title: Spt7_Taf13_DMSO_B

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2  using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
Signal per gene was normalized by the number of all S. pombe reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number). Genes classified as dubious, pseudogenes or transposable elements were excluded leaving 5797 genes for the downstream analysis.
Genome_build: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed CSV files contain normalized signal for all analyzed features (5797 mRNA genes).

extract_protocol:
Newly synthesized RNAs were labeled as previously described (Bonnet et al., 2014; PMID: 25228644). S. cerevisiae and previously labeled S. pombe cells were mixed in an 8:1 ratio and total RNA was extracted using the RiboPure yeast kit (Ambion, Life Technologies) using the following volumes:  480 μl lysis buffer, 48 μl 10% SDS, 480 μl phenol:CHCl3:IAA (25:24:1)  per S. cerevisiae pellet + 50 μl S. pombe (from a single S. pombe pellet resuspended in 850 μl lysis buffer). Total RNA was then biotinylated and purified essentially as described (Duffy et al., 2015; PMID: 26340425; Duffy and Simon, 2016; PMID: 27925666) using 40 μl (~40 μg) total RNA. In the last step 50 μl each of RNA sample eluted from streptavidin beads was adjusted to 100 μl with nuclease-free water and purified on RNeasy columns (Qiagen) using the modified protocol as described (Duffy and Simon, 2016; PMID: 27925666). RNAs were eluted into 14 μl nuclease-free water.
Ovation SoLo RNA-seq System and Ovation Universal RNA-seq System kits (Tecan)

treatment_protocol: DMSO for 30 minutes followed by 6 minute RNA labeling with 4-tU

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 TAF13-3xV5 IAA7::KanMX Spt7-3xV5 IAA7::URA3

value: DMSO for 30 minutes


title: Spt7_Taf13_3IAA_B

status: Public on Jan 08 2020

type: SRA

city: Oklahoma City

first: Rafal

last: Donczew

state: OK

address: 825 NE 13th St

department: Cell Cycle and Cancer Biology

country: USA

institute: Oklahoma Medical Research Foundation

library_source: transcriptomic

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: 30 degrees in synthetic medium to mid-log phase

treatment_protocol: 500 μM 3-IAA for 30 minutes followed by 6 minute RNA labeling with 4-tU

tag: strain

tag: genotype

tag: treatment

value: 500 μM 3-IAA for 30 minutes


title: Spt7_Taf13_3IAA_C


title: Spt7_Taf13_DMSO_A


title: Young_EALL_P2_15

city: Singapore

first: Hassen

last: Kared

address: 8A Biomedical Grove - Immunos Building - Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN) - A*STAR

description:
RHT1562
TPM_sc_young.txt

data_processing:
Pair-end raw reads were aligned to human reference genome using RSEM version 1.3.0.
Transcript Per Million read (TPM) values were calculated using RSEM version 1.3.0.
We filtered out low-quality cells from our data set based on a threshold for the number of genes detected (a minimum of 200 unique genes per cell). All genes that were not detected in at least 0.4% of all our single cells were discarded.
Genome_build: GRCh38 version 25
Supplementary_files_format_and_content: tab-delimited text files include TPM values for Young donors (716 cells) and Old donors (725 cells)

organism: Homo sapiens

source_name: Naïve CD4 T cell

extract_protocol:
1mg/ml BSA Lysis buffer (Ambion Thermo Fisher Scientific, Waltham, MA, USA);
Single cell cDNA libraries were using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: Use of 250 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x51 cycles on an Illumina HiSeq 2000 system (Illumina, San Diego, CA, USA) (192 samples/lane).

tag: donorid

value: EALL

tag: plateid

tag: batch

tag: cell type

value: Naive CD4 T cell

tag: developmental stage

value: Young


title: Spt7_C

description: Library strategy: ChEC-Seq

library_source: genomic

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and D. melanogaster reference genome (release 6.06) with Bowtie2 (Langmead and Salzberg, 2012) using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all D. melanogaster reads mapped for the sample and multiplied by 10000 (arbitrarily chosen number).
Genome_build: sacCer3 (S. cerevisiae), release 6.06 (D. melanogaster)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains spike-in normalized signal per base pair.

molecule: genomic DNA

extract_protocol:
ChEC-seq was performed as previously described (Grünberg et al., 2016; PMID: 27797823; Zentner et al., 2015; PMID: 26490019) with following modifications. The final calcium concentration in the reaction mixture was 0.2 mM (2 mM in the original protocol) and MNase digestion was done for 5 min for all collected samples. Stop buffer was supplemented with D. melanogaster MNase-digested DNA (1 ng/ml stock concentration) in the amount calculated based on S. cerevisiae culture A600 measurement (volume = A600 x 8 ul).
Sequencing libraries were prepared similarly as described (Warfield et al., 2017; PMID: 28918900) with several modifications. 1/6 vol of the final ChEC DNA sample was used as an input. Final adapter concentration during ligation was 6.5 nM. Following ligation, two-step cleanup was performed using 0.25X vol AMPure XP reagent in the first step and 1.1X vol in the second step. 18 cycles were used for library amplification.

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 SPT7-3xFlag-MNase::TRP1


title: Young_EALL_P2_14

description:
RHT1561
TPM_sc_young.txt


title: Spt7_Taf13_DMSO_C


title: Young_EALL_P2_12

description:
RHT1559
TPM_sc_young.txt


title: Spt7_Taf13_3IAA_A


title: Young_EALL_P2_9

description:
RHT1556
TPM_sc_young.txt


title: Young_EALL_P2_10

description:
RHT1557
TPM_sc_young.txt


title: Young_EALL_P2_8

description:
RHT1555
TPM_sc_young.txt


title: Young_EALL_P2_5

description:
RHT1552
TPM_sc_young.txt


title: Taf7_YPD_B_DMSO

growth_protocol: 30 degrees in YPD to mid-log phase

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 TAF7-3xV5 IAA7::KanMX


title: Spt3_Taf13_3IAA_A

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 TAF13-3xV5 IAA7::KanMX Spt3 -3xV5 IAA7::URA3


title: Young_EALL_P2_13

description:
RHT1560
TPM_sc_young.txt


title: Spt3_Taf13_3IAA_B


title: Young_EALL_P2_11

description:
RHT1558
TPM_sc_young.txt


title: Spt3_Taf13_DMSO_A


title: Young_EALL_P2_6

description:
RHT1553
TPM_sc_young.txt


title: Spt3_Taf13_3IAA_C


title: Young_EALL_P2_3

description:
RHT1550
TPM_sc_young.txt


title: Taf7_YPD_A_DMSO


title: Young_EALL_P2_2

description:
RHT1549
TPM_sc_young.txt


title: Taf7_YPD_B_3IAA


title: Taf7_YPD_A_3IAA


title: Spt3_Taf13_DMSO_B


title: Young_EALL_P2_1

description:
RHT1548
TPM_sc_young.txt


title: Young_EALL_P1_90

description:
RHT1545
TPM_sc_young.txt


title: Young_EALL_P1_91

description:
RHT1546
TPM_sc_young.txt


title: spt3del_input_A

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2  using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
For each base pair in the genome, we counted the number of paired-end fragments aligned over it.
Signal per base pair was normalized by the number of all S. pombe reads mapped for the sample, multiplied by 10000 (arbitrarily chosen number) and multiplied by the ratio of S. pombe to S. cerevisiae reads in the corresponding input sample.
Genome_build: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary_files_format_and_content: Processed data is provided in a wig format and contains normalized signal per base pair.

extract_protocol:
ChIP-seq was performed similarly as described (Rodriguez et al., 2014; PMID:  25271716 ) with following modifications. Zirconia/silica beads were used for bead beating. Chromatin was sonicated for three rounds of 15 min. S. pombe (strain 972h) chromatin used as a spike-in was prepared the same way as S. cerevisiae samples (including cross linking, bead beating and sonication) and kindly supplied by Toshi Tsukiyama. Each IP reaction contained 1 ug of S. cerevisiae chromatin, 10 ng of S. pombe chromatin and 20 ul of Protein G dynabeads (Invitrogen, #10004D) conjugated with 4 ul of anti-H3K18Ac antibody (EMD Milipore, #07-354) and the final volume was brought to 500 ul with FA buffer. 25 ul of the S. cerevisiae/S. pombe chromatin mix was transferred to a separate tube as an ?input? sample before addition of beads and combined with 25 ul of the stop buffer. Chromatin-antibody complexes were eluted with two 25 ul volumes of stop buffer. IP and input samples were processed together from this point. After Proteinase K digestion DNA was purified by phenol extraction (two step extraction for input samples) followed by ethanol precipitation in the presence of 20 ug glycogen. Pelleted DNA was washed with 70% ethanol and resuspended in 15 ul 10 mM Tris-HCl (pH 7.5).
Sequencing libraries were prepared similarly as described (Warfield et al., 2017; PMID: 28918900) with few modifications. 2 ng of DNA was used as an input. Final adapter concentration during ligation was 6.5 nM. 15 cycles were used for library amplification.

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3 - Flag3 ::KanMX spt3 delta::NAT MX

value: 6 minute RNA labeling with 4-tU

tag: growth

value: 30 degrees in synthetic medium to mid-log phase


title: Young_EALL_P2_7

description:
RHT1554
TPM_sc_young.txt


title: Taf1_YPD_B_3IAA

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 TAF1-3xV5 IAA7::KanMX


title: Young_EALL_P2_4

description:
RHT1551
TPM_sc_young.txt


title: Taf1_YPD_B_DMSO


title: Young_EALL_P1_88

description:
RHT1543
TPM_sc_young.txt


title: Taf1_YPD_A_DMSO


title: Taf1_YPD_A_3IAA


title: Young_EALL_P1_89

description:
RHT1544
TPM_sc_young.txt


title: Taf13_YPD_B_3IAA

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 TAF13-3xV5 IAA7::KanMX


title: Taf13_YPD_A_DMSO


title: Young_EALL_P1_82

description:
RHT1524
TPM_sc_young.txt


title: Young_EALL_P1_86

description:
RHT1541
TPM_sc_young.txt


title: Young_EALL_P1_85

description:
RHT1540
TPM_sc_young.txt


title: Taf13_GC_B_DMSO


title: Young_EALL_P1_84

description:
RHT1526
TPM_sc_young.txt


title: Taf13_YPD_B_DMSO


title: Young_EALL_P1_83

description:
RHT1525
TPM_sc_young.txt


title: Taf13_GC_B_3IAA


title: Young_EALL_P1_81

description:
RHT1523
TPM_sc_young.txt


title: Young_EALL_P1_80

description:
RHT1522
TPM_sc_young.txt


title: Taf13_GC_A_DMSO


title: Taf13_GC_A_3IAA


title: Young_EALL_P2_71

description:
RHT1618
TPM_sc_young.txt


title: spt7del_GC_C

treatment_protocol: 6 minute RNA labeling with 4-tU

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 spt7 delta::HPH

value: control


title: Young_EALL_P1_77

description:
RHT1519
TPM_sc_young.txt


title: Young_EALL_P1_87

description:
RHT1542
TPM_sc_young.txt


title: spt7del_GC_A


title: spt7del_GC_B


title: Young_EALL_P1_76

description:
RHT1518
TPM_sc_young.txt


title: Young_EALL_P1_78

description:
RHT1520
TPM_sc_young.txt


title: spt3del_GC_C


title: Spt3_Taf13_DMSO_C


title: spt3del_GC_B


title: Young_EALL_P1_74

description:
RHT1515
TPM_sc_young.txt


title: Taf13_YPD_A_3IAA


title: spt20del_GC_C

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 spt20 delta::KanMx


title: Young_EALL_P1_72

description:
RHT1513
TPM_sc_young.txt


title: Young_EALL_P1_71

description:
RHT1512
TPM_sc_young.txt


title: Young_EALL_P1_69

description:
RHT1510
TPM_sc_young.txt


title: WT_565_GC_B

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3 - Flag3 ::KanMX


title: Young_EALL_P1_75

description:
RHT1517
TPM_sc_young.txt


title: spt20del_GC_A


title: Young_EALL_P1_68

description:
RHT1509
TPM_sc_young.txt


title: WT_565_GC_A


title: spt20del_GC_B


title: Young_EALL_P1_70

description:
RHT1511
TPM_sc_young.txt


title: WT_4705_GC_B

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0


title: Young_EALL_P1_66

description:
RHT1507
TPM_sc_young.txt


title: Young_EALL_P1_63

description:
RHT1504
TPM_sc_young.txt


title: Young_EALL_P1_65

description:
RHT1506
TPM_sc_young.txt


title: Spt3_7_YPD_C_DMSO

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 SPT7-3xV5 IAA7::KanMX SPT3-3xV5 IAA7degron::URA3

