title: Mac1cell_R15_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R15_C24

status: Public on Oct 01 2019

type: SRA

city: Houston

first: Qingnan

last: Liang

state: TX

address: One Baylor Plaza

department: HGSC

country: USA

institute: Baylor College of Medicine

description: P1_Mac.txt (matrix)

library_source: transcriptomic

data_processing:
Illumina Casava software used for basecalling. Individual FASTQ files obtained were demultiplexed using the well-specific barcode identifiers for downstream data processing and analysis.
FASTQ sequences were mapped to human genome hg19 (GRCh37) downloaded from UCSC genome browser website and aligned using TopHat2
Transcript structure and abundance were estimated using HTseq and Cufflink
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: retina

extract_protocol:
Single nuclear capture and sequencing were performed on the ICELL8 single cell platform (Wafergen Biosytems). ICELL8 platform comprised of a multi-sample nano-dispenser that precisely dispensed 50nl of the single nuclei suspension into an ICELL8 nanowell microchip-containing 5184 wells (150nl capacity). Assuming a Poisson distribution frequency for the number of cells per well, about 30% of the nanowells were expected to contain a single nucleus under optimal conditions. Automated scanning fluorescent microscopy of the microchip was performed using an Olympus BX43 fluorescent microscope with a robotic stage to visualize wells containing single nuclei (see Table 1 for single cell capture number across different experimental repeats). The automated well selection was performed using the CellSelect software (Wafergen Biosystems), which identified nanowells containing single nuclei and excluded wells with >1 nuclear, debris, nuclei clumps or empty wells. The candidate wells were manually evaluated for debris or clumps as an additional QC.
The chip was subjected to freeze-thaw in order to lyse the cells and 50 nl of reverse transcription and amplification solution (following ICELL8 protocol) was dispensed using the multi-sample nano-dispenser to candidate wells. Each well had a preprinted primer that contains an 11-nucleotide-well-specific barcode. This barcode was added to the 3’ (A)n RNA tail of the nuclear transcripts during reverse transcription and cDNA amplification, the latter of which was performed on candidate wells using SCRB-seq chemistry. After RT, the cDNA products from candidate wells were pooled, concentrated (Zymo Clean and Concentrator kit, Zymogen) and purified using 0.6x AMPure XP beads. A 3’ transcriptome enriched library was made using Nextera XT Kit and 3’-specific P5 primer, which was sequenced on the Illumina Hiseq2500.

treatment_protocol: Nuclei from frozen neural retinal tissue was isolated using RNase-free lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl¬2, 0.1% NP40). The frozen tissue was resuspended in ice-cold lysis buffer and triturated to break the tissue structure. The tissue aggregates were then homogenized using a Wheaton™ Dounce Tissue Grinder and centrifuged (500g) to pellet the nuclei. The pellet was re-suspended in fresh lysis buffer and homogenized to yield clean single-nuclei suspension. The collected nuclei were stained with DAPI (4',6-diamidino-2-phenylindole, 10ug/ml) and were diluted to 1000 μl of 3E4/ml with 1× PBS (without Ca and Mg ions, pH 7.4, Thermo Fisher), RNase inhibitor (NEB, 40KU/ml) and Cell Diluent Buffer.

tag: sample

tag: tissue

value: Retina


title: Mac1cell_R15_C17

description: P1_Mac.txt (matrix)


title: 50_MED24 knockout, IL-1b at 30 ng/mL, 4h

city: Cambridge

first: Paul

last: Blainey

state: MA

address: 415 Main Street

institute: Broad Institute

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Transcript counts were quantified using the command "kallisto quant" with default parameters and human reference Homo_sapiens.GRCh37.75.cdna.abinitio.fa.gz (kallisto v0.45).
Genome_build: GRCh37.75
Supplementary_files_format_and_content: Transcript counts determined by kallisto are stored in a tab-delimited table with one row per transcript feature.

molecule: polyA RNA

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum and 100U/mL penicillin/streptomycin

extract_protocol:
Cells were washed once with PBS and lysed in 1X TCL buffer (Qiagen, supplemented with 1% beta-mercaptoethanol).
Smart-seq2 was performed as described (Trombetta et al., 2014).

treatment_protocol: Cytokines were added directly to culture media.

tag: cell line

value: HeLa

tag: genotype

tag: stimulation

tag: timepoint

tag: clone

value: MED24 KO 2.1


title: Mac1cell_R15_C15

description: P1_Mac.txt (matrix)


title: 10_MED24 knockout, IL-1b at 30 ng/mL, 4h


title: 47_MED24 knockout, TNFa at 1 ng/mL, 1h


title: Mac1cell_R15_C14

description: P1_Mac.txt (matrix)


title: 12_MED24 knockout, IL-1b at 30 ng/mL, 4h


title: 34_MED24 knockout, IL-1b at 30 ng/mL, 1h


title: Mac1cell_R15_C11

description: P1_Mac.txt (matrix)


title: 74_MED24 knockout, IL-1b at 30 ng/mL, 1h


title: 52_MED24 knockout, IL-1b at 30 ng/mL, 4h


title: Mac1cell_R14_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C9

description: P1_Mac.txt (matrix)


title: 76_MED24 knockout, IL-1b at 30 ng/mL, 1h


title: 36_MED24 knockout, IL-1b at 30 ng/mL, 1h


title: Mac1cell_R14_C67

description: P1_Mac.txt (matrix)


title: 62_MED24 knockout, IL-1b at 1 ng