title: whole_blood-SLE_P_NC_1-rep21

description:
9269325097_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep40

status: Public on Mar 22 2019

type: RNA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

description:
9339657020_J
Early version of manifest, only 47,231 probes

hyb_protocol: Amplified labeled RNA were hybridized overnight to Illumina HumanHT-12 v4 Beadchips (Illumina) following manufacturer's protocols. Following hybridization each chip was washed, blocked and stained following the manufacturer’s protocols.

scan_protocol: Scanned on an Illumina Beadstation 500

data_processing: Data was normalized using GenomeStudio's Global Average Normalization. Sample name is included in 'description' field. Two samples (whole blood_SLE+_<16 weeks_3 [9269325029_K], whole blood_SLE+_PP_8 [9269325029_J]) were processed separately and raw and processed data for these samples were included in separate files.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Following extraction, a LabChip GX instrument (Caliper Life Sciences Inc.) was used to measure the RNA Quality Score (RQS) for each sample. RNA concentration was measured using a Nanodrop 8000 (Nanodrop Technologies). Following RNA extraction and quality control analysis, Globin mRNA was depleted from a portion of each total RNA sample using the GLOBINclear™ 96-well format kit (Ambion). This was followed by another round of RQS and concentration determinations for quality control purposes. 250ng of globin reduced RNA from all samples passing quality control were then amplified and labeled using the Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion).

extract_protocol: Blood was collected in PAXgene tubes (Qiagen), immediately placed on ice and stored within 2-4 hours at -20°C until further analyses in batches. RNA was extracted, amplified, quantified and globin reduced according to manufacturer’s instructions.

tag: tissue

value: whole blood

value: <16 weeks

tag: age

tag: gender

value: Female

tag: race

value: C

tag: ethnicity

value: Not Hispanic or Latino

tag: sle

tag: apl

tag: lac

tag: tp

tag: pe

tag: fd

tag: nnd

tag: iugr

tag: sga

tag: batch


title: whole_blood-SLE_P_NC_1-rep32

description:
9339657008_H
Early version of manifest, only 47,231 probes

value: Hispanic or Latino


title: whole_blood-SLE_P_NC_1-rep20

description:
9269325082_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep1

description:
9269325021_D
Early version of manifest, only 47,231 probes

value: AA


title: whole_blood-SLE_P_NC_1-rep4

description:
9269325031_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep16

description:
9269325067_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep6

description:
9339657013_E
Early version of manifest, only 47,231 probes

value: PP

value: Before


title: whole_blood-SLE_P_NC_1-rep41

description:
9339657021_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep5

description:
9339657010_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep4

description:
9339657002_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep2

description:
9269325033_K
Early version of manifest, only 47,231 probes

value: After


title: whole_blood-SLE_P_PE_5-rep3

description:
9270006084_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep1

description:
9269325031_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep7

description:
9339657016_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_5-rep8

description:
9339657019_K
Early version of manifest, only 47,231 probes

value: Other


title: whole_blood-SLE_P_PE_4-rep6

description:
9339657009_J
Early version of manifest, only 47,231 probes

value: 32-40 weeks


title: whole_blood-SLE_P_PE_4-rep5

description:
9270006084_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_4-rep4

description:
9270006063_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_4-rep7

description:
9339657014_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_4-rep3

description:
9270006063_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_4-rep1

description:
9269325025_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep4

description:
9269325033_B
Early version of manifest, only 47,231 probes

value: 24-31 weeks


title: whole_blood-SLE_P_NC_1-rep42

description:
9339657021_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep15

description:
9339657020_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep7

description:
9269325037_B
Early version of manifest, only 47,231 probes

value: As


title: whole_blood-SLE_P_PE_3-rep3

description:
9269325030_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep14

description:
9339657015_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep1

description:
9269325021_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep8

description:
9269325043_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep6

description:
9269325037_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep5

description:
9269325034_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep13

description:
9339657015_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep10

description:
9269325097_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep12

description:
9339657012_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep2

description:
9269325033_D
Early version of manifest, only 47,231 probes

value: 16-23 weeks


title: whole_blood-SLE_P_PE_2-rep15

description:
9339657008_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep3

description:
9269325034_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep9

description:
9269325048_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep11

description:
9270006076_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_4-rep2

description:
9270006058_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep16

description:
9339657014_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep5

description:
9269325038_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep14

description:
9339657008_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep10

description:
9270006076_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep18

description:
9339657020_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep7

description:
9269325061_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep17

description:
9339657014_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep9

description:
9270006063_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep13

description:
9339657002_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep12

description:
9271668036_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_NC_1-rep29

description:
9339657006_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep6

description:
9269325041_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep8

description:
9270006058_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep1

description:
9269325023_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_2-rep4

description:
9269325035_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep10

description:
9271668036_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep9

description:
9271668022_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep11

description:
9270006067_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep17

description:
9339657013_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep12

description:
9339657006_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep5

description:
9269325057_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep11

description:
9339657002_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep7

description:
9270006058_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep18

description:
9339657013_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep16

description:
9339657010_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep8

description:
9270006063_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep13

description:
9339657008_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep1

description:
9269325023_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep6

description:
9269325078_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep6

description:
9269325091_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep14

description:
9339657009_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep4

description:
9269325043_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep15

description:
9339657009_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep1

description:
9269325029_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep2

description:
9269325048_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep8

description:
9339657017_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep3

description:
9269325061_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep19

description:
9339657013_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep3

description:
9269325039_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_4-rep5

description:
9270006076_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep7

description:
9339657016_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_4-rep3

description:
9269325057_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_4-rep4

description:
9270006063_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_3-rep2

description:
9269325025_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep2

description:
9269325035_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_4-rep6

description:
9339657017_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep11

description:
9339657018_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_4-rep2

description:
9269325044_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep20

description:
9339657018_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep8

description:
9269325091_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep10

description:
9339657015_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep4

description:
9269325061_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep6

description:
9269325039_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep7

description:
9269325067_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep2

description:
9269325030_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep9

description:
9271668036_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_5-rep5

description:
9269325061_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep6

description:
9269325048_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep5

description:
9269325035_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep18

description:
9339657020_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep4

description:
9269325037_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep14

description:
9271668036_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep13

description:
9271668022_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep16

description:
9339657012_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep4

description:
9269325034_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep3

description:
9269325031_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_4-rep1

description:
9269325021_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep2

description:
9269325029_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep17

description:
9339657017_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep8

description:
9269325082_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep5

description:
9269325043_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep15

description:
9339657010_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep12

description:
9271668022_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep1

description:
9269325025_F
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep9

description:
9270006058_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep10

description:
9270006084_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep13

description:
9339657013_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep10

description:
9269325097_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep15

description:
9339657016_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep11

description:
9271668022_A
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep9

description:
9269325091_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep16

description:
9339657016_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep12

description:
9339657009_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep7

description:
9269325078_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep5

description:
9269325041_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep8

description:
9269325091_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep17

description:
9339657020_H
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep3

description:
9269325030_L
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep6

description:
9269325057_J
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep2

description:
9269325029_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep1

description:
9269325021_E
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep7