value: DMSO for 30 minutes


title: spt3del_GC_A


title: WT_4705_GC_C


title: WT_4705_GC_A


title: Young_EALL_P1_73

description:
RHT1514
TPM_sc_young.txt

value: EALL

value: Naive CD4 T cell


title: Spt3_7_YPD_C_3IAA

value: 500 μM 3-IAA for 30 minutes


title: Spt3_7_YPD_A_3IAA


title: Spt3_7_YPD_B_DMSO


title: Spt3_7_YPD_B_3IAA


title: Young_EALL_P1_62

description:
RHT1503
TPM_sc_young.txt

value: Young


title: Young_EALL_P1_61

description:
RHT1502
TPM_sc_young.txt


title: Young_EALL_P1_59

description:
RHT1500
TPM_sc_young.txt


title: Spt3_7_GC_C_DMSO


title: Young_EALL_P1_64

description:
RHT1505
TPM_sc_young.txt


title: Young_EALL_P1_58

description:
RHT1499
TPM_sc_young.txt


title: Young_EALL_P1_67

description:
RHT1508
TPM_sc_young.txt


title: Young_EALL_P1_56

description:
RHT1497
TPM_sc_young.txt


title: Spt3_7_GC_B_DMSO


title: Spt3_7_GC_B_3IAA


title: Young_EALL_P1_60

description:
RHT1501
TPM_sc_young.txt


title: Young_EALL_P1_55

description:
RHT1496
TPM_sc_young.txt


title: Young_EALL_P1_79

description:
RHT1521
TPM_sc_young.txt


title: Spt3_7_GC_A_DMSO


title: Young_EALL_P1_54

description:
RHT1495
TPM_sc_young.txt


title: Spt3_7_GC_A_3IAA


title: Spt3_20_GC_C_DMSO

value: mat alpha delta ade2::hisG his3 delta 200 leu2 delta 0 lys2 delta 0 met15 delta 0 trp1 delta 63 ura3 delta 0 RPB3-3x Flag::NAT MX pGPD1-OSTIR::HIS3 SPT20-3xV5-mini degron IAA7::KanMX SPT3-3xV5 IAA7degron::URA3


title: Young_EALL_P1_52

description:
RHT1493
TPM_sc_young.txt


title: Spt3_20_GC_C_3IAA


title: Young_EALL_P1_53

description:
RHT1494
TPM_sc_young.txt


title: Spt3_7_YPD_A_DMSO


title: Spt3_7_GC_C_3IAA


title: Young_EALL_P1_51

description:
RHT1492
TPM_sc_young.txt


title: Spt3_20_GC_B_3IAA


title: Spt3_20_GC_A_DMSO


title: Young_EALL_P1_49

description:
RHT1490
TPM_sc_young.txt


title: Young_EALL_P1_50

description:
RHT1491
TPM_sc_young.txt


title: Young_EALL_P1_57

description:
RHT1498
TPM_sc_young.txt


title: Spt3_20_GC_A_3IAA


title: Young_EALL_P1_48

description:
RHT1489
TPM_sc_young.txt


title: Young_EALL_P1_45

description:
RHT1486
TPM_sc_young.txt


title: Young_EALL_P1_44

description:
RHT1485
TPM_sc_young.txt


title: Young_EALL_P1_43

description:
RHT1484
TPM_sc_young.txt


title: W303 Euploid Rep2

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

description:
Gasch 956
07172018_HTSeq_results.txt

data_processing:
Reads trimmed w/ Trimmomatic-0.30
Read alignment done w/ BWA mem Version: 0.7.12-r1039
Reas sorting and indexing w/ Samtools 1.2 (htslib 1.2.1)
Gene counts generated w/ HTSeq version 0.6.0
RPKM Calculated w/ Gasch Laboratory python script
Genome_build: SGD S288C R58-1-1 w/ YPS1009 snps subsitution
Supplementary_files_format_and_content: HTSeq count tables w/ gene counts for each sample

growth_protocol: All strains were grown 7+ generations in YPD to OD600 0.3-0.6 except noted samples grown 3 generations in YPD to OD600 0.3-0.6 to minimize loss of aneuploidy

extract_protocol:
RNA was extracted with hot phenol protocol; RNA was rRNA-depleted with Illumina's Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat)
cDNA library was prepared with Illumina's TruSeq Total RNA Stranded Kit

tag: hapoid or diploid

value: Haploid

tag: euploid or aneuploid

value: Euploid


title: W303 Disome8,15 Rep2

description:
Gasch 958
07172018_HTSeq_results.txt

value: Aneuploid


title: W303 Disome8 Rep2

description:
Gasch 957
07172018_HTSeq_results.txt


title: Young_EALL_P1_47

description:
RHT1488
TPM_sc_young.txt


title: W303 Disome8,10,16 Rep2

description:
Gasch 959
07172018_HTSeq_results.txt


title: Young_EALL_P1_41

description:
RHT1482
TPM_sc_young.txt


title: W303 Disome8,15 Rep1

description:
Gasch 954
07172018_HTSeq_results.txt


title: W303 Disome8 Rep1

description:
Gasch 953
07172018_HTSeq_results.txt


title: Spt3_20_GC_B_DMSO


title: WA1_Chr8.4n ssd1Δ/ssd1Δ Rep3

description:
Gasch 951
07172018_HTSeq_results.txt

value: Diploid


title: Young_EALL_P1_39

description:
RHT1480
TPM_sc_young.txt


title: Young_EALL_P1_40

description:
RHT1481
TPM_sc_young.txt


title: Young_EALL_P1_38

description:
RHT1479
TPM_sc_young.txt


title: WA1 Euploid ssd1Δ/ssd1Δ Rep3

description:
Gasch 950
07172018_HTSeq_results.txt


title: WA1_Chr8.4n Wild-Type Rep3

description:
Gasch 949
07172018_HTSeq_results.txt


title: W303 Euploid Rep1

description:
Gasch 952
07172018_HTSeq_results.txt


title: Young_EALL_P1_37

description:
RHT1478
TPM_sc_young.txt


title: Young_EALL_P1_46

description:
RHT1487
TPM_sc_young.txt


title: Young_EALL_P1_35

description:
RHT1476
TPM_sc_young.txt


title: W303 Disome8,10,16 Rep1

description:
Gasch 955
07172018_HTSeq_results.txt


title: Young_EALL_P1_36

description:
RHT1477
TPM_sc_young.txt


title: YPS1009 Dis12 ssd1Δ Rep3

description:
Gasch 947
07172018_HTSeq_results.txt


title: Young_EALL_P1_34

description:
RHT1475
TPM_sc_young.txt


title: YPS1009 Euploid ssd1Δ Rep3

description:
Gasch 946
07172018_HTSeq_results.txt


title: Young_EALL_P1_42

description:
RHT1483
TPM_sc_young.txt


title: YPS1009 Euploid Wild-type Rep3

description:
Gasch 944
07172018_HTSeq_results.txt


title: Young_EALL_P1_31

description:
RHT1472
TPM_sc_young.txt


title: Young_EALL_P1_30

description:
RHT1471
TPM_sc_young.txt


title: WA1_Chr8.4n ssd1Δ/ssd1Δ Rep2

description:
Gasch 943
07172018_HTSeq_results.txt


title: Young_EALL_P1_29

description:
RHT1470
TPM_sc_young.txt


title: WA1_Chr8.4n Wild-Type Rep2

description:
Gasch 941
07172018_HTSeq_results.txt


title: YPS1009 Dis12 ssd1Δ Rep4

description:
Gasch 939
07172018_HTSeq_results.txt


title: Young_EALL_P1_28

description:
RHT1469
TPM_sc_young.txt


title: WA1 Euploid Wild-type Rep3

description:
Gasch 948
07172018_HTSeq_results.txt


title: WA1 Euploid Wild-type Rep2

description:
Gasch 940
07172018_HTSeq_results.txt


title: Young_EALL_P1_27

description:
RHT1468
TPM_sc_young.txt


title: Young_EALL_P1_26

description:
RHT1467
TPM_sc_young.txt


title: YPS1009 Euploid ssd1Δ Rep4

description:
Gasch 938
07172018_HTSeq_results.txt


title: Young_EALL_P1_25

description:
RHT1466
TPM_sc_young.txt


title: YPS1009 Euploid Wild-type Rep4

description:
Gasch 936
07172018_HTSeq_results.txt


title: Young_EALL_P1_24

description:
RHT1465
TPM_sc_young.txt


title: WA1_Chr8.4n Wild-Type Rep1

description:
Gasch 933
07172018_HTSeq_results.txt


title: WA1_Chr8.4n ssd1Δ/ssd1Δ Rep1

description:
Gasch 935
07172018_HTSeq_results.txt


title: Young_EALL_P1_33

description:
RHT1474
TPM_sc_young.txt


title: Young_EALL_P1_23

description:
RHT1464
TPM_sc_young.txt


title: Young_EALL_P1_22

description:
RHT1463
TPM_sc_young.txt


title: YPS1009 Dis12 Wild-type Rep3

description:
Gasch 945
07172018_HTSeq_results.txt


title: WA1 Euploid ssd1Δ/ssd1Δ Rep1

description:
Gasch 934
07172018_HTSeq_results.txt


title: WA1 Euploid Wild-type Rep1

description:
Gasch 932
07172018_HTSeq_results.txt


title: Young_EALL_P1_20

description:
RHT1461
TPM_sc_young.txt


title: Young_EALL_P1_21

description:
RHT1462
TPM_sc_young.txt


title: Young_EALL_P1_32

description:
RHT1473
TPM_sc_young.txt


title: Young_EALL_P1_18

description:
RHT1459
TPM_sc_young.txt


title: Young_EALL_P1_17

description:
RHT1458
TPM_sc_young.txt


title: Young_EALL_P1_19

description:
RHT1460
TPM_sc_young.txt


title: WA1 Euploid ssd1Δ/ssd1Δ Rep2

description:
Gasch 942
07172018_HTSeq_results.txt


title: Young_EALL_P1_16

description:
RHT1457
TPM_sc_young.txt


title: Young_EALL_P1_13

description:
RHT1454
TPM_sc_young.txt


title: Young_EALL_P1_14

description:
RHT1455
TPM_sc_young.txt


title: Young_EALL_P1_15

description:
RHT1456
TPM_sc_young.txt


title: Young_EALL_P1_12

description:
RHT1453
TPM_sc_young.txt


title: R848-treated Peyer's patch TIM-4+ LysoMac, replicate 2

type: RNA

city: Marseille

first: Hugues

last: Lelouard

address: parc Scientifique de Luminy case 906

country: France

institute: CIML CNRS UMR 7280

description:
Peyer's patch TIM4+ macrophages 9h after R848 treatment
PP TIM-4+ LysoMac R848 # 2

hyb_protocol: Following fragmentation and end-labelling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene. The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix).

scan_protocol: Chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: Raw data (.CEL files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

organism: Mus musculus

source_name: Mouse Peyer's patch, R848, 9h

label_protocol: Biotinylated double strand cDNA targets were prepared from 2 to 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol: Extraction of total RNA was performed using the Qiagen RNeasy Plus Micro Kit following the manufacturer's instructions.

treatment_protocol: Peyer's patches (PP) were collected from 42 C57BL/6 mice per replicate (6–8 week-old). Groups of PP from 3 mice were cut into pieces and digested in 7mL of RPMI containing 100 µg/mL of type 2 collagenase (Worthington) and 140 µg/mL of DNase I (Sigma) for 40 min at room temperature. CD11c+ cells were enriched using anti-CD11c microbeads and the program posselD2 of an autoMACS pro separator according to manufacturer’s instructions (Miltenyi Biotec) before staining and cell sorting using a a FACSAria III (BD Biosciences).