description:
9269325061_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep18

description:
9339657020_I
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_2-rep11

description:
9270006096_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep15

description:
9339657015_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep13

description:
9339657014_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep6

description:
9269325044_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep8

description:
9269325067_K
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep14

description:
9339657015_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep2

description:
9269325025_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep1

description:
9269325023_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep14

description:
9339657014_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep7

description:
9269325067_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep16

description:
9339657016_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep17

description:
9339657017_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep11

description:
9270006067_H
Early version of manifest, only 47,231 probes

value: 7.5 WPP


title: whole_blood-HC_P_5-rep5

description:
9269325037_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep4

description:
9269325033_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep12

description:
9270006084_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep10

description:
9270006067_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep33

description:
9339657019_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep3

description:
9269325033_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_5-rep9

description:
9269325078_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep6

description:
9269325034_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep23

description:
9339657008_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep17

description:
9269325078_G
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_1-rep4

description:
9269325036_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep4

description:
9269325031_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep13

description:
9269325041_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep30

description:
9339657016_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep5

description:
9269325033_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep12

description:
9269325039_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep31

description:
9339657016_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep2

description:
9269325029_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep1

description:
9269325023_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep34

description:
9339657019_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep32

description:
9339657018_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep16

description:
9269325048_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep7

description:
9269325036_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep24

description:
9339657008_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep19

description:
9270006063_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep27

description:
9339657012_D
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep1

description:
9269325021_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep21

description:
9339657003_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep35

description:
9339657021_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep28

description:
9339657013_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep22

description:
9339657003_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep3

description:
9269325030_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep15

description:
9269325043_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep26

description:
9339657010_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep20

description:
9270006076_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep9

description:
9269325036_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep8

description:
9269325036_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep18

description:
9269325082_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep14

description:
9269325043_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep17

description:
9269325043_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep14

description:
9269325038_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep28

description:
9270006084_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep6

description:
9269325033_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep7

description:
9269325033_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep31

description:
9270006096_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep18

description:
9269325048_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep10

description:
9269325039_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep19

description:
9269325057_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep35

description:
9339657010_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep25

description:
9270006058_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep22

description:
9269325078_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep29

description:
9339657014_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep1

description:
9269325021_B
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_PE_1-rep21

description:
9339657020_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep21

description:
9269325078_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep9

description:
9269325033_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep27

description:
9270006063_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep5

description:
9269325029_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep2

description:
9269325023_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep36

description:
9339657019_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep4

description:
9269325025_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep20

description:
9269325067_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep34

description:
9339657003_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep33

description:
9271668036_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep15

description:
9269325038_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep8

description:
9269325033_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep37

description:
9339657021_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep3

description:
9269325025_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep10

description:
9269325034_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep11

description:
9269325035_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep29

description:
9270006084_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep32

description:
9271668022_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep16

description:
9269325041_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep12

description:
9269325035_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep24

description:
9269325091_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep13

description:
9269325037_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep26

description:
9270006058_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep23

description:
9269325082_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep17

description:
9269325061_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep33

description:
9339657009_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep1

description:
9269325021_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep21

description:
9269325091_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep29

description:
9271668036_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep22

description:
9269325097_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_4-rep25

description:
9339657009_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep23

description:
9269325097_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep25

description:
9270006058_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep11

description:
9269325043_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_3-rep30

description:
9270006084_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep16

description:
9269325057_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep14

description:
9269325044_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep37

description:
9339657015_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep8

description:
9269325037_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep31

description:
9339657008_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep3

description:
9269325029_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep28

description:
9271668022_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep6

description:
9269325034_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep30

description:
9339657002_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep12

description:
9269325043_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep32

description:
9339657008_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep27

description:
9270006076_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep2

description:
9269325025_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep19

description:
9269325067_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep13

description:
9269325043_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep10

description:
9269325039_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep15

description:
9269325057_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep9

description:
9269325038_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep24

description:
9269325097_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep26

description:
9270006067_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep36

description:
9339657013_C
Early version of manifest, only 47,231 probes


title: whole_blood-SLE_P_OC_3-rep3

description:
9269325031_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep34

description:
9339657010_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep20

description:
9269325067_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep4

description:
9269325029_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep7

description:
9269325035_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep21

description:
9270006067_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep5

description:
9269325030_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep35

description:
9339657012_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_2-rep18

description:
9269325061_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep25

description:
9271668036_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep14

description:
9269325061_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep36

description:
9339657019_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep20

description:
9270006063_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep3

description:
9269325025_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep9

description:
9269325037_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep31

description:
9339657015_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep33

description:
9339657016_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep28

description:
9339657008_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep24

description:
9271668036_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep10

description:
9269325038_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep17

description:
9269325091_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep26

description:
9339657003_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep15

description:
9269325067_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep13

description:
9269325044_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep5

description:
9269325031_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep4

description:
9269325029_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep11

description:
9269325041_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep16

description:
9269325078_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep1

description:
9269325023_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep29

description:
9339657009_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep35

description:
9339657018_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep27

description:
9339657006_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep23

description:
9270006096_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep8

description:
9269325037_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep37

description:
9339657019_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep19

description:
9269325097_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep7

description:
9269325036_J
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep34

description:
9339657018_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep32

description:
9339657015_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep30

description:
9339657012_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep38

description:
9339657021_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep18

description:
9269325091_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep2

description:
9269325023_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep23

description:
9339657019_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep12

description:
9269325043_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep22

description:
9270006076_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_P_1-rep6

description:
9269325035_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep21

description:
9339657014_K
Early version of manifest, only 47,231 probes

value: H


title: whole_blood-HC_NP_5-rep20

description:
9339657012_J
Early version of manifest, only 47,231 probes

value: whole blood


title: whole_blood-HC_NP_5-rep17

description:
9339657002_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep18

description:
9339657006_E
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep16

description:
9271668022_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep19

description:
9339657006_K
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep15

description:
9270006096_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep14

description:
9269325097_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep13

description:
9269325082_G
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep12

description:
9269325082_A
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep10

description:
9269325044_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep11

description:
9269325048_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep9

description:
9269325044_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep7

description:
9269325044_B
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep6

description:
9269325041_D
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep8

description:
9269325044_F
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep4

description:
9269325038_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep5

description:
9269325039_H
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep3

description:
9269325037_I
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep1

description:
9269325023_L
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep2