tag: gender

value: Female

tag: age

value: 10 to 8 weeks-old

tag: tissue

value: Peyer's patch

tag: main location

value: Interfollicular region (T cell zone)

value: Macrophages

tag: phenotype


title: Young_EALL_P1_10

description:
RHT1451
TPM_sc_young.txt


title: Young_EALL_P1_6

description:
RHT1447
TPM_sc_young.txt


title: Young_EALL_P1_9

description:
RHT1450
TPM_sc_young.txt


title: R848-treated Peyer's patch TIM-4- LysoMac, replicate 3

description:
Peyer's patch TIM4- macrophages 9h after R848 treatment
PP TIM-4- LysoMac R848 # 3

value: 8 to 8 weeks-old

value: Subepithelial dome


title: Young_EALL_P1_8

description:
RHT1449
TPM_sc_young.txt


title: YPS1009 Dis12 Wild-type Rep4

description:
Gasch 937
07172018_HTSeq_results.txt


title: Young_EALL_P1_7

description:
RHT1448
TPM_sc_young.txt


title: R848-treated Peyer's patch DP LysoDC, replicate 3

description:
Peyer's patch DP LysoDC 9h after R848 treatment
PP DP LysoDC R848 # 3

value: 6 to 8 weeks-old

value: Monocyte-derived Dendritic Cell


title: Young_EALL_P1_11

description:
RHT1452
TPM_sc_young.txt

value: EALL

value: Naive CD4 T cell


title: R848-treated Peyer's patch DP LysoDC, replicate 2

description:
Peyer's patch DP LysoDC 9h after R848 treatment
PP DP LysoDC R848 # 2


title: Young_EALL_P1_2

description:
RHT1443
TPM_sc_young.txt

value: Young


title: R848-treated Peyer's patch TIM-4- LysoMac, replicate 1

description:
Peyer's patch TIM4- macrophages 9h after R848 treatment
PP TIM-4- LysoMac R848 # 1


title: Young_EALL_P1_1

description:
RHT1442
TPM_sc_young.txt


title: R848-treated Peyer's patch TIM-4- LysoMac, replicate 2

description:
Peyer's patch TIM4- macrophages 9h after R848 treatment
PP TIM-4- LysoMac R848 # 2

value: 7 to 8 weeks-old


title: R848-treated Peyer's patch TP LysoDC, replicate 1

description:
Peyer's patch TP LysoDC 9h after R848 treatment
PP TP LysoDC R848 # 1


title: Peyer's patch TN LysoDC, steady state, replicate 4

description:
Peyer's patch TN LysoDC at steady state
PP TN LysoDC # 4

source_name: Mouse Peyer's patch, steady state

value: Follicle


title: R848-treated Peyer's patch TP LysoDC, replicate 2

description:
Peyer's patch TP LysoDC 9h after R848 treatment
PP TP LysoDC R848 # 2


title: R848-treated Peyer's patch DP LysoDC, replicate 4

description:
Peyer's patch DP LysoDC 9h after R848 treatment
PP DP LysoDC R848 # 4


title: R848-treated Peyer's patch TP LysoDC, replicate 3

description:
Peyer's patch TP LysoDC 9h after R848 treatment
PP TP LysoDC R848 # 3


title: Young_DZQV_P2_89

description:
RHT1254
TPM_sc_young.txt

value: DZQV


title: Peyer's patch TN LysoDC, steady state, replicate 3

description:
Peyer's patch TN LysoDC at steady state
PP TN LysoDC # 3


title: R848-treated Peyer's patch DP LysoDC, replicate 1

description:
Peyer's patch DP LysoDC 9h after R848 treatment
PP DP LysoDC R848 # 1


title: Peyer's patch TN LysoDC, steady state, replicate 2

description:
Peyer's patch TN LysoDC at steady state
PP TN LysoDC # 2


title: Young_EALL_P1_5

description:
RHT1446
TPM_sc_young.txt


title: Peyer's patch TN LysoDC, steady state, replicate 1

description:
Peyer's patch TN LysoDC at steady state
PP TN LysoDC # 1


title: Young_DZQV_P2_88

description:
RHT1253
TPM_sc_young.txt


title: Young_EALL_P1_3

description:
RHT1444
TPM_sc_young.txt


title: Young_DZQV_P2_87

description:
RHT1252
TPM_sc_young.txt


title: Young_DZQV_P2_86

description:
RHT1251
TPM_sc_young.txt


title: Peyer's patch SP LysoDC, steady state, replicate 2

description:
Peyer's patch SP LysoDC at steady state
PP SP LysoDC # 2


title: Young_DZQV_P2_85

description:
RHT1250
TPM_sc_young.txt


title: Young_DZQV_P2_82

description:
RHT1247
TPM_sc_young.txt


title: R848-treated Peyer's patch TIM-4+ LysoMac, replicate 3

description:
Peyer's patch TIM4+ macrophages 9h after R848 treatment
PP TIM-4+ LysoMac R848 # 3

value: 11 to 8 weeks-old


title: Young_EALL_P1_4

description:
RHT1445
TPM_sc_young.txt


title: Young_DZQV_P2_83

description:
RHT1248
TPM_sc_young.txt


title: Young_DZQV_P2_78

description:
RHT1243
TPM_sc_young.txt


title: Young_DZQV_P2_77

description:
RHT1242
TPM_sc_young.txt


title: R848-treated Peyer's patch TIM-4+ LysoMac, replicate 1

description:
Peyer's patch TIM4+ macrophages 9h after R848 treatment
PP TIM-4+ LysoMac R848 # 1

value: 9 to 8 weeks-old


title: Young_DZQV_P2_76

description:
RHT1241
TPM_sc_young.txt


title: Young_DZQV_P2_81

description:
RHT1246
TPM_sc_young.txt


title: Peyer's patch DP LysoDC, steady state, replicate 5

description:
Peyer's patch DP LysoDC at steady state
PP DP LysoDC # 5

value: Female


title: Peyer's patch SP LysoDC, steady state, replicate 4

description:
Peyer's patch SP LysoDC at steady state
PP SP LysoDC # 4


title: Peyer's patch DP LysoDC, steady state, replicate 3

description:
Peyer's patch DP LysoDC at steady state
PP DP LysoDC # 3


title: Peyer's patch DP LysoDC, steady state, replicate 2

description:
Peyer's patch DP LysoDC at steady state
PP DP LysoDC # 2


title: G03T3_CardiogenicShock

city: Milano

first: Matteo

last: Barcella

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description:
Ribo and Globin depleted library
processed data file: rawcounts_CS_SS.xlsx

data_processing:
Basecalls performed using CASAVA version 1.8.2
Trimming performed with Trimmomatic v0.35, with following parameters: MINLEN:40, AVGQUAL:25 and TRAILING:15
Trimmed reads aligned to GRCh38 using STAR v.2.5.2b using as reference transcript the gencode (v.25) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.5.1 with custom parameters: --minOverlap 5; only both reads, no multimapping.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file including raw counts for each sample (columns) across 58096 genes (rows) [counts matrix]

source_name: CardiogenicShock_T3_whole blood

extract_protocol:
Peripheral blood was collected in EDTA tubes at T1,T2 and T3 and stored at -20°C after adding 400µl of 2X Denaturing solution (Ambion, USA).Total RNA was extracted from 800 µl of blood with MirVana Paris Kit and treated with Turbo DNA-free Kit (Ambion, USA). RNA Quality was assessed on Agilent Bioanalyzer with the RNA 6000 Nano Kit (Agilent, Santa Clara, CA) and samples were considered suitable for processing if RNA Integrity Number was greater than 7.5
Sequencing libraries were prepared with the TruSeq Stranded Total RNA with Ribo-Zero Globin Kit (Illumina, San Diego, CA) using 800 ng of total RNA

tag: patient

tag: timepoint

tag: clinical classification

value: CS

value: Whole blood


title: Peyer's patch DP LysoDC, steady state, replicate 1

description:
Peyer's patch DP LysoDC at steady state
PP DP LysoDC # 1

tag: strain

value: Peyer's patch

tag: treatment


title: Peyer's patch DP LysoDC, steady state, replicate 4

description:
Peyer's patch DP LysoDC at steady state
PP DP LysoDC # 4


title: Peyer's patch TP LysoDC, steady state, replicate 4

description:
Peyer's patch TP LysoDC at steady state
PP TP LysoDC # 4


title: Peyer's patch TP LysoDC, steady state, replicate 3

description:
Peyer's patch TP LysoDC at steady state
PP TP LysoDC # 3


title: Young_DZQV_P2_75

description:
RHT1240
TPM_sc_young.txt

tag: donorid

tag: plateid


title: Peyer's patch TP LysoDC, steady state, replicate 1

description:
Peyer's patch TP LysoDC at steady state
PP TP LysoDC # 1

tag: cell type


title: G03T1_CardiogenicShock

source_name: CardiogenicShock_T1_whole blood


title: Peyer's patch TP LysoDC, steady state, replicate 2

description:
Peyer's patch TP LysoDC at steady state
PP TP LysoDC # 2


title: G03T2_CardiogenicShock

source_name: CardiogenicShock_T2_whole blood


title: Young_DZQV_P2_74

description:
RHT1239
TPM_sc_young.txt

tag: batch

tag: developmental stage


title: Young_DZQV_P2_73

description:
RHT1237
TPM_sc_young.txt


title: Young_DZQV_P2_72

description:
RHT1236
TPM_sc_young.txt


title: G01T3_SepticShock

source_name: SepticShock_T3_whole blood

value: SS


title: G07T1_SepticShock [re-analysis]

source_name: SepticShock_T1_whole blood


title: G07T2_SepticShock [re-analysis]

source_name: SepticShock_T2_whole blood


title: Young_DZQV_P2_70

description:
RHT1234
TPM_sc_young.txt


title: Young_DZQV_P2_71

description:
RHT1235
TPM_sc_young.txt


title: G01T2_SepticShock [re-analysis]


title: G01T1_SepticShock [re-analysis]


title: Young_DZQV_P2_69

description:
RHT1232
TPM_sc_young.txt


title: Peyer's patch SP LysoDC, steady state, replicate 3

description:
Peyer's patch SP LysoDC at steady state
PP SP LysoDC # 3


title: Young_DZQV_P2_84

description:
RHT1249
TPM_sc_young.txt


title: Young_DZQV_P2_66

description:
RHT1229
TPM_sc_young.txt


title: Young_DZQV_P2_68

description:
RHT1231
TPM_sc_young.txt


title: G07T3_SepticShock


title: Young_DZQV_P2_63

description:
RHT1226
TPM_sc_young.txt


title: Young_DZQV_P2_65

description:
RHT1228
TPM_sc_young.txt


title: Young_DZQV_P2_67

description:
RHT1230
TPM_sc_young.txt


title: Young_DZQV_P2_64

description:
RHT1227
TPM_sc_young.txt


title: Young_DZQV_P2_62

description:
RHT1225
TPM_sc_young.txt


title: Young_DZQV_P2_60

description:
RHT1223
TPM_sc_young.txt


title: Young_DZQV_P2_61

description:
RHT1224
TPM_sc_young.txt


title: Young_DZQV_P2_59

description:
RHT1222
TPM_sc_young.txt


title: VA Responder-12

city: New Delhi

first: Ritushree

last: Kukreti

state: Delhi

address: CSIR-IGIB, Mall road, Opp. Jubilee Hall, University of Delhi

department: Genomics and Molecular Medicine Unit

country: India

institute: CSIR-IGIB

description: Valproate Responder

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw intensity files were extracted from GenomeStudio and then uploaded in R software ('limma' package in R) to perform background correction. Further, filtration of probes with detection p<0.05 for at least 50% arrays per chip was performed on the background-corrected data which reduced the number of probes to only 13,165 from the initial 47,231 probes. Finally, the filtered data were normalised using log2 transformation followed by Supervised Normalization of Microarrays (SNM) where sex, age and batch-effects between the samples were adjusted.

source_name: Whole blood

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy Minelute Clean-up kit in accordance with the prescribed protocol provided with the kit.

tag: age (in years)

tag: Sex

value: Male

tag: epilepsy type

value: Cryptogenic

value: Valproate

tag: drug response

value: Responder

tag: ethnicity

value: North Indian


title: VA Responder-14

description: Valproate Responder

value: Idiopathic


title: CBZ Non-responder-9

description: Carbamazepine Non-responder

value: Carbamazepine

value: Non-responder


title: VA Responder-16

description: Valproate Responder


title: PHT Non-responder-6

description: Phenytoin Non-responder

value: Phenytoin


title: Young_DZQV_P2_57

description:
RHT1220
TPM_sc_young.txt

value: DZQV

value: Naive CD4 T cell

value: Young


title: CBZ Responder-10

description: Carbamazepine Responder

value: Female


title: Young_DZQV_P2_58

description:
RHT1221
TPM_sc_young.txt


title: Peyer's patch SP LysoDC, steady state, replicate 1

description:
Peyer's patch SP LysoDC at steady state
PP SP LysoDC # 1

tag: gender

tag: age

value: 6 to 8 weeks-old

tag: tissue

tag: main location

value: Subepithelial dome

value: Monocyte-derived Dendritic Cell


title: Young_DZQV_P2_55

description:
RHT1218
TPM_sc_young.txt


title: Young_DZQV_P2_56

description:
RHT1219
TPM_sc_young.txt


title: VA Responder-13

description: Valproate Responder


title: CBZ Responder-9

description: Carbamazepine Responder


title: Young_DZQV_P2_53

description:
RHT1216
TPM_sc_young.txt


title: Young_DZQV_P2_54

description:
RHT1217
TPM_sc_young.txt


title: PHT Responder-7

description: Phenytoin Responder


title: Healthy Control-17

description: Healthy Control


title: Young_DZQV_P2_52

description:
RHT1215
TPM_sc_young.txt


title: Healthy Control-10

description: Healthy Control


title: VA Responder-15

description: Valproate Responder


title: VA Responder-10

description: Valproate Responder


title: Healthy Control-16

description: Healthy Control


title: Healthy Control-9

description: Healthy Control


title: Healthy Control-15

description: Healthy Control


title: Young_DZQV_P2_50

description:
RHT1213
TPM_sc_young.txt


title: Healthy Control-8

description: Healthy Control


title: Young_DZQV_P2_49

description:
RHT1212
TPM_sc_young.txt


title: Young_DZQV_P2_48

description:
RHT1211
TPM_sc_young.txt


title: Young_DZQV_P2_46

description:
RHT1209
TPM_sc_young.txt


title: Young_DZQV_P2_45

description:
RHT1208
TPM_sc_young.txt


title: Young_DZQV_P2_44

description:
RHT1207
TPM_sc_young.txt


title: Young_DZQV_P2_43

description:
RHT1206
TPM_sc_young.txt


title: Young_DZQV_P2_51

description:
RHT1214
TPM_sc_young.txt


title: Young_DZQV_P2_41

description:
RHT1204
TPM_sc_young.txt


title: Young_DZQV_P2_40

description:
RHT1203
TPM_sc_young.txt


title: Healthy Control-13

description: Healthy Control


title: Healthy Control-12

description: Healthy Control


title: Healthy Control-14

description: Healthy Control


title: Healthy Control-1

description: Healthy Control


title: Young_DZQV_P2_47

description:
RHT1210
TPM_sc_young.txt


title: Young_DZQV_P2_42

description:
RHT1205
TPM_sc_young.txt


title: PHT Responder-6

description: Phenytoin Responder

value: Symptomatic


title: Drug-naïve_SE-12

description: Drug-naïve

value: Male

value: Drug-naïve


title: Young_DZQV_P2_39

description:
RHT1202
TPM_sc_young.txt


title: Healthy Control-2

description: Healthy Control


title: Healthy Control-19

description: Healthy Control


title: Young_DZQV_P2_38

description:
RHT1201
TPM_sc_young.txt


title: Drug-naïve_IE-13

description: Drug-naïve


title: Drug-naïve_IE-11

description: Drug-naïve


title: Young_DZQV_P2_35

description:
RHT1198
TPM_sc_young.txt


title: Healthy Control-4

description: Healthy Control


title: Young_DZQV_P2_37

description:
RHT1200
TPM_sc_young.txt


title: Young_DZQV_P2_36

description:
RHT1199
TPM_sc_young.txt


title: Drug-naïve_IE-15

description: Drug-naïve


title: Drug-naïve_IE-10

description: Drug-naïve


title: Young_DZQV_P2_34

description:
RHT1197
TPM_sc_young.txt


title: Young_DZQV_P2_33

description:
RHT1196
TPM_sc_young.txt


title: Healthy Control-3 (Replicate)