description:
9269325031_C
Early version of manifest, only 47,231 probes


title: whole_blood-HC_NP_5-rep22

description:
9339657018_H
Early version of manifest, only 47,231 probes


title: HCT116-posi-2_S63

status: Public on Feb 22 2019

type: SRA

library_source: transcriptomic

data_processing:
Raw sequence image files from the Illumina HiSeq 2500 in the form of bcl were converted to the fastq format using CASAVA v1.8.2
2 raw fastq files were concatenated together and the combined fastq file was used for all subsequent analysis. Which 2 samples were combined is designated by column 'characteristics: combined ID'.
Adapters from the 3′ end were clipped using cutadapt v.1.10 (http://cutadapt.readthedocs.io/en/stable/guide.html)
All of the reads shorter than 15 nt and 3′ bases below a quality score of 30 were discarded
sRNABench (http://bioinfo5.ugr.es/sRNAbench/sRNAbench.php) was used to map the reads to RNA libraries. The algorithm used in sRNABench was based on mirAnalyzer, where the reads with the same sequence were collapsed and mapped to the human genome and the miRBase v21 miRNA database (http://www.mirbase.org/).
Alignments were performed with Bowtie v0.12.9.
Differentially expressed miRNAs were identified using DESeq2 and selected based on adjusted p-values (p < 0.05), absolute value of log2 fold change >1, and a base mean value >20.
Genome_build: GRCh38 and the miRBase v21 miRNA database
Supplementary_files_format_and_content: both files are .txt format; one contains the raw read counts for the combined samples, and the other the deseq2 normalized read counts

source_name: colorectal cancer cell line HCT116

growth_protocol: Cell lines and materials  CRC cell line HCT116 was purchased from the American Type Culture Collection (Manassas, VA, USA), and 5-fluorouracil (5FU)-resistant (5FUR) cell lines were established by a method described previously (Yu Y, Kanwar SS, Patel BB, Nautiyal J, Sarkar FH, and Majumdar AP. Elimination of Colon Cancer Stem-Like Cells by the Combination of Curcumin and FOLFOX. Transl Oncol. 2009;2(4):321-8). The cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM; Gibco™, Invitrogen, Carlsbad, CA, USA) with 10% fetal bovine serum and 1% penicillin–streptomycin and maintained at 37°C in a humidified incubator at 5% CO2. CRC SDCSCs were generated from HCT116 and HT29 cell lines in serum-free medium (DMEM/F12) supplemented with B27 and N2 supplements (Gibco™), 10 ng/ml human recombinant basic fibroblast growth factor (Gibco™), and 20 ng/ml epidermal growth factor (Sigma-Aldrich, St. Louis, MO, USA) cultured in a Costar® ultra-low-attachment flask (Corning Inc., Corning, NY, USA). 5FU and oxaliplatin (Sigma-Aldrich) were dissolved in DMSO, and diluted to appropriate experimental concentrations with the culture medium.    Cell sorting  Spheroid derived cancer stem cells (SDCSCs) derived from HCT116 and HT26 cell lines were stained with CD44v6-FITC monoclonal antibody (Cat. # MA5-16966; Invitrogen), and propidium iodide was used to eliminate dead cells. Cell sorting was performed using BD FACS Aria II (BD Biosciences, San Jose, CA, USA) with a 100-µm nodule. The number of sorted cells was monitored with an antibody specific for CD44v6-FITC, and stained cells were deemed to be positive for CD44v6.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kits (Qiagen, Germantown, MD, USA) following the manufacturer’s instructions.
Next-generation sequencing library construction for miRNAs from tissue was performed using a Truseq Small RNA Kit (Illumina, San Diego, CA) with up to 1 µg of total RNA input, in accordance with the manufacturer’s protocol. The quality of individual libraries was assessed using a High Sensitivity DNA Kit (Agilent, Santa Clara, CA, USA). Libraries were pooled together prior to size selection (~148 nt) by gel electrophoresis using a Pippin HT instrument (Sage Science Inc., Beverly, MA, USA). The efficiency of size selection was assessed using the High Sensitivity DNA Kit (Agilent), and the pooled libraries were thereafter quantified by qPCR using a KAPA Library Quantification Kit, Universal (KAPA Biosystems, Wilmington, MA).

value: colorectal cancer cell line

tag: cell line

tag: cell sub-population

tag: combined id


title: HCT116-neg-2_S65

tag: tissue


title: HCT116-posi-1_S174


title: HCT116-neg-2_S177


title: HCT116-neg-1_S176


title: HCT116-posi-2_S175


title: HCT116-posi-1_S62


title: whole_blood-HC_P_4-rep11

description:
9269325039_F
Early version of manifest, only 47,231 probes

tag: age

tag: gender

value: Female


title: NA_12

status: Public on Jan 24 2019

city: Birmingham

first: Tamas

last: Jilling

state: AL

address: UAB Station

department: Department of Pediatrics

institute: The University of Alabama at Birmingham

description:
replicate 3
SAMPLE 12

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were processed with Illumina's GenomeStudio V2011.1. Quantile normalization and background subtraction was performed.

organism: Mus musculus

source_name: ileum

label_protocol: Illumina

extract_protocol:
The right lung and a 5 mm section of the terminal ileum was processed for RNA extration.
RNA was extracted and treated with DNase I using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Neonatal mice were exposed from postnatal day 3 (P3) to P14 to either normoxia (FiO2=21%) or hyperoxia (FiO2=85%).

tag: strain

value: 14 days

tag: treatment

value: hyperoxia

value: ileum


title: HCT116-neg-1_S64


title: NA_3

description:
replicate 3
SAMPLE 3

source_name: lung

value: normoxia

value: lung


title: NA_10

description:
replicate 1
SAMPLE 10


title: NA_5

description:
replicate 2
SAMPLE 5


title: NA_11

description:
replicate 2
SAMPLE 11


title: NA_9

description:
replicate 3
SAMPLE 9


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851090_E

status: Public on Dec 26 2018

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HumanHT-12 v4 Beadchips (Illumina) following manufacturer's protocols. Following hybridization each chip was washed, blocked and stained following the manufacturer’s protocols.

scan_protocol: Illumina Beadstation 500

data_processing: llumina GenomeStudio software was used to subtract background and scale average samples’ signal intensity

source_name: whole_blood-NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

extract_protocol: Total RNA was isolated from whole blood lysed in Tempus™ Blood RNA Tubes (Applied Biosystems™) using the MagMAX™-96 Blood RNA Isolation Kit (Ambion) according to the manufacturer's instructions for high throughput applications.

tag: sample name

value: NCH 998

tag: bacterial organism

tag: viral organism

value: RSV

tag: analysis group

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

tag: age (mo.)

value: F

tag: race

value: White

tag: ethnicity

value: Not Hispanic or Latino

tag: condition

value: Pneumonia


title: NA_1

description:
replicate 1
SAMPLE 1


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_L

source_name: whole_blood-NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 866

value: Rhinovirus


title: NA_8

description:
replicate 2
SAMPLE 8


title: NONE-RSV+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_I

source_name: whole_blood-NONE-RSV+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1016

value: RSV+Rhinovirus


title: NONE-Rhinovirus+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851091_C

source_name: whole_blood-NONE-Rhinovirus+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 969

value: Rhinovirus+Adenovirus

value: M


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_K

value: NCH 815


title: NONE-Rhinovirus+Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851087_I

source_name: whole_blood-NONE-Rhinovirus+Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 966


title: NONE-RSV+Coronavirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_D

source_name: whole_blood-NONE-RSV+Coronavirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1000

value: RSV+Coronavirus


title: NA_2

description:
replicate 2
SAMPLE 2

value: 14 days

value: normoxia

value: lung


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_E

value: PN NCH 1006

value: RSV

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: White


title: NA_6

description:
replicate 3
SAMPLE 6

value: ileum


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_K

value: NCH 914

value: F

value: Not Hispanic or Latino

value: Pneumonia


title: NA_7

description:
replicate 1
SAMPLE 7

value: hyperoxia


title: NA_4

description:
replicate 1
SAMPLE 4


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851092_I

value: NCH 987


title: NONE-Rhinovirus+Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_K

source_name: whole_blood-NONE-Rhinovirus+Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 865