description: Healthy Control


title: Young_DZQV_P2_32

description:
RHT1195
TPM_sc_young.txt


title: Young_DZQV_P2_30

description:
RHT1193
TPM_sc_young.txt


title: Young_DZQV_P2_29

description:
RHT1192
TPM_sc_young.txt


title: Young_DZQV_P2_31

description:
RHT1194
TPM_sc_young.txt


title: Young_DZQV_P2_28

description:
RHT1191
TPM_sc_young.txt


title: Healthy Control-11

description: Healthy Control


title: Healthy Control-7

description: Healthy Control


title: VA Responder-11

description: Valproate Responder

value: Valproate


title: Young_DZQV_P2_27

description:
RHT1190
TPM_sc_young.txt


title: Drug-naïve_IE-5

description: Drug-naïve


title: Young_DZQV_P2_26

description:
RHT1189
TPM_sc_young.txt


title: Young_DZQV_P2_25

description:
RHT1188
TPM_sc_young.txt


title: VA Responder-9

description: Valproate Responder

value: Responder


title: Young_DZQV_P2_24

description:
RHT1187
TPM_sc_young.txt


title: Young_DZQV_P2_23

description:
RHT1186
TPM_sc_young.txt


title: Young_DZQV_P2_22

description:
RHT1185
TPM_sc_young.txt


title: Young_DZQV_P2_21

description:
RHT1184
TPM_sc_young.txt


title: Young_DZQV_P2_20

description:
RHT1183
TPM_sc_young.txt


title: Drug-naïve_IE-9

description: Drug-naïve

value: North Indian


title: Healthy Control-18

description: Healthy Control


title: Drug-naïve_SE-2

description: Drug-naïve


title: Young_DZQV_P2_18

description:
RHT1181
TPM_sc_young.txt


title: Young_DZQV_P2_19

description:
RHT1182
TPM_sc_young.txt


title: Healthy Control-6

description: Healthy Control


title: Healthy Control-5

description: Healthy Control


title: Drug-naïve_IE-6

description: Drug-naïve

value: Idiopathic


title: VA Responder-8

description: Valproate Responder


title: Young_DZQV_P2_17

description:
RHT1180
TPM_sc_young.txt


title: Drug-naïve_SE-7

description: Drug-naïve


title: Drug-naïve_IE-4

description: Drug-naïve


title: Drug-naïve_CE-36

description: Drug-naïve

value: Cryptogenic


title: Healthy Control-3

description: Healthy Control


title: Young_DZQV_P2_16

description:
RHT1179
TPM_sc_young.txt


title: Healthy Control-63

description: Healthy Control


title: Young_DZQV_P2_15

description:
RHT1178
TPM_sc_young.txt


title: PHT Non-responder-5

description: Phenytoin Non-responder

value: Non-responder


title: Young_DZQV_P2_14

description:
RHT1177
TPM_sc_young.txt


title: PHT Non-responder-4

description: Phenytoin Non-responder

value: Phenytoin


title: Healthy Control-64

description: Healthy Control


title: Drug-naïve_CE-33

description: Drug-naïve


title: Young_DZQV_P2_12

description:
RHT1175
TPM_sc_young.txt

value: DZQV


title: Young_DZQV_P2_13

description:
RHT1176
TPM_sc_young.txt

value: Naive CD4 T cell


title: Young_DZQV_P2_10

description:
RHT1173
TPM_sc_young.txt

value: Young


title: Young_DZQV_P2_80

description:
RHT1245
TPM_sc_young.txt


title: CBZ Non-responder-8

description: Carbamazepine Non-responder

value: Carbamazepine


title: Young_DZQV_P2_79

description:
RHT1244
TPM_sc_young.txt


title: Young_DZQV_P2_7

description:
RHT1170
TPM_sc_young.txt


title: Young_DZQV_P2_9

description:
RHT1172
TPM_sc_young.txt


title: Young_DZQV_P2_11

description:
RHT1174
TPM_sc_young.txt


title: PHT Non-responder-3

description: Phenytoin Non-responder


title: Young_DZQV_P2_4

description:
RHT1166
TPM_sc_young.txt


title: Young_DZQV_P2_6

description:
RHT1169
TPM_sc_young.txt


title: Young_DZQV_P2_5

description:
RHT1167
TPM_sc_young.txt


title: Young_DZQV_P2_8

description:
RHT1171
TPM_sc_young.txt


title: Young_DZQV_P2_3

description:
RHT1165
TPM_sc_young.txt


title: Drug-naïve_IE-1

description: Drug-naïve

value: Female


title: Drug-naïve_CE-26

description: Drug-naïve


title: VA Non-responder-8

description: Valproate Non-responder


title: Young_DZQV_P2_2

description:
RHT1164
TPM_sc_young.txt


title: Young_DZQV_P2_1

description:
RHT1163
TPM_sc_young.txt


title: Young_DZQV_P1_81

description:
RHT1161
TPM_sc_young.txt


title: Young_DZQV_P1_78

description:
RHT1158
TPM_sc_young.txt


title: VA Non-responder-7

description: Valproate Non-responder


title: Young_DZQV_P1_80

description:
RHT1160
TPM_sc_young.txt


title: Young_DZQV_P1_79

description:
RHT1159
TPM_sc_young.txt


title: CBZ Non-responder-7

description: Carbamazepine Non-responder


title: Young_DZQV_P1_76

description:
RHT1156
TPM_sc_young.txt


title: PHT Responder-5

description: Phenytoin Responder


title: Young_DZQV_P1_77

description:
RHT1157
TPM_sc_young.txt


title: CBZ Responder-8

description: Carbamazepine Responder


title: Healthy Control-61

description: Healthy Control


title: Young_DZQV_P1_75

description:
RHT1155
TPM_sc_young.txt


title: Young_DZQV_P1_74

description:
RHT1154
TPM_sc_young.txt


title: VA Non-responder-9

description: Valproate Non-responder


title: Drug-naïve_SE-35

description: Drug-naïve


title: Healthy Control-62

description: Healthy Control


title: CBZ Responder-7

description: Carbamazepine Responder


title: Healthy Control-60

description: Healthy Control


title: Healthy Control-54

description: Healthy Control


title: CBZ Non-responder-6

description: Carbamazepine Non-responder


title: VA Responder-7

description: Valproate Responder


title: Drug-naïve_SE-31

description: Drug-naïve


title: Young_DZQV_P1_73

description:
RHT1153
TPM_sc_young.txt


title: Young_DZQV_P1_71

description:
RHT1151
TPM_sc_young.txt


title: Drug-naïve_CE-23

description: Drug-naïve


title: Young_DZQV_P1_70

description:
RHT1150
TPM_sc_young.txt


title: Drug-naïve_SE-32

description: Drug-naïve


title: VA Non-responder-6

description: Valproate Non-responder


title: Young_DZQV_P1_68

description:
RHT1148
TPM_sc_young.txt


title: Healthy Control-65

description: Healthy Control


title: Young_DZQV_P1_69

description:
RHT1149
TPM_sc_young.txt


title: CBZ Non-responder-5

description: Carbamazepine Non-responder


title: Drug-naïve_CE-34

description: Drug-naïve


title: Drug-naïve_SE-22

description: Drug-naïve


title: Drug-naïve_SE-30

description: Drug-naïve


title: Young_DZQV_P1_67

description:
RHT1147
TPM_sc_young.txt


title: Young_DZQV_P1_66

description:
RHT1146
TPM_sc_young.txt


title: Drug-naïve_CE-28

description: Drug-naïve


title: Young_DZQV_P1_65

description:
RHT1145
TPM_sc_young.txt


title: Young_DZQV_P1_72

description:
RHT1152
TPM_sc_young.txt


title: Young_DZQV_P1_63

description:
RHT1143
TPM_sc_young.txt


title: Young_DZQV_P1_64

description:
RHT1144
TPM_sc_young.txt


title: Young_DZQV_P1_62

description:
RHT1132
TPM_sc_young.txt


title: Young_DZQV_P1_61

description:
RHT1131
TPM_sc_young.txt


title: Young_DZQV_P1_59

description:
RHT1129
TPM_sc_young.txt


title: CBZ Non-responder-4

description: Carbamazepine Non-responder


title: Young_DZQV_P1_60

description:
RHT1130
TPM_sc_young.txt


title: Drug-naïve_SE-25

description: Drug-naïve


title: Drug-naïve_CE-29

description: Drug-naïve


title: PHT Non-responder-2

description: Phenytoin Non-responder


title: Young_DZQV_P1_58

description:
RHT1128
TPM_sc_young.txt


title: Young_DZQV_P1_56

description:
RHT1126
TPM_sc_young.txt


title: CBZ Non-responder-3

description: Carbamazepine Non-responder


title: PHT Responder-4

description: Phenytoin Responder


title: Young_DZQV_P1_55

description:
RHT1125
TPM_sc_young.txt


title: Healthy Control-53

description: Healthy Control


title: Young_DZQV_P1_54

description:
RHT1124
TPM_sc_young.txt


title: Healthy Control-42

description: Healthy Control


title: Drug-naïve_CE-20

description: Drug-naïve


title: CBZ Responder-5

description: Carbamazepine Responder


title: Drug-naïve_CE-27

description: Drug-naïve


title: Drug-naïve_IE-21

description: Drug-naïve


title: Drug-naïve_SE-24

description: Drug-naïve


title: CBZ Responder-4

description: Carbamazepine Responder


title: Young_DZQV_P1_52

description:
RHT1121
TPM_sc_young.txt


title: Young_DZQV_P1_53

description:
RHT1123
TPM_sc_young.txt


title: Young_DZQV_P1_57

description:
RHT1127
TPM_sc_young.txt


title: Healthy Control-25

description: Healthy Control


title: Healthy Control-51

description: Healthy Control


title: Young_DZQV_P1_49

description:
RHT1118
TPM_sc_young.txt


title: Young_DZQV_P1_50

description:
RHT1119
TPM_sc_young.txt


title: Young_DZQV_P1_46

description:
RHT1114
TPM_sc_young.txt


title: Young_DZQV_P1_51

description:
RHT1120
TPM_sc_young.txt


title: Young_DZQV_P1_47

description:
RHT1116
TPM_sc_young.txt


title: Young_DZQV_P1_48

description:
RHT1117
TPM_sc_young.txt


title: Young_DZQV_P1_45

description:
RHT1113
TPM_sc_young.txt


title: Healthy Control-27

description: Healthy Control


title: VA Non-responder-5

description: Valproate Non-responder


title: Drug-naïve_IE-14

description: Drug-naïve


title: Healthy Control-28

description: Healthy Control


title: Healthy Control-24

description: Healthy Control


title: Young_DZQV_P1_42

description:
RHT1110
TPM_sc_young.txt


title: Young_DZQV_P1_41

description:
RHT1109
TPM_sc_young.txt


title: Young_DZQV_P1_40

description:
RHT1108
TPM_sc_young.txt


title: Young_DZQV_P1_39

description:
RHT1107
TPM_sc_young.txt


title: Young_DZQV_P1_38

description:
RHT1106
TPM_sc_young.txt


title: Young_DZQV_P1_36

description:
RHT1104
TPM_sc_young.txt


title: Young_DZQV_P1_37

description:
RHT1105
TPM_sc_young.txt


title: Young_DZQV_P1_43

description:
RHT1111
TPM_sc_young.txt


title: VA Responder-6

description: Valproate Responder


title: CBZ Non-responder-2

description: Carbamazepine Non-responder


title: Young_DZQV_P1_44

description:
RHT1112
TPM_sc_young.txt


title: VA Responder-4

description: Valproate Responder


title: Young_DZQV_P1_34

description:
RHT1102
TPM_sc_young.txt


title: Young_DZQV_P1_33

description:
RHT1101
TPM_sc_young.txt


title: PHT Responder-2

description: Phenytoin Responder


title: VA Responder-5

description: Valproate Responder


title: VA Non-responder-3

description: Valproate Non-responder


title: Healthy Control-36

description: Healthy Control


title: Young_DZQV_P1_35

description:
RHT1103
TPM_sc_young.txt


title: CBZ Responder-3

description: Carbamazepine Responder


title: Healthy Control-50

description: Healthy Control


title: VA Non-responder-4

description: Valproate Non-responder


title: Healthy Control-33

description: Healthy Control


title: Healthy Control-40

description: Healthy Control


title: Healthy Control-38

description: Healthy Control


title: Drug-naïve_IE-19

description: Drug-naïve


title: Healthy Control-49

description: Healthy Control


title: PHT Responder-3

description: Phenytoin Responder


title: PHT Responder-1

description: Phenytoin Responder


title: Young_DZQV_P1_30

description:
RHT1098
TPM_sc_young.txt


title: Young_DZQV_P1_31

description:
RHT1099
TPM_sc_young.txt


title: CBZ Responder-2

description: Carbamazepine Responder


title: Young_DZQV_P1_28

description:
RHT1096
TPM_sc_young.txt


title: Young_DZQV_P1_32

description:
RHT1100
TPM_sc_young.txt


title: Young_DZQV_P1_27

description:
RHT1093
TPM_sc_young.txt


title: Healthy Control-39

description: Healthy Control


title: Healthy Control-30

description: Healthy Control


title: Young_DZQV_P1_26

description:
RHT1092
TPM_sc_young.txt


title: Young_DZQV_P1_25

description:
RHT1091
TPM_sc_young.txt


title: PHT Non-responder-1

description: Phenytoin Non-responder


title: Drug-naïve_IE-17

description: Drug-naïve


title: Young_DZQV_P1_24

description:
RHT1090
TPM_sc_young.txt


title: Young_DZQV_P1_23

description:
RHT1089
TPM_sc_young.txt


title: CBZ Non-responder-1

description: Carbamazepine Non-responder


title: Healthy Control-29

description: Healthy Control


title: Young_DZQV_P1_19

description:
RHT1085
TPM_sc_young.txt


title: Young_DZQV_P1_20

description:
RHT1086
TPM_sc_young.txt


title: Young_DZQV_P1_29

description:
RHT1097
TPM_sc_young.txt


title: CBZ Responder-1

description: Carbamazepine Responder


title: Young_DZQV_P1_18

description:
RHT1084
TPM_sc_young.txt


title: Young_DZQV_P1_21

description:
RHT1087
TPM_sc_young.txt


title: Young_DZQV_P1_17

description:
RHT1083
TPM_sc_young.txt


title: Young_DZQV_P1_22

description:
RHT1088
TPM_sc_young.txt


title: Young_DZQV_P1_16

description:
RHT1082
TPM_sc_young.txt


title: Young_DZQV_P1_15

description:
RHT1081
TPM_sc_young.txt


title: Young_DZQV_P1_14

description:
RHT1080
TPM_sc_young.txt


title: Healthy Control-37

description: Healthy Control


title: VA Responder-3

description: Valproate Responder


title: Young_DZQV_P1_13

description:
RHT1079
TPM_sc_young.txt


title: Young_DZQV_P1_12

description:
RHT1077
TPM_sc_young.txt


title: VA Responder-2

description: Valproate Responder


title: Healthy Control-23

description: Healthy Control


title: Healthy Control-20

description: Healthy Control


title: VA Non-responder-2

description: Valproate Non-responder


title: Healthy Control-44

description: Healthy Control


title: VA Responder-1

description: Valproate Responder


title: Drug-naïve_SE-16

description: Drug-naïve


title: Young_DZQV_P1_11

description:
RHT1076
TPM_sc_young.txt


title: Young_DZQV_P1_10

description:
RHT1075
TPM_sc_young.txt


title: Drug-naïve_SE-18

description: Drug-naïve


title: Young_DZQV_P1_9

description:
RHT1074
TPM_sc_young.txt


title: Young_DZQV_P1_7

description:
RHT1072
TPM_sc_young.txt


title: Healthy Control-31

description: Healthy Control


title: Young_DZQV_P1_8

description:
RHT1073
TPM_sc_young.txt


title: Young_DZQV_P1_6

description:
RHT1071
TPM_sc_young.txt


title: VA Non-responder-1

description: Valproate Non-responder


title: Young_DZQV_P1_5

description:
RHT1070
TPM_sc_young.txt


title: Healthy Control-22

description: Healthy Control


title: Young_DZQV_P1_4

description:
RHT1069
TPM_sc_young.txt


title: Young_DZQV_P1_3

description:
RHT1068
TPM_sc_young.txt


title: Young_DZQV_P1_1

description:
RHT1066
TPM_sc_young.txt


title: Young_GDHD_P2_88

description:
RHT1065
TPM_sc_young.txt

value: GDHD


title: Young_GDHD_P2_87

description:
RHT1064
TPM_sc_young.txt


title: Young_GDHD_P2_86

description:
RHT1063
TPM_sc_young.txt


title: Young_GDHD_P2_85

description:
RHT1062
TPM_sc_young.txt


title: Young_GDHD_P2_83

description:
RHT1060
TPM_sc_young.txt


title: Young_DZQV_P1_2

description:
RHT1067
TPM_sc_young.txt


title: Young_GDHD_P2_84

description:
RHT1061
TPM_sc_young.txt


title: Young_GDHD_P2_82

description:
RHT1059
TPM_sc_young.txt


title: Healthy Control-26

description: Healthy Control


title: monocytes from HIV+ART subject h121

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Expression with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

source_name: monocytes

label_protocol: RNA (100ng) was amplified with Epicentre TargetAmp Nano-g Biotin-aRNA Labeling Kit to generate biotinylated amplified RNA.

growth_protocol: PBMCs were separated by Ficoll-gradient centrifugation followed by purification of CD14+ monocytes by negative selection with antibody-conjugated magnetic beads according to the manufacturer’s instructions (Miltenyi Biotech)

extract_protocol: Total RNA was isolated from purified monocytes using the Qiagen DNA/RNA mini kit (catalog no. 80204).  RNA quality was assayed by Eukaryote total RNA nano Bioanalyzer (Agilent) assay, and all RNA used had an RNA Integrity number (RIN) >7.

value: monocytes

tag: patient id

tag: hiv status

value: HIV+ART


title: monocytes from HIV+ART subject h118


title: Young_GDHD_P2_81

description:
RHT1058
TPM_sc_young.txt


title: Healthy Control-21

description: Healthy Control

tag: treatment


title: monocytes from HIV+ART subject h122


title: monocytes from HIV+ART subject h124


title: monocytes from HIV+ART subject h117


title: Young_GDHD_P2_79

description:
RHT1056
TPM_sc_young.txt

tag: donorid


title: CBZ Responder-6

description: Carbamazepine Responder

value: Male


title: monocytes from HIV+ART subject h125


title: Young_GDHD_P2_78

description:
RHT1055
TPM_sc_young.txt

tag: plateid


title: Young_GDHD_P2_77

description:
RHT1054
TPM_sc_young.txt

tag: cell type


title: Young_GDHD_P2_76

description:
RHT1053
TPM_sc_young.txt

tag: batch


title: Young_GDHD_P2_80

description:
RHT1057
TPM_sc_young.txt

tag: developmental stage


title: Young_GDHD_P2_75

description:
RHT1052
TPM_sc_young.txt


title: Young_GDHD_P2_74

description:
RHT1051
TPM_sc_young.txt


title: monocytes from HIV+ART subject h101


title: monocytes from control subject c469

value: control


title: Young_GDHD_P2_72

description:
RHT1049
TPM_sc_young.txt


title: Young_GDHD_P2_73

description:
RHT1050
TPM_sc_young.txt


title: monocytes from control subject c458


title: monocytes from control subject c550


title: monocytes from control subject c534


title: monocytes from HIV+ART subject h119


title: monocytes from HIV+ART subject h102


title: monocytes from HIV+ART subject h123


title: Young_GDHD_P2_71

description:
RHT1048
TPM_sc_young.txt


title: Young_GDHD_P2_69

description:
RHT1046
TPM_sc_young.txt


title: Young_GDHD_P2_70

description:
RHT1047
TPM_sc_young.txt


title: Young_GDHD_P2_68

description:
RHT1045
TPM_sc_young.txt


title: monocytes from control subject c420


title: Young_GDHD_P2_66

description:
RHT1043
TPM_sc_young.txt


title: monocytes from control subject c227


title: monocytes from control subject c345


title: Young_GDHD_P2_65

description:
RHT1042
TPM_sc_young.txt


title: monocytes from control subject c188


title: monocytes from control subject c030


title: monocytes from HIV+ART subject h120


title: Young_GDHD_P2_63

description:
RHT1040
TPM_sc_young.txt


title: Young_GDHD_P2_62

description:
RHT1039
TPM_sc_young.txt


title: Young_GDHD_P2_64

description:
RHT1041
TPM_sc_young.txt


title: monocytes from control subject c121


title: monocytes from control subject c383


title: Young_GDHD_P2_61

description:
RHT1038
TPM_sc_young.txt


title: Young_GDHD_P2_67

description:
RHT1044
TPM_sc_young.txt


title: Young_GDHD_P2_57

description:
RHT1034
TPM_sc_young.txt


title: Young_GDHD_P2_58

description:
RHT1035
TPM_sc_young.txt


title: Young_GDHD_P2_56

description:
RHT1033
TPM_sc_young.txt


title: Young_GDHD_P2_52

description:
RHT1028
TPM_sc_young.txt


title: Young_GDHD_P2_53

description:
RHT1029
TPM_sc_young.txt


title: Young_GDHD_P2_51

description:
RHT1027
TPM_sc_young.txt


title: Young_GDHD_P2_50

description:
RHT1026
TPM_sc_young.txt


title: Young_GDHD_P2_46

description:
RHT1022
TPM_sc_young.txt


title: Young_GDHD_P2_60

description:
RHT1037
TPM_sc_young.txt


title: Young_GDHD_P2_44

description:
RHT1020
TPM_sc_young.txt


title: Young_GDHD_P2_45

description:
RHT1021
TPM_sc_young.txt


title: Young_GDHD_P2_47

description:
RHT1023
TPM_sc_young.txt


title: Young_GDHD_P2_59

description:
RHT1036
TPM_sc_young.txt


title: Young_GDHD_P2_42

description:
RHT1018
TPM_sc_young.txt


title: Young_GDHD_P2_48

description:
RHT1024
TPM_sc_young.txt


title: Young_GDHD_P2_40

description:
RHT1016
TPM_sc_young.txt


title: Young_GDHD_P2_39

description:
RHT1015
TPM_sc_young.txt


title: Young_GDHD_P2_43

description:
RHT1019
TPM_sc_young.txt


title: Young_GDHD_P2_49

description:
RHT1025
TPM_sc_young.txt


title: Young_GDHD_P2_38

description:
RHT1014
TPM_sc_young.txt


title: Young_GDHD_P2_41

description:
RHT1017
TPM_sc_young.txt


title: Young_GDHD_P2_37

description:
RHT1013
TPM_sc_young.txt


title: Young_GDHD_P2_36

description:
RHT1012
TPM_sc_young.txt


title: Young_GDHD_P2_35

description:
RHT1011
TPM_sc_young.txt


title: Young_GDHD_P2_55

description:
RHT1031
TPM_sc_young.txt


title: Young_GDHD_P2_54

description:
RHT1030
TPM_sc_young.txt


title: Young_GDHD_P2_32

description:
RHT1008
TPM_sc_young.txt


title: Young_GDHD_P2_28

description:
RHT1004
TPM_sc_young.txt


title: Young_GDHD_P2_29

description:
RHT1005
TPM_sc_young.txt


title: Young_GDHD_P2_31

description:
RHT1007
TPM_sc_young.txt


title: Young_GDHD_P2_33

description:
RHT1009
TPM_sc_young.txt


title: Young_GDHD_P2_30

description:
RHT1006
TPM_sc_young.txt


title: Young_GDHD_P2_27

description:
RHT1003
TPM_sc_young.txt


title: Young_GDHD_P2_23

description:
RHT999
TPM_sc_young.txt


title: Young_GDHD_P2_21

description:
RHT997
TPM_sc_young.txt


title: Young_GDHD_P2_24

description:
RHT1000
TPM_sc_young.txt


title: Young_GDHD_P2_22

description:
RHT998
TPM_sc_young.txt


title: Young_GDHD_P2_26

description:
RHT1002
TPM_sc_young.txt


title: Young_GDHD_P2_25

description:
RHT1001
TPM_sc_young.txt


title: Young_GDHD_P2_18

description:
RHT993
TPM_sc_young.txt


title: Young_GDHD_P2_20

description:
RHT995
TPM_sc_young.txt


title: Young_GDHD_P2_17

description:
RHT992
TPM_sc_young.txt


title: Young_GDHD_P2_15

description:
RHT990
TPM_sc_young.txt


title: Young_GDHD_P2_14

description:
RHT989
TPM_sc_young.txt


title: Young_GDHD_P2_13

description:
RHT988
TPM_sc_young.txt


title: Young_GDHD_P2_19

description:
RHT994
TPM_sc_young.txt


title: Young_GDHD_P2_16

description:
RHT991
TPM_sc_young.txt


title: Young_GDHD_P2_12

description:
RHT985
TPM_sc_young.txt


title: Young_GDHD_P2_9

description:
RHT982
TPM_sc_young.txt


title: Young_GDHD_P2_10

description:
RHT983
TPM_sc_young.txt


title: Young_GDHD_P2_8

description:
RHT981
TPM_sc_young.txt


title: Young_GDHD_P2_34

description:
RHT1010
TPM_sc_young.txt


title: Young_GDHD_P2_7

description:
RHT980
TPM_sc_young.txt


title: Young_GDHD_P2_6

description:
RHT979
TPM_sc_young.txt


title: Young_GDHD_P2_5

description:
RHT978
TPM_sc_young.txt


title: Young_GDHD_P2_3

description:
RHT976
TPM_sc_young.txt


title: Young_GDHD_P2_2

description:
RHT975
TPM_sc_young.txt


title: Young_GDHD_P2_4

description:
RHT977
TPM_sc_young.txt


title: Young_GDHD_P2_1

description:
RHT974
TPM_sc_young.txt


title: Young_GDHD_P1_89

description:
RHT971
TPM_sc_young.txt


title: Young_GDHD_P1_91

description:
RHT973
TPM_sc_young.txt


title: Young_GDHD_P1_90

description:
RHT972
TPM_sc_young.txt


title: Young_GDHD_P1_86

description:
RHT968
TPM_sc_young.txt


title: Young_GDHD_P1_85

description:
RHT967
TPM_sc_young.txt


title: Young_GDHD_P1_88

description:
RHT970
TPM_sc_young.txt


title: Young_GDHD_P2_11

description:
RHT984
TPM_sc_young.txt


title: Young_GDHD_P1_81

description:
RHT963
TPM_sc_young.txt


title: Young_GDHD_P1_79

description:
RHT961
TPM_sc_young.txt


title: Young_GDHD_P1_80

description:
RHT962
TPM_sc_young.txt


title: Young_GDHD_P1_82

description:
RHT964
TPM_sc_young.txt


title: Young_GDHD_P1_78

description:
RHT960
TPM_sc_young.txt


title: Young_GDHD_P1_75

description:
RHT957
TPM_sc_young.txt


title: Young_GDHD_P1_77

description:
RHT959
TPM_sc_young.txt


title: Young_GDHD_P1_74

description:
RHT956
TPM_sc_young.txt


title: Young_GDHD_P1_83

description:
RHT965
TPM_sc_young.txt


title: Young_GDHD_P1_72

description:
RHT953
TPM_sc_young.txt


title: Young_GDHD_P1_76

description:
RHT958
TPM_sc_young.txt


title: Young_GDHD_P1_70

description:
RHT951
TPM_sc_young.txt


title: Young_GDHD_P1_73

description:
RHT955
TPM_sc_young.txt


title: Young_GDHD_P1_69

description:
RHT950
TPM_sc_young.txt


title: Young_GDHD_P1_68

description:
RHT949
TPM_sc_young.txt


title: Young_GDHD_P1_67

description:
RHT948
TPM_sc_young.txt


title: Young_GDHD_P1_84

description:
RHT966
TPM_sc_young.txt


title: Young_GDHD_P1_71

description:
RHT952
TPM_sc_young.txt


title: Young_GDHD_P1_66

description:
RHT947
TPM_sc_young.txt


title: Young_GDHD_P1_64

description:
RHT945
TPM_sc_young.txt


title: Young_GDHD_P1_65

description:
RHT946
TPM_sc_young.txt


title: Young_GDHD_P1_60

description:
RHT941
TPM_sc_young.txt


title: Young_GDHD_P1_58

description:
RHH4950
TPM_sc_young.txt


title: Young_GDHD_P1_57

description:
RHH4948
TPM_sc_young.txt


title: Young_GDHD_P1_63

description:
RHT944
TPM_sc_young.txt


title: Young_GDHD_P1_61

description:
RHT942
TPM_sc_young.txt


title: Young_GDHD_P1_54

description:
RHH4945
TPM_sc_young.txt


title: Young_GDHD_P1_56

description:
RHH4947
TPM_sc_young.txt


title: Young_GDHD_P1_59

description:
RHH4951
TPM_sc_young.txt


title: Young_GDHD_P1_55

description:
RHH4946
TPM_sc_young.txt


title: Young_GDHD_P1_48

description:
RHH4939
TPM_sc_young.txt


title: Young_GDHD_P1_49

description:
RHH4940
TPM_sc_young.txt


title: Young_GDHD_P1_50

description:
RHH4941
TPM_sc_young.txt


title: Young_GDHD_P1_47

description:
RHH4938
TPM_sc_young.txt


title: Young_GDHD_P1_46

description:
RHH4937
TPM_sc_young.txt


title: Young_GDHD_P1_87

description:
RHT969
TPM_sc_young.txt


title: Young_GDHD_P1_43

description:
RHH4934
TPM_sc_young.txt


title: Young_GDHD_P1_45

description:
RHH4936
TPM_sc_young.txt


title: Young_GDHD_P1_44

description:
RHH4935
TPM_sc_young.txt


title: Young_GDHD_P1_42

description:
RHH4933
TPM_sc_young.txt


title: Young_GDHD_P1_40

description:
RHH4931
TPM_sc_young.txt


title: Young_GDHD_P1_41

description:
RHH4932
TPM_sc_young.txt


title: Young_GDHD_P1_39

description:
RHH4930
TPM_sc_young.txt


title: Young_GDHD_P1_62

description:
RHT943
TPM_sc_young.txt


title: Young_GDHD_P1_38

description:
RHH4929
TPM_sc_young.txt


title: Young_GDHD_P1_37

description:
RHH4928
TPM_sc_young.txt


title: Young_GDHD_P1_35

description:
RHH4926
TPM_sc_young.txt


title: Young_GDHD_P1_36

description:
RHH4927
TPM_sc_young.txt


title: Young_GDHD_P1_53

description:
RHH4944
TPM_sc_young.txt


title: Young_GDHD_P1_34

description:
RHH4925
TPM_sc_young.txt


title: Young_GDHD_P1_51

description:
RHH4942
TPM_sc_young.txt


title: Young_GDHD_P1_52

description:
RHH4943
TPM_sc_young.txt


title: Young_GDHD_P1_29

description:
RHH4920
TPM_sc_young.txt


title: Young_GDHD_P1_28

description:
RHH4919
TPM_sc_young.txt


title: Young_GDHD_P1_32

description:
RHH4923
TPM_sc_young.txt


title: Young_GDHD_P1_30

description:
RHH4921
TPM_sc_young.txt


title: Young_GDHD_P1_25

description:
RHH4916
TPM_sc_young.txt


title: Young_GDHD_P1_27

description:
RHH4918
TPM_sc_young.txt


title: Young_GDHD_P1_26

description:
RHH4917
TPM_sc_young.txt


title: Young_GDHD_P1_24

description:
RHH4915
TPM_sc_young.txt


title: Young_GDHD_P1_31

description:
RHH4922
TPM_sc_young.txt


title: Young_GDHD_P1_23

description:
RHH4914
TPM_sc_young.txt


title: Young_GDHD_P1_21

description:
RHH4912