value: Rhinovirus+Parainfluenza

value: M


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851089_C

value: NCH 823

value: Rhinovirus


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_B

value: NCH 847


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851088_B

value: NCH 828


title: NONE-Rhinovirus+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851073_J

value: NCH 967

value: Rhinovirus+Adenovirus


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_K

value: NCH 901

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: White


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851073_I

value: PN NCH 1012


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851089_E

value: NCH 868

value: Not Hispanic or Latino


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_K

value: NCH 854

value: F

value: Pneumonia


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_K

value: NCH 816


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851072_L

value: NCH 894


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851079_A

source_name: whole_blood-NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 817

value: Rhinovirusuman metapneumovirus

value: M


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851087_A

value: PN NCH 1003

value: Rhinovirus


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_J

value: PN NCH 1014


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_A

value: NCH 874


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_B

value: NCH 189

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851089_D

value: NCH 961

value: White


title: NONE-Coronavirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851092_J

source_name: whole_blood-NONE-Coronavirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1001

value: Coronavirus

value: Not Hispanic or Latino


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851079_I

value: NCH 983

value: Pneumonia


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851090_D

value: NCH 838


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_F

value: NCH 958

value: F


title: NONE-Rhinovirusuman metapneumovirusnfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_D

source_name: whole_blood-NONE-Rhinovirusuman metapneumovirusnfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 831

value: Rhinovirusuman metapneumovirusnfluenza

value: M


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_L

value: NCH 979

value: Rhinovirusuman metapneumovirus


title: NONE-Rhinovirusuman metapneumovirusnfluenza+RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851073_A

source_name: whole_blood-NONE-Rhinovirusuman metapneumovirusnfluenza+RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 814


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_C

value: NCH 902

value: Rhinovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: NONE-Bocavirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_H

source_name: whole_blood-NONE-Bocavirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1018

value: Bocavirus+Rhinovirus

value: White


title: NONE-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_B

source_name: whole_blood-NONE-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 826

value: Parainfluenza

value: Not Hispanic or Latino


title: NONE-Not tested-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_G

source_name: whole_blood-NONE-Not tested-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 906

value: Not tested

value: Pneumonia


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_J

value: NCH 827


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_B

value: NCH 819

value: M


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_J

value: NCH 985

value: F

value: Unknown


title: NONE-Adenovirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851073_C

source_name: whole_blood-NONE-Adenovirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 856

value: Adenovirus+Rhinovirus


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851090_L

value: NCH 844

value: Rhinovirusuman metapneumovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: NONE-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_L

value: NCH 888

value: White


title: NONE-Adenovirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_A

value: PN NCH 1015

value: Not Hispanic or Latino


title: NONE-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_B

value: PN NCH 1017

value: Parainfluenza

value: Black or African American


title: NONE-Adenovirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_F

value: PN NCH 1011

value: Pneumonia


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_J

value: PN NCH 1002

value: RSV


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_A

value: NCH 811

value: F

value: Other


title: NONE-Rhinovirusuman metapneumovirusnfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851089_L

value: NCH 809

value: Rhinovirusuman metapneumovirusnfluenza

value: M

value: Hispanic or Latino


title: NONE-Coronavirus+Bocavirus+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851090_F

source_name: whole_blood-NONE-Coronavirus+Bocavirus+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 989

value: Coronavirus+Bocavirus+Adenovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_C

value: PN NCH 1005

value: Not Hispanic or Latino


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851087_G

value: NCH 800


title: NONE-RSV+Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_B

source_name: whole_blood-NONE-RSV+Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 974

value: RSV+Parainfluenza


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_H

value: NCH 821

value: Rhinovirusuman metapneumovirus

value: Pneumonia


title: NONE-RSV+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_C

source_name: whole_blood-NONE-RSV+Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1009

value: RSV+Adenovirus

value: F

value: Black or African American


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_E

source_name: whole_blood-NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 805

value: RSV

value: Other


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851088_D

source_name: whole_blood-NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 988

value: Rhinovirus

value: M


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_D

value: NCH 842

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: Not Hispanic or Latino


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_D

value: NCH 895

value: Asian


title: NONE-Rhinovirusuman metapneumovirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_G

source_name: whole_blood-NONE-Rhinovirusuman metapneumovirus+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 835


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_E

value: NCH 825

value: Pneumonia


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_D

value: NCH 841

value: Hispanic or Latino


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_L

value: NCH 955


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851089_H

value: NCH 873

value: F

value: Black or African American


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851079_H

value: NCH 872


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_I

value: NCH 810

value: Rhinovirus

value: Other


title: NONE-Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_B

source_name: whole_blood-NONE-Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 837

value: Parainfluenza+Rhinovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: M


title: NONE-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_A

value: NCH 882

value: Rhinovirusuman metapneumovirus

value: Not Hispanic or Latino


title: NONE-Rhinovirus+Bocavirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851088_A

source_name: whole_blood-NONE-Rhinovirus+Bocavirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 968

value: Rhinovirus+Bocavirus

value: Pneumonia


title: NONE-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_J

value: NCH 836

value: Parainfluenza


title: NONE-Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_A

value: NCH 858

value: F

value: Black or African American


title: NONE-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_L

value: NCH 898


title: NONE-Rhinovirusuman metapneumovirusnfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851092_K

value: NCH 803

value: Rhinovirusuman metapneumovirusnfluenza

value: Other


title: NONE-RSV+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851079_C

source_name: whole_blood-NONE-RSV+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1019

value: RSV+Rhinovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: NONE-Bocavirus+Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_G

source_name: whole_blood-NONE-Bocavirus+Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 908

value: Bocavirus+Parainfluenza+Rhinovirus


title: NONE-RSV-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_I

value: NCH 997

value: RSV

value: Hispanic or Latino


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851092_F

source_name: whole_blood-NONE-Negative-pneumonia vs healthy ctrl-Pneumonia

value: NCH 864

value: Negative

value: pneumonia vs healthy ctrl

value: M

value: White

value: Not Hispanic or Latino

value: Pneumonia


title: NONE-Not tested-pneumonia vs healthy ctrl-Pneumonia 8363851091_F

source_name: whole_blood-NONE-Not tested-pneumonia vs healthy ctrl-Pneumonia

value: NCH 980

value: Not tested

value: F


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851073_D

value: NCH 962


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851087_D

value: NCH 834


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851088_E

value: NCH 804


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851090_H

value: NCH 855


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851081_F

value: NCH 802


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851092_H

value: PN NCH 1007


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851088_I

value: PN NCH 1010


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851083_L

value: PN NCH 1013


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851074_G

value: NCH 890

value: Negative


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851078_H

value: NCH 904

value: pneumonia vs healthy ctrl

value: Black or African American


title: NONE-Not tested-pneumonia vs healthy ctrl-Pneumonia 8363851085_C

value: NCH 900

value: White

value: Not Hispanic or Latino

value: Pneumonia


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851088_J

value: NCH 824

value: M


title: NONE-Not tested-pneumonia vs healthy ctrl-Pneumonia 8363851080_H

value: NCH 917

value: Not tested


title: NONE-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851072_F

value: NCH 829

value: Rhinovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: F


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851089_B

value: NCH 953


title: NONE-Negative-pneumonia vs healthy ctrl-Pneumonia 8363851073_B

value: NCH 862

value: Negative


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851073_K

source_name: whole_blood-Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia

value: NCH 896

value: Mycoplasma

value: pneumonia vs healthy ctrl


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851079_L

value: NCH 993

value: White


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851083_I

value: NCH 884

value: Black or African American

value: Not Hispanic or Latino

value: Pneumonia


title: Mycoplasma-Rhinovirus+Adenovirus-pneumonia vs healthy ctrl-Pneumonia 8363851087_L

source_name: whole_blood-Mycoplasma-Rhinovirus+Adenovirus-pneumonia vs healthy ctrl-Pneumonia

value: NCH 956

value: Rhinovirus+Adenovirus


title: Mycoplasma-Parainfluenza-pneumonia vs healthy ctrl-Pneumonia 8363851074_L

source_name: whole_blood-Mycoplasma-Parainfluenza-pneumonia vs healthy ctrl-Pneumonia

value: NCH 877

value: Parainfluenza


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851078_I

value: NCH 954

value: Rhinovirus

value: M

value: Other


title: Mycoplasma-Parainfluenza-pneumonia vs healthy ctrl-Pneumonia 8363851088_F

value: NCH 879


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851072_H

value: NCH 910

value: Mycoplasma


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851076_H

value: NCH 892

value: pneumonia vs healthy ctrl


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851081_E

value: NCH 965

value: F

value: White


title: Mycoplasma-Rhinovirus-pneumonia vs healthy ctrl-Pneumonia 8363851084_D

value: NCH 975

value: Hispanic or Latino

value: Pneumonia


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_A

source_name: whole_blood-Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 889

value: Negative

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: Not Hispanic or Latino


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851073_F

value: NCH 857

value: M


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851079_K

value: NCH 850


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851091_L

value: NCH 863


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851091_E

value: NCH 952

value: Mycoplasma


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851092_A

value: NCH 867


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_B

value: NCH 986


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_F

value: NCH 859


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_G

value: NCH 845

value: White


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851079_J

value: NCH 852


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_F

value: NCH 851

value: F

value: Pneumonia


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851092_B

value: NCH 860

value: Negative

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_D

value: NCH 887

value: Not Hispanic or Latino


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851088_C

value: NCH 891


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_G

value: PN NCH 1008


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851091_A

value: NCH 918

value: Mycoplasma

value: M


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_J

value: NCH 996


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851073_L

value: NCH 951


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_A

value: NCH 964

value: Other


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_E

value: NCH 916

value: White


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_A

value: NCH 861

value: F

value: Black or African American

value: Pneumonia


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851086_E

value: NCH 853

value: Negative

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: Asian


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851072_J

value: NCH 960

value: Not Hispanic or Latino


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_E

value: NCH 869

value: Mycoplasma

value: M


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851088_L

value: NCH 915


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851085_G

value: NCH 982


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851092_E

value: NCH 899


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_H

value: NCH 992


title: S. pneumoniae-RSV+Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851087_B

source_name: whole_blood-Streptococcus pneumoniae-RSV+Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 999

value: Streptococcus pneumoniae

value: RSV+Rhinovirusuman metapneumovirus

value: White


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851081_C

value: NCH 886

value: Black or African American

value: Pneumonia


title: S. pneumoniae-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_I

source_name: whole_blood-Streptococcus pneumoniae-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 991

value: Rhinovirus

value: infection vs healthy ctrl+pneumonia vs healthy ctrl


title: S. pneumoniae-Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851084_J

value: NCH 832

value: Not Hispanic or Latino


title: Mycoplasma-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_B

value: NCH 909

value: Mycoplasma

value: Negative

value: M


title: S. pyogenes-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_H

source_name: whole_blood-Streptococcus pyogenes-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 843

value: Streptococcus pyogenes

value: Rhinovirusuman metapneumovirus

value: F


title: S. pyogenes-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851078_F

value: NCH 822

value: White


title: S. pneumoniae-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851087_F

source_name: whole_blood-Streptococcus pneumoniae-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 973

value: Streptococcus pneumoniae


title: S. pneumoniae-Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851089_A

source_name: whole_blood-Streptococcus pneumoniae-Adenovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 990

value: Adenovirus

value: Asian

value: Pneumonia


title: MSSA-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_I

source_name: whole_blood-MSSA-Parainfluenza-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 885

value: MSSA

value: Parainfluenza

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: Other

value: Not Hispanic or Latino


title: S. pneumoniae-Not tested-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851074_A

source_name: whole_blood-Streptococcus pneumoniae-Not tested-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 820

value: Not tested

value: Black or African American


title: S. pyogenes-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851076_D

value: NCH 976

value: Streptococcus pyogenes

value: Rhinovirusuman metapneumovirus

value: F


title: S. pneumoniae-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851080_J

value: NCH 903

value: Streptococcus pneumoniae

value: Negative

value: M

value: White


title: S. pneumoniae-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851077_K

source_name: whole_blood-Streptococcus pneumoniae-Rhinovirusuman metapneumovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: PN NCH 1004

value: Pneumonia


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851080_E

source_name: whole_blood-N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: Healthy Control


title: MRSA-RSV+Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851088_K

source_name: whole_blood-MRSA-RSV+Parainfluenza+Rhinovirus-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 818

value: MRSA

value: RSV+Parainfluenza+Rhinovirus

value: Not Hispanic or Latino


title: S. pneumoniae+Mycoplasma-Parainfluenza-pneumonia vs healthy ctrl-Pneumonia 8363851089_K

source_name: whole_blood-Streptococcus pneumoniae+Mycoplasma-Parainfluenza-pneumonia vs healthy ctrl-Pneumonia

value: NCH 970

value: Streptococcus pneumoniae+Mycoplasma

value: Parainfluenza

value: pneumonia vs healthy ctrl


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851076_I


title: S. pneumoniae-Not tested-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851091_B

value: NCH 808

value: Not tested

value: Black or African American


title: S. pyogenes-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia 8363851083_K

source_name: whole_blood-Streptococcus pyogenes-Negative-inf vs healthy ctrl+pneumonia vs healthy ctrl-Pneumonia

value: NCH 833

value: Streptococcus pyogenes

value: Negative

value: F


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851085_L

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: White


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851089_J

value: Healthy Control


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851090_B


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851074_C

value: M


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851080_C


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851092_C

value: Asian


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851091_H

value: Hispanic or Latino


title: HESC_Input

status: Public on Dec 04 2018

city: Houston

first: Maria

last: Szwarc

address: One Baylor Plaza

institute: Baylor College of MEdicine

library_source: genomic

data_processing:
50-nt sequence reads identified using Ilumina's Hi-seq were mapped to the genome using the BWA algorithm at default settings.
Only reads that passed Illumina’s purity filter, align with no more than 2 mismatches, and mapped uniquely to the genome were used.
32122151 of total 35761720 SRC2 peaks aligned (32237127 of total 33513636 input peaks)
Reads were extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp
32122151 of total 35761720 SRC2 peaks aligned (32237127 of total 33513636 input peaks), and fragment density was determined on genomic 32-nt bins.
Genomic binding sites ('intervals') were defined using MACS 1.3.7.1 (using balanced Input files, # tag size = 36, # band width = 150, # model fold 16, d (shift) 179, pvalue cutoff 1.00E-07)
Genome_build: GRCh37.p2-Primary Assembly
Supplementary_files_format_and_content: BED = standard BED file containing the MACS peaks

molecule: genomic DNA

source_name: human endometrial stromal cells (hESCs)

growth_protocol: DMEM/F12, 10% fetal bovine serum, antibiotic-antimycotic, HEPES and NaHCO3

extract_protocol:
Lysates were clarified from sonicated nuclei and DNA complexes were isolated with antibody Bethyl A300-346A.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the  3'-ends. Illumina genomic adapters were ligated and the sample was  size-fractionated (200-300 bp) on a 2% agarose gel. After a final PCR  amplification step (18 cycles), the resulting DNA libraries were  quantified and sequenced on HiSeq 2000.