TPM_sc_young.txt


title: Young_GDHD_P1_20

description:
RHH4911
TPM_sc_young.txt


title: Young_GDHD_P1_22

description:
RHH4913
TPM_sc_young.txt


title: Young_GDHD_P1_15

description:
RHH4906
TPM_sc_young.txt


title: Young_GDHD_P1_18

description:
RHH4909
TPM_sc_young.txt


title: Young_GDHD_P1_14

description:
RHH4905
TPM_sc_young.txt


title: Young_GDHD_P1_16

description:
RHH4907
TPM_sc_young.txt


title: Young_GDHD_P1_17

description:
RHH4908
TPM_sc_young.txt


title: Young_GDHD_P1_19

description:
RHH4910
TPM_sc_young.txt


title: Young_GDHD_P1_12

description:
RHH4903
TPM_sc_young.txt


title: Young_GDHD_P1_13

description:
RHH4904
TPM_sc_young.txt


title: Young_GDHD_P1_10

description:
RHH4901
TPM_sc_young.txt


title: Young_GDHD_P1_11

description:
RHH4902
TPM_sc_young.txt


title: Young_GDHD_P1_33

description:
RHH4924
TPM_sc_young.txt


title: Young_GDHD_P1_8

description:
RHH4899
TPM_sc_young.txt


title: Young_GDHD_P1_7

description:
RHH4898
TPM_sc_young.txt


title: Young_GDHD_P1_6

description:
RHH4897
TPM_sc_young.txt


title: Young_GDHD_P1_5

description:
RHH4896
TPM_sc_young.txt


title: Young_GDHD_P1_4

description:
RHH4895
TPM_sc_young.txt


title: Young_GDHD_P1_2

description:
RHH4893
TPM_sc_young.txt


title: Young_GDHD_SCM

description:
RHT2459
read_count_bulk.txt
rpkm_bulk.txt

data_processing:
The paired-end reads were mapped to Human GRCh38 reference genome version 25 using STAR alignment tool.
The number of reads mapped to each gene was counted using feature Counts and the human reference genome to obtain the read count table.
RPKM (Reads Per Kilobase of transcript per Million mapped reads) values were computed using edgeR R package by filtering the genes that have zeros total count and by normalizing the count with TMM algorithm.
Genome_build: GRCh38 version 25
Supplementary_files_format_and_content: tab-delimited text files include read count values and RPKM values for the 36 samples from bulk data

source_name: SCM

extract_protocol:
Total RNA was extracted following the double extraction protocol: RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction (TRIzol, Thermo Fisher Scientific, Waltham, MA, USA) followed by a Qiagen RNeasy Micro clean-up procedure (Qiagen, Hilden, Germany). All human RNAs were analyzed on Agilent Bioanalyzer for quality assessment with RNA Integrity Number (RIN) range from 6.2 to 9.6 and median RIN 8.9 (Agilent, Santa Clara, CA, USA)
cDNA libraries were prepared using 1ng of total RNA and 0.5ul of a 1:50,000 dilution of ERCC RNA Spike in Controls (Ambion Thermo Fisher Scientific, Waltham, MA, USA) using SMARTSeq v2 protocol (Picelli et al., 2014) except for the following modifications: 1. Use of 20µM TSO, 2. Use of 250pg of cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (16 samples/lane).

value: SCM


title: Young_GDHD_RTE

description:
RHT2458
read_count_bulk.txt
rpkm_bulk.txt

source_name: RTE

value: RTE


title: Young_GDHD_P1_3

description:
RHH4894
TPM_sc_young.txt


title: Young_DZQV_NaiveCD4T

description:
RHT2449
read_count_bulk.txt
rpkm_bulk.txt

source_name: Naive CD4 T cells

value: Naive CD4 T cells


title: Young_GDHD_P1_9

description:
RHH4900
TPM_sc_young.txt


title: Young_DZQV_TMNP

description:
RHT2452
read_count_bulk.txt
rpkm_bulk.txt

source_name: TMNP

value: TMNP


title: Young_CM8K_TMNP

description:
RHT2448
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1949_SCM

description:
RHT2443
read_count_bulk.txt
rpkm_bulk.txt

value: Old


title: Young_CM8K_SCM

description:
RHT2447
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1949_TMNP

description:
RHT2444
read_count_bulk.txt
rpkm_bulk.txt


title: Young_DZQV_RTE

description:
RHT2450
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1157_SCM

description:
RHT2439
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1157_RTE

description:
RHT2438
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1157_NaiveCD4T

description:
RHT2437
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1949_NaiveCD4T

description:
RHT2441
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1157_TMNP

description:
RHT2440
read_count_bulk.txt
rpkm_bulk.txt


title: Old_5541_TMNP

description:
RHT2435
read_count_bulk.txt
rpkm_bulk.txt


title: Old_5541_SCM

description:
RHT2436
read_count_bulk.txt
rpkm_bulk.txt


title: Young_GDHD_P1_1

description:
RHH4892
TPM_sc_young.txt


title: Young_EALL_RTE

description:
RHT2454
read_count_bulk.txt
rpkm_bulk.txt

value: EALL


title: Young_EALL_NaiveCD4T

description:
RHT2453
read_count_bulk.txt
rpkm_bulk.txt


title: Young_DZQV_SCM

description:
RHT2451
read_count_bulk.txt
rpkm_bulk.txt


title: Young_GDHD_NaiveCD4T

description:
RHT2457
read_count_bulk.txt
rpkm_bulk.txt


title: Old_5541_NaiveCD4T

description:
RHT2433
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1997_SCM

description:
RHT2432
read_count_bulk.txt
rpkm_bulk.txt


title: Old_5541_RTE

description:
RHT2434
read_count_bulk.txt
rpkm_bulk.txt


title: Young_EALL_TMNP

description:
RHT2456
read_count_bulk.txt
rpkm_bulk.txt


title: Young_CM8K_NaiveCD4T

description:
RHT2445
read_count_bulk.txt
rpkm_bulk.txt


title: Young_G486_SCM

description:
RHT2428
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1949_RTE

description:
RHT2442
read_count_bulk.txt
rpkm_bulk.txt


title: Old_1997_NaiveCD4T

description:
RHT2429
read_count_bulk.txt
rpkm_bulk.txt


title: Young_EALL_SCM

description:
RHT2455
read_count_bulk.txt
rpkm_bulk.txt


title: Young_G486_TMNP

description:
RHT2427
read_count_bulk.txt
rpkm_bulk.txt


title: Young_G486_RTE

description:
RHT2426
read_count_bulk.txt
rpkm_bulk.txt


title: RNA-Seq deltaYB-1 polyA rep1 (total_polyA_del_1), run 2

city: Pushchino

first: Ivan

middle: V

last: Kulakovskiy

address: Institutskaya 4

country: Russia

institute: Institute of Protein Research

description: Control for RIP-Seq

data_processing:
Trimming was performed with cutadapt v1.18 with the following parameters: "-a AGATCGGAAGAGCACACGTCT -j 32 --minimum-length 20 --discard-untrimmed --maximum-length 60 --trim-n" for the Ribo-Seq and the size-matched RNA-Seq samples, "-a AGATCGGAAGAGCACACGTCT -j 32 --minimum-length 20 --trim-n -o" for the RIP-Seq and the respective control RNA-Seq samples. Quality parameter was set as "-q 20" for HiSeq-sequences samples and "--nextseq-trim=20" for NextSeq-sequenced samples.
Mapping to the hg38 genome assembly with GENCODE v29 genome annotation and read counting was performed with STAR v2.6.1d (default parameters).
Genome_build: GRCh38 - hg38
Supplementary_files_format_and_content: Tab-separated plain text files with read counts per gene.

molecule: polyA RNA

source_name: Human embryonic kidney

growth_protocol: HEK293T cells were routinely cultured in DMEM supplemented with 10% fetal bovine serum, 2 mM glutamine, 100 U/ml penicillin, and 100 µg streptomycin.

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. PolyA RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module.

tag: cell line

tag: experiment type

value: RNA-Seq

tag: genotype


title: RNA-Seq wt polyA rep1 (total_polyA_1), run 2

description: Control for RIP-Seq

value: wild type


title: RNA-Seq deltaYB-1 polyA rep1 (total_polyA_del_1), run 1

description: Control for RIP-Seq


title: RNA-Seq wt polyA rep1 (total_polyA_1), run 1

description: Control for RIP-Seq


title: Old_1997_TMNP

description:
RHT2431
read_count_bulk.txt
rpkm_bulk.txt


title: YB-1 RIP-Seq wt PolyA (IP_YB1_polyA), run 1

extract_protocol:
Cells were lysed in two pellet volumes of lysis buffer and centrifuged at 16,000 g for 10 min. YB-1-RNA complex was isolated by antibody-coated Protein-G sepharose. RNA was isolated using TRIzol LS Reagent.
Library was prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina. PolyA RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module.

value: RIP-Seq

tag: rip antibody


title: YB-1 RIP-Seq wt PolyA (IP_YB1_polyA), run 2


title: Size-matched RNA-Seq deltaYB-1 (RP_tot_del), run 1

description: Control for Ribo-Seq

extract_protocol:
Cells washed with PBS supplemented with cycloheximide 100 µg/ml, lysed in polysome lysis buffer and cleared by centrifugation at 20,000 g for 10 min.
Library was prepared with TruSeq Ribo Profile Kit. rRNA depletion was performed using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat).

value: Size-matched RNA-Seq


title: Ribo-Seq deltaYB-1 (RP_del), run 2

value: Ribo-Seq


title: Size-matched RNA-Seq deltaYB-1+HA (RP_tot_del_HA), run 2

description: Control for Ribo-Seq


title: Ribo-Seq deltaYB-1+HA (RP_del_HA), run 2


title: Size-matched RNA-Seq wt+HA-YB-1 (RP_tot_wt_YB1), run 2

description: Control for Ribo-Seq

value: wild type+HA-YB-1


title: Ribo-Seq deltaYB-1 (RP_del), run 3


title: Size-matched RNA-Seq deltaYB-1 (RP_tot_del), run 2

description: Control for Ribo-Seq


title: Ribo-Seq deltaYB-1 (RP_del), run 1


title: Old_1997_RTE

description:
RHT2430
read_count_bulk.txt
rpkm_bulk.txt


title: Young_G486_NaiveCD4T

description:
RHT2425
read_count_bulk.txt
rpkm_bulk.txt

value: Young


title: Size-matched RNA-Seq wt (RP_tot_wt), run 1

description: Control for Ribo-Seq


title: Size-matched RNA-Seq wt (RP_tot_wt), run 2

description: Control for Ribo-Seq


title: Ribo-Seq wt+HA (RP_wt_HA), run 2

value: wild type+HA


title: Size-matched RNA-Seq wt+HA (RP_tot_wt_HA), run 2

description: Control for Ribo-Seq


title: 85 tumor

city: South San Francisco

first: Steffen

last: Durinck

state: CA

address: 1 DNA Way

institute: Genentech

hyb_protocol: default agilent

scan_protocol: default agilent

data_processing: limma R package

source_name: mammary gland

label_protocol: default agilent

growth_protocol: mouse tumors

extract_protocol: RNeasy Kit (Qiagen, Hilden, Germany)

treatment_protocol: mouse tumors

tag: tag

value: adenocarcinoma


title: 17 tumor


title: Ribo-Seq wt (RP_wt), run 3


title: 470 tumor


title: Ribo-Seq wt (RP_wt), run 1


title: 131 tumor


title: 594 tumor

value: sarcomatoid carcinoma


title: Ribo-Seq wt (RP_wt), run 2


title: 105 tumor


title: 307 transplanted tumor in lung

source_name: lung met

value: sarcomatoid adenocarcinoma


title: Ribo-Seq wt+HA-YB-1 (RP_wt_YB1), run 2


title: 323 transplanted tumor in lung


title: 307 tumor


title: donor b

city: Moncton

first: Rodney

last: Ouellette

address: 35 Providence St.

country: Canada

institute: ATLANTIC CANCER RESEARCH INSTITUTE

description: small RNA

data_processing:
RNA-seq reads were mapped using bowtie2 (version 2.2.5)  using mirbase build 20 version of index files.
parameters used are as follows with Bowtie2: --end-to-end --norc --very-sensitive
FeatureCounts (version 1.4.6-p4) to extract the raw counts
We calculated normalized TMM values using edgeR  ( version 3.18.1)
Genome_build: hg19
Supplementary_files_format_and_content: Csv files with samples raw  and normalized TMM counts from all 4 samples.

source_name: Vn96-plasma Evs

extract_protocol:
RNA was extracted with miRVana Total RNA kit
RNA quality was assayed on Agilent Tape Station 2200 using RNA HS screen tape assay. RNA (25 ng) was used to prepare a small RNA library using Clean Tag Small RNA library kit (TriLink biotech). For each individual library, RNA was ligated to chemically modified adapters to suppress adaptor dimer formation. Modified adapters were added to both 3′ and 5′ ends following manufacturer recommended conditions. Adapter ligated RNA was reverse transcribed using Ion Torrent specific primer. cDNA was then amplified using Ion convert barcode primers containing a unique index to allow libraries to be pooled during Ion Torrent sequencing (Life Technologies). Library QC was assayed on Agilent Tape Station using D1000 screen tape. Equally-pooled libraries (pmol) were clonally amplified onto Ion Sphere™ Particles (ISPs) supplied by Ion Pi HiQ OT2 kit. ISPs were then loaded onto Ion PI chip and sequenced using Ion Torrent Proton Sequencer.

value: Plasma Evs

value: Normal


title: 323 tumor


title: donor d

description: small RNA


title: donor c

description: small RNA


title: donor a

description: small RNA


title: OCCC 1-1697

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

institute: National University of Singapore

description: epithelial ovarian cancer of clear cell histology

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Fragmented and biotin labeled cDNA was hybridized to Affymetrix Human Transcriptome Array 2.0 for 18 hours at 45C with rotation at 60 rpm. Arrays were then washed and stained using the FS450_0007 fluidics protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
RMA normalization using Affymetrix Powertools 1.15.0
probe group file: HTA-2_0.r3.pgf
meta-probeset file: HTA-2_0.r3.Psrs.mps

source_name: frozen archival epithelial ovarian cancer tumors samples

label_protocol: Samples were enzymatically fragmented and biotinylated using the NuGEN Applause WT-Amp ST System and Encore Biotin Module.

extract_protocol: Total RNA was extracted by Qiagen miRNEasy Mini kit according to the manufacturer's instructions.

tag: histology

value: clear cell

tag: occc subtype

value: EpiCC


title: OCCC 1-1628

tag: age


title: OCCC 1-1571


title: OCCC 1-1589


title: OCCC 1-1598


title: Zn resupply root-rep2 miRNA-seq

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

country: China

institute: Hangzhou Normal University

data_processing:
The raw reads were performed on an in-house program ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adaptor sequences, low-complexity sequences, junk reads, repeat sequences, and the reads that matched the common non-coding RNA families (tRNA, rRNA, snoRNA, and snRNA) deposited in Rfam database (http://www.sanger.ac.uk/software/Rfam).
Subsequently, unique sequences with length of 20-24 nucleotide (nt) were mapped to rice miRNA precursors in miRBase 22.0 by BLAST to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends, and one nt mismatch of the miRNA sequence for the alignment were allowed. The unique sequences mapping to rice mature miRNAs in the precursors were identified as known miRNAs. The unique sequences mapping to the opposite arm of known rice miRNA precursor hairpin were considered to be novel 5p- or 3p- derived miRNA candidates.
The remaining sequences were mapped to miRNA precursors of other plant species in miRBase 22.0 by BLAST, and the mapped pre-miRNAs were further aligned with the rice genome to determine their genomic locations. The remaining unmapped sequences were further aligned with the rice genome, and the flanking sequences with a length of 120 nt were collected for secondary structure prediction using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).
The criteria for novel miRNA prediction and characterization were based on the previous study (Axtell and Meyers 2018), described as follows: (1) number of nucleotides in one bulge in stem is ≤12; (2) number of base pairs in the stem region of the predicted hairpin is ≥16; (3) the free energy for miRNA precursor should be ≤ -15 kCal/mol; (4) length of hairpin is larger than 50 but less than 300 nt; (5) number of nucleotides in one bulge of the mature region should be ≤4; (6) number of biased errors in one bulge of the mature region should be ≤2; (7) number of biased bulges in the mature region should be ≤2; (8) number of mismatches in mature region should be ≤4; (9) number of base pairs in the mature region of the predicted hairpin should be ≥12; (10) percent of mature sequence in the stem should be ≥80.
Genome_build: Rfam database (http://www.sanger.ac.uk/software/Rfam)
Supplementary_files_format_and_content: Excel file, with all miRNAs detected and their expression levels in samples

organism: Oryza sativa Japonica Group

source_name: Root

growth_protocol: Seeds of the rice (Oryza sativa L. japonica) were surface sterilized in 10% (v/v) H2O2 for 20 min and rinsed with sterile water. Seeds were then transferred to seedling trays floating on sterile water for germination. After growing in the sterile water for 10 days, seedlings were transferred to a plastic container with 2.5 L Yoshida solution (Yoshida et al. 1976). The fresh nutrient solution was replenished every 2 day, and the pH was adjusted to 5.6. Plants were grown in a growth chamber under controlled conditions. The light intensity was approximately 180 μmol m-2 s-1 at shoot height with a day/night cycle of 16 h/8 h at 26°C/24°C. The relative humidity was 50%.

extract_protocol:
Rice shoots and roots were collected after Zn-deficiency and Zn-resupply treatments.
Eighteen samples (Zn-plus shoot, Zn-minus shoot, Zn-resupply shoot, Zn-plus root, Zn-minus root, Zn-resupply root, each with three biological replicates) were harvested for small RNA library construction and sequencing. Roots and shoots from three rice seedlings were collected and mixed together as one sample. Total RNAs were extracted from samples using Trizol reagent (Invitrogen, Carlsbad, CA). RNA abundances and purity were tested following the manufacture of RNA 6000 Nano LabChip Kit (Agilent, CA, USA). Approximately 1.0 μg of total RNA was used to prepare a small RNA library according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Single-end sequencing with a length of about 50 bp was conducted on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China).

treatment_protocol: After growing in the nutrient solution (with 1.5 µM ZnSO4) for one week, uniform seedlings were used for Zn deficiency treatment. For Zn deficiency, no ZnSO4 was added to the nutrient solution, while normal 1.5 µM ZnSO4 was used for the control treatment. Roots and shoots of rice seedlings were collected after Zn-deficient treatment for two weeks. For Zn-resupply treatment, Zn-deficient seedlings were transferred to nomal nutrient solution containing 1.5 µM ZnSO4 for three days. After Zn-resupply treatment, roots and shoots were collected for analyses at the same time point as collecting the Zn-deficient samples (four hours after illumination).

tag: cultivar

value: Nipponbare

tag: tissue

value: the whole root system

value: 4 week old seedling


title: Zn resupply root-rep3 miRNA-seq


title: Zn resupply root-rep1 miRNA-seq


title: OCCC 1-1618

tag: patient id


title: OCCC 1-1637


title: OCCC 1-1558

value: MesCC


title: OCCC 1-1462


title: OCCC 1-1622


title: OCCC 1-1625


title: OCCC 1-1528


title: OCCC 1-1449


title: OCCC 1-1695


title: OCCC 1-1590


title: OCCC 1-1498


title: OCCC 1-1546


title: OCCC 1-1432AS

source_name: cells from ovarian cancer patient's ascites fluid


title: OCCC 1-1450


title: OCCC 1-1420


title: OCCC 1-1582


title: OCCC 1-1392


title: Zn resupply shoot-rep3 miRNA-seq

source_name: Shoot

value: the leaf and stem


title: OCCC 1-1706


title: Zn resupply shoot-rep2 miRNA-seq


title: OCCC 1-1493


title: Zn plus root-rep2 miRNA-seq


title: Zn plus root-rep3 miRNA-seq


title: Zn resupply shoot-rep1 miRNA-seq


title: OCCC 1-1384


title: Zn plus root-rep1 miRNA-seq


title: Zn plus shoot-rep3 miRNA-seq


title: Zn plus shoot-rep2 miRNA-seq


title: Zn minus root-rep1 miRNA-seq


title: Zn minus shoot-rep2 miRNA-seq


title: Zn minus shoot-rep3 miRNA-seq


title: Zn minus root-rep3 miRNA-seq


title: Zn minus root-rep2 miRNA-seq


title: Zn minus shoot-rep1 miRNA-seq


title: 872 G1E-ER4+E2

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

data_processing:
Illumina's bcl2fastq2 to generate fastq files
Custom script to trim reads to 30nts
Map reads with Bowtie 0.12.8 with parameters -y -v 2 -p 7 --best --strata -k 1 --sam-nohead --sam
Samtools v1.6 to filter chrM and unmapped reads
Fseq v1.85 to generate wiggles.  Use parameters -v -of wig -f 0
Homer v36 to call peaks.  Use parameter -style dnase.
Custom script to format peaks in bed format and bedtools to remove blacklist regions
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Fseq
Supplementary_files_format_and_content: bed, peaks from Homer

source_name: cell line

extract_protocol:
Approximately 50,000 cells were collected by centrifugation at 600 xg for 10 min at 4 °C. Cells were washed once with cold 1x PBS and centrifuged as above. Cells were lysed by gently pipetting to resuspend cell pellet in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged as above.
Cells were suspended in the following mix: 25 μl 2X Tagment DNA buffer (Illumina cat# FC-121-1030), 3 μl Tn5 Transposase (Illumina cat#FC-121-1030), 22 μl nuclease-free H2O and incubated for 30 min at 37 °C. Reactions were terminated by adding 5 μl of 1% SDS solution and purified using SPRIselect beads. Following purification, library fragments were amplified using NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min.  Libraries were amplified for a total of 17–19 cycles and then purified using AMPure XP beads (Beckman Coulter cat #A63881).

value: G1E clone rescued by expression of an E2-dependent GATA1-ER hybrid protein


title: 871 G1E

value: GATA1-deficient, erythroid-committed progenitor cell line


title: 1199 NEU

source_name: peripheral blood

tag: strain

value: adult

value: neutrophil


title: 1198 MON

value: monocyte


title: 1196 LSK

source_name: bone marrow

value: Lin-, Sca1+, cKit+


title: 870 G1E


title: 1200 NEU


title: 1197 MON


title: NEU 1157

description: neutrophil

data_processing:
Illumina's bcl2fastq2 to generate fastq files
The sequence reads were processed using the ENCODE3 long RNA-seq pipeline (https://www.encodeproject.org/pipelines/ENCPL002LPE/). In brief, reads were mapped to the mouse genome using STAR, followed by RSEM for gene quantifications using Gencode vM4 genes.
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from STAR
Supplementary_files_format_and_content: tsv, expression levels from RSEM

extract_protocol:
After Ficoll separation of peripheral blood, neutrophils were collected from the cell pellet following red cell lysis
Total RNA was extracted using TRIzol and the Ambion PureLink RNA Mini Kit (Life Technologies, cat# 12183018), treated with DNase to remove genomic DNA using the DNAfree Kit (Life Technologies, cat# AM1906).
Sequencing libraries were constructed from 100 ng of DNase-treated, total RNA using the ScriptSeqv2 Complete Kit (Illumina cat# BHMR1224). The RNA depleted for rRNA using the Ribo-Zero removal reagents and fragmented. First strand cDNA was then synthesized using a 5’ tagged random hexamer and reverse transcription, followed by annealing of a 5’ tagged, 3’-end blocked terminal-tagged oligo and second strand synthesis. The Di-tagged cDNA fragments were purified, barcoded, and PCR-amplified for 15 cycles.

value: neutrophils


title: Zn plus shoot-rep1 miRNA-seq


title: MON 1208

description: monocyte

extract_protocol:
After Ficoll separation of peripheral blood, monocytes (Gr-1+Mac-1+) were sorted from the mononuclear fraction.
Total RNA was extracted using TRIzol and the Ambion PureLink RNA Mini Kit (Life Technologies, cat# 12183018), treated with DNase to remove genomic DNA using the DNAfree Kit (Life Technologies, cat# AM1906).
Sequencing libraries were constructed from 100 ng of DNase-treated, total RNA using the ScriptSeqv2 Complete Kit (Illumina cat# BHMR1224). The RNA depleted for rRNA using the Ribo-Zero removal reagents and fragmented. First strand cDNA was then synthesized using a 5’ tagged random hexamer and reverse transcription, followed by annealing of a 5’ tagged, 3’-end blocked terminal-tagged oligo and second strand synthesis. The Di-tagged cDNA fragments were purified, barcoded, and PCR-amplified for 15 cycles.

value: monocytes (Gr-1+Mac-1+)


title: MON 1233

description: monocyte


title: NEU 1156

description: neutrophil