treatment_protocol: 10nM beta-estradiol, 100nM medroxyprogesterone acetate, and 1mM cAMP in Opti-MEM I Reduced Serum Media with 2% charcoal-stripped fetal bovine serum

tag: cell type

value: endometrial stromal cells

tag: antibody


title: FD41489 P37 NT siRNA day 0 EPC

status: Public on Oct 23 2018

description:
nontargeting siRNA day 0 EPC
FD41489

data_processing:
Raw reads in fastq file format were mapped to human genome hg19 (Human assembly:  GRCh37/hg19;  http://genome.ucsc.edu) through use of the ultrafast universal RNA-seq aligner: Spliced Transcripts Alignment to a Reference (STAR) software
To reduce possible PCR bias, read duplicates were removed with Picard Tools (http://broadinstitute.github.io/picard/).
The number of reads aligned to known genes was determined by the Python-based software package HTSeq
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt; 13 columns; headers: "GeneSymbol" and raw count data for each of the 12 samples: "FD41481" "FD41482" "FD41483" "FD41484" "FD41485" "FD41486" "FD41694" "FD41488" "FD41489" "FD41490" "FD41491" "FD41494"

source_name: endometrial stromal cells

growth_protocol: Plated 8x10^4 cells per well in 6-well format. 48 hours allowed for growth before siRNA transfection

extract_protocol:
RNeasy Plus kit (Qiagen Inc., Germantown, MD)
250ng of total RNA as input, the TruSeqTM RNA library preparation kit v2 (Illumina®, Inc., San Diego, CA) was used for mRNA isolation, fragmentation, and subsequent first and second strand DNA synthesis.  The kit also was used for follow up end-repair along with base- and adaptor- ligation before products were purified and then enriched by PCR (15 cycles) to create the cDNA libraries.  The resulting libraries were quantitated using the NanoDropTM spectrometer and fragment size assessed using a DNA 1000 chip on the Agilent 2100 Bioanalyzer. A qPCR assay was performed on the libraries to determine the concentration of adapter-ligated fragments using the Applied Biosystems ViiATM 7 Real-Time PCR System (Thermo Fisher Scientific®) with a KAPA library Quant kit (Kapabiosystems, Inc., Wilmington, MA). Relevant samples were pooled in equimolar amounts and re-quantitated by qPCR. Library pools (27pM) were loaded into a high output flow cell for clonal cluster generation by bridge amplification using the cBot 2 system (Illumina®, Inc.). Indexed paired-end sequencing (2x100bp read lengths) was performed using the ultrahigh-throughput HiSeq 2500 sequencing system (Illumina®, Inc.).

treatment_protocol: nontargeting vs. SRC-2/NCOA2 siRNA transfection for 48 hours; followed by EPC (estradiol, medroxprogesterone acetate, cAMP) treatment for 0 or 3 days

tag: sirna

value: nontargeting siRNA

tag: genotype

value: control

tag: agent

value: untreated

tag: time

value: day 0 EPC

tag: individual

value: volunteer P37


title: FD41490 P37 SRC-2/NCOA2 siRNA day 0 EPC

description:
SRC-2/NCOA2 siRNA day 0 EPC
FD41490

value: SRC-2/NCOA2 siRNA

value: SRC-2/NCOA2 knockdown


title: FD41694 P35 NT siRNA day 3 EPC

description:
nontargeting siRNA day 3 EPC
FD41694

value: EPC

value: day 3 EPC

value: volunteer P35


title: FD41488 P35 SRC-2/NCOA2 siRNA day 3 EPC

description:
SRC-2/NCOA2 siRNA day 3 EPC
FD41488


title: FD41482 P30 SRC-2/NCOA2 siRNA day 0 EPC

description:
SRC-2/NCOA2 siRNA day 0 EPC
FD41482

value: volunteer P30


title: FD41486 P35 SRC-2/NCOA2 siRNA day 0 EPC

description:
SRC-2/NCOA2 siRNA day 0 EPC
FD41486


title: FD41483 P30 NT siRNA day 3 EPC

description:
nontargeting siRNA day 3 EPC
FD41483


title: FD41484 P30 SRC-2/NCOA2 siRNA day 3 EPC

description:
SRC-2/NCOA2 siRNA day 3 EPC
FD41484


title: FD41485 P35 NT siRNA day 0 EPC

description:
nontargeting siRNA day 0 EPC
FD41485


title: FD41481 P30 NT siRNA day 0 EPC

description:
nontargeting siRNA day 0 EPC
FD41481


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851091_K

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

tag: gender

value: F

value: White

value: Not Hispanic or Latino


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851091_I

value: M

value: Asian

value: Healthy Control


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851088_H

value: NCH 692

value: Black or African American


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851072_K


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851077_C

value: NCH 684


title: PUM1CLIP_293T_NoDice_4-25_rep2

status: Public on Oct 17 2018

city: Riverside

first: Fedor

last: Karginov

state: California

address: 900 University Ave

department: MCSB

institute: UC Riverside

description:
crosslinked PUM1-bound RNA
Pum1Peaks.bed

data_processing:
3' adapter (GTGTCAGTCACTTCCAGCGG) was clipped off and the resulting reads filtered for a length of 20nt or more (4nt random ligation barcode + G + 15nt of insert)
reads that have identical barcode + G + insert (i.e. PCR duplicates) were collapsed to unique reads and filtered for the presence of G at position 5
4nt barcode + G were trimmed off, and remaining insert (peak) sequences collapsed to unique sequences, preserving their count of barcodes (unique 5' ligation events during library construction) as the readcount for quantification
reads were aligned by bowtie2 to the hg19 genome build; unmapped reads were further mapped by Tophat to a transcriptome file combining refseq gene information and lincRNAs; matches with a mapping quality of 20 or more were retained; distinct reads with identical mapping coordinates (i.e. sequencing or allelic variants) were collapsed by readcount
reads were annotated by microRNA, refseq/lincRNA, and repeatmasker annotation positions
combined reads from all conditions were pooled to define peaks using FindPeaks4, and readcounts underneath each peak were re-extracted for each replicate
peak readcounts were filtered for a sum of more than 6 (for PUM1) or 3 (for PUM2) across all replicates, and peak signal and differential signal was computed by DESeq2, and further intersected with external data on mRNA level changes as described
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text, extended .bed file with processed, filtered PUM peak coordinates, annotations, quantification and overlap information

growth_protocol: Cells were grown in DMEM (Corning Cellgro) with 10 % Fetal Bovine Serum (HyClone) and 10 units/ml of Penicillin-Streptomycin (HyClone). Cultured plates were grown in a humidified incubator at 37 °C with 5 % CO2

extract_protocol:
Cells were crosslinked, lysed and immunoprecipitated with antibodies against endogenous PUM1 or PUM2 as described in the Materials and Methods
The HITS-CLIP (CLIP-seq) protocol for library construction was performed, as described in the Materials and Methods

tag: cell line

tag: dicer protein status

value: NoDice_4-25 KO

tag: cliped protein


title: PUM1CLIP_293T_NoDice_2-20_rep2

value: NoDice_2-20 KO


title: PUM2CLIP_293T_rep1

description:
crosslinked PUM2-bound RNA
Pum2Peaks.bed

value: WT


title: HESC_SRC-2/NCOA2 ChIP-seq

value: endometrial stromal cells

tag: treatment

value: 10nM beta-estradiol, 100nM medroxyprogesterone acetate, and 1mM cAMP

value: SRC-2/NCOA2 (Bethyl A300-346A)


title: PUM2CLIP_293T_NoDice_4-25_rep1


title: FD41491 P37 NT siRNA day 3 EPC

description:
nontargeting siRNA day 3 EPC
FD41491

value: nontargeting siRNA

value: control

value: EPC

value: day 3 EPC

value: volunteer P37


title: FD41494 P37 SRC-2/NCOA2 siRNA day 3 EPC

description:
SRC-2/NCOA2 siRNA day 3 EPC
FD41494

value: SRC-2/NCOA2 siRNA

value: SRC-2/NCOA2 knockdown


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851090_J

tag: sample name

value: NCH 693

tag: bacterial organism

tag: viral organism

tag: analysis group

value: infection vs healthy ctrl+pneumonia vs healthy ctrl

value: M

value: White

value: Not Hispanic or Latino

value: Healthy Control


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851073_H

value: NCH 688

tag: age (mo.)

tag: race

tag: ethnicity

tag: condition


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851092_D

value: F


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851088_G


title: PUM1CLIP_293T_rep2

value: WT


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851076_L

value: NCH 679


title: N/A-N/A-inf vs healthy ctrl+pneumonia vs healthy ctrl-Healthy Control 8363851077_I

value: NCH 680


title: PUM2CLIP_293T_NoDice_2-20_rep1

value: NoDice_2-20 KO


title: PUM1CLIP_293T_NoDice_4-25_rep1

value: NoDice_4-25 KO


title: PUM1CLIP_293T_rep1


title: Ago2CLIP_dsiPUM2-2_PUM2KD_rep4

description: crosslinked Ago2-bound RNA

data_processing:
3' adapter (GTGTCAGTCACTTCCAGCGG) was clipped off and the resulting reads filtered for a length of 20nt or more (4nt random ligation barcode + G + 15nt of insert)
reads that have identical barcode + G + insert (i.e. PCR duplicates) were collapsed to unique reads and filtered for the presence of G at position 5
4nt barcode + G were trimmed off, and remaining insert (peak) sequences collapsed to unique sequences, preserving their count of barcodes (unique 5' ligation events during library construction) as the readcount for quantification
reads were aligned by bowtie2 to the hg19 genome build; unmapped reads were further mapped by Tophat to a transcriptome file combining refseq gene information and lincRNAs; matches with a mapping quality of 20 or more were retained; distinct reads with identical mapping coordinates (i.e. sequencing or allelic variants) were collapsed by readcount
reads were annotated by microRNA, refseq/lincRNA, and repeatmasker annotation positions
combined reads from all conditions were pooled to define peaks using FindPeaks4, and readcounts underneath each peak were re-extracted for each replicate
peak readcounts were filtered for a sum of more than 21 across all replicates, peaks containing complements to nucleotides 3-7 of the knockdown siRNAs were eliminated to avoid off-targeting artefacts, and peak signal and differential signal was computed by DESeq2, and further intersected with external data on mRNA level changes as described
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text, extended .bed file with processed, filtered Ago2 peak coordinates, annotations, quantification and overlap information

source_name: T-REx-293 cells

extract_protocol:
Cells were crosslinked, lysed and immunoprecipitated with antibodies against endogenous Ago2 as described in the Materials and Methods
The HITS-CLIP (CLIP-seq) protocol for library construction was performed, as described in the Materials and Methods

treatment_protocol: T-REx-293 cells were separately transfected with two distinct siRNAs each against PUM1 or PUM2, or with a gl3.1 siRNA control. TransIT-TKO (Mirus) transfections with 100nM of siRNA were performed for the first PUM1 and PUM2 KD replicates, and calcium phosphate transfections with 100nM siRNA were carried out for the later replicates. For each replicate set, three successive transfections 2-3 days apart were performed to get sufficient knockdown of HuR.

tag: sirna

tag: knockdown protein


title: Ago2CLIP_dsiPUM2-1_PUM2KD_rep4

description: crosslinked Ago2-bound RNA


title: PUM1CLIP_293T_NoDice_2-20_rep1


title: Ago2CLIP_gl3.1_PUM2KD_rep4

description: crosslinked Ago2-bound RNA

value: luciferase (control, not present)


title: Ago2CLIP_dsiPUM2-2_PUM2KD_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM2-1_PUM2KD_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_PUM2KD_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM2-1_PUM2KD_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_PUM2KD_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_PUM2KD_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM2-1_PUM2KD_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM2-2_PUM2KD_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM1-3_PUM1KD_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM1-1_PUM1KD_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_PUM1KD_rep3

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM1-3_PUM1KD_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM1-1_PUM1KD_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM1-1_PUM1KD_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM1-3_PUM1KD_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_PUM1KD_rep1

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_gl3.1_PUM1KD_rep2

description: crosslinked Ago2-bound RNA


title: Ago2CLIP_dsiPUM2-2_PUM2KD_rep3

description: crosslinked Ago2-bound RNA


title: SLE445-PD1POS

status: Public on Sep 26 2018

description:
project2.csv
cDNA3666

data_processing:
Sequences were aligned with HISAT2, duplicates removed with Samtools, and counts generated with HTSeq using the annotations from Gencode V20. Genes identified as globins, ribosomal RNAs, and pseudogenes were removed.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: csv; raw counts

source_name: whole blood

growth_protocol: Blood samples were obtained from patients fulfilling the diagnosis of SLE according to the criteria established by the American College of Rheumatology. Healthy pediatric controls were children visiting the clinic either for reasons not related to autoimmunity or for surgery not associated with any inflammatory diseases

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen)
Total RNA was converted to cDNA using 20 ng RNA as input for the Ovation RNA-Seq System V2, and barcoded Illumina library constructs were produced using Ovation Ultralow Library System V2 (NuGEN Technologies) following the manufacturer’s instructions. Library fragment size and molar concentration were determined using Agilent High Sensitivity DNA Chip on 2100 Bioanalyzer, and quantitative PCR data were obtained by the KAPA BioSystems Library Quantification qPCR Kit for Illumina Platform on a Viia7 Real-Time PCR System (Thermo Fisher Scientific). RNA-seq libraries were sequenced on the Illumina HiSeq 2500 sequencing system using SBS v3 chemistry and two high-output flow cells targeting 70–80 million 2 × 75 paired-end reads per library.

treatment_protocol: Cell isolation: For pDC isolation, the total dendritic cell fraction was obtained from healthy buffy coats by magnetic cell sorting with pan-DC Enrichment Kit (Stem Cell Technology). Highly pure (>99%) pDCs (Lin- HLADR+ CD11c- CD123+) were then isolated from this fraction by FACS sorting. Fresh peripheral blood naïve CD4 T cells (>99% pure) were isolated using Total CD4 T cell enrichment kit (Stem Cell Technology) followed by cell sorting as CD4+ CD45RA+ CD45RO- cells. Naïve CD4+ T cells where labeled with 5 μM carboxy-fluorescein diacetate succinimidyl ester (CFSE; Thermo Fisher) following the manufacturer’s instructions. Were described, primed (CFSElow) CD4+ T cells were sorted from pDC/CD4 T cell co-cultures at day 6. 7ADD and anti-CD123 antibody were used to remove dead cells and contaminating pDCs, respectively (Extended Data Fig. 2a). For B cell isolation, positively selected CD19+ B cells (Stem Cell Technology) were stained with anti-IgD APC, anti-CD27 PE and anti-CD19 FITC and then sorted as IgD+CD27−CD19+ cells (naïve) or IgD-CD27+CD19+ cells (memory). For blood CD4+ T cell subset sorting, frozen PBMCs from SLE patients were stained with anti-CD4 PE-Cy7, anti-CXCR5 AlexaFluor 647, anti-CD45RA APC-H7, anti-PD1 Brilliant Violet 421, anti-CD3 V500 and anti-CXCR3 Brilliant Violet 785. Then, CXCR3+ PD1low CD4+ T cells, CXCR3- PD1hi CD4+ T cells, CXCR3+ PD1hi CD4+ T cells populations were sorted from the CD3+ CD4+ CD45RA- CXCR5- cells fraction. CD3+ CD4+ CD45RA− CXCR5+ CD4+ T cells (Tfh cells) were also sorted for comparison.    CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.     Proliferation assay: CD4 T cell proliferation was measured by resazurin reduction, as previously described3. Briefly, primed (CFSElow) CD4+ T cells were seeded at 5 × 105 cells and re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3) and 2 μg/ml of soluble anti-CD28 mAbs. After incubation for 20 h, medium supplemented with 40 μM resazurin was added for an additional 4 hr. Resazurin reduction to resorufin was measured fluorometrically using a SpectraMax M5 (Molecular Devices). Results obtained were expressed in fluorescence arbitrary units (AU). Alternatively, proliferation was assessed by flow cytometry using the Click-IT EdU Proliferation Kit, according to the manufacturer’s instructions (Thermo Fisher).     In vitro Tfh cell generation: Human Tfh cells were generated as previously described. Briefly, after overnight stimulation of naive CD4+ T cells with Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) in complete RPMI medium, cells were transferred to 96-well plates coated with anti-CD3 and supplemented with 2 μg/ml of soluble anti-CD28 mAb (Biolegend), human recombinant IL-23 (25 ng/ml) and human recombinant TGFβ (5 ng/ml). After 4 d cells were collected and used for analysis.

tag: tissue

value: whole blood

tag: subject id

tag: diagnosis

value: Systemic Lupus Erythematosus (SLE)

tag: cell population (pd1pos=cxcr3+ pd1hi cd4+ t)

tag: activation

tag: project


title: SLE434-Tfh

description:
project2.csv
cDNA3665

value: Tfh

tag: treatment


title: SLE434-PD1POS

description:
project2.csv
cDNA3662


title: SLE424-Tfh

description:
project2.csv
cDNA3661


title: SLE445-Tfh

description:
project2.csv
cDNA3669


title: SLE451-PD1POS

description:
project2.csv
cDNA3670


title: SLE451-Tfh

description:
project2.csv
cDNA3673


title: SLE424-PD1POS

description:
project2.csv
cDNA3658


title: SLE415-Tfh

description:
project2.csv
cDNA3657


title: SLE413-Tfh

description:
project2.csv
cDNA3653


title: SLE415-PD1POS

description:
project2.csv
cDNA3654


title: SLE382-PD1POS

description:
project2.csv
cDNA3646


title: SLE267-Tfh

description:
project2.csv
cDNA3645


title: SLE382-Tfh

description:
project2.csv
cDNA3649


title: SLE267-PD1POS

description:
project2.csv
cDNA3642


title: SLE111-PD1POS

description:
project2.csv
cDNA3634


title: SLE111-Tfh

description:
project2.csv
cDNA3637


title: SLE224-PD1POS

description:
project2.csv
cDNA3638


title: N_II_S8

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3278

source_name: T-cells

value: T-cells

value: II

value: healthy control

value: Ox mtDNA

value: Ox mtDNA generation and pDC activation:Ox mtDNA was generated as previously described. Briefly, healthy neutrophils were pre-incubated with IFNα2β (2000 U/ml; Schering Corp.) for 90 min at 370C and then extensively washed before incubation with anti-RNP IgG (50 μg/ml) purified from SLE patient sera. Neutrophil supernatants were then collected, centrifuged for 10 min at 1400g and stored at -80C. PDCs (5x105 cells/well – 96 U bottom plate) were cultured with 40% v/v Ox mtDNA-containing neutrophil supernatants (referred in the text as “Ox mtDNA”) or with 5 μg/ml of either CpGA (ODN-2216; Invivogen) for 24 h. The volume of Ox mtDNA-containing neutrophil supernatants and the concentration of CpGA were selected based on their capacity to trigger similar levels of IFNα production by pDCs.


title: SLE224-Tfh

description:
project2.csv
cDNA3641


title: N_III_S9

description:
CD4 T cell differentiation, activation and analysis: 12 x 104 freshly sorted allogeneic naïve CD4+ T cells were co-cultured with activated pDCs (DC/T cell ratio of 1:6) in round-bottom 96-wells culture plates for 6 days. Were described, MitoTempo (MT – 50 μM – SantaCruz Biotechnology) or anti-PD1 antibody (clone EH12.2H7 – 10 μg/ml - Biolegend) were added during the co-culture. As a control, 12 x 104 naïve CD4+ T cells were activated with 1 μl of Dynabeads human T cell activator CD3/CD28 (Thermo Fisher) for 6 days (referred in the text as “Th0”). For intracellular cytokine staining, primed CD4+ T cells were re-stimulated with 50 ng/ml PMA, 2 μg/ml Ionomycin and GolgiPlug (BD Biosciences) for 5 h. Cells were then stained with a combination of anti-IL10 and IFNγ mAbs (BD Biosciences) with Cytofix/Cytoperm Fixation and Permeabilization Solution (BD Biosciences) following the manufacturer’s instructions. For re-stimulation experiments, 5 x 104 primed (CFSElow) CD4+ T cells or sorted SLE patient CD4+ T cells were re-stimulated with 10 μg/ml of plate-bound anti-CD3 (OKT3 - Biolegend) and 2 μg/ml of soluble anti-CD28 mAb (Biolegend) for 24 h. Cytokine levels in the corresponding supernatants were measured with Flex Set Kit (BD Biosciences). For HIF1α intracellular staining, CD4+ T cells were stained with anti-HIF-1α antibody (Biolegend) with Foxp3 fix/perm buffer set (Biolegend) following the manufacturer’s instructions. Dead cells were excluded from the analysis by labeling with LIVE/DEAD fixable Aqua (Thermo Fisher) prior to fixation/permeabilization.
project1.csv
cDNA3279

value: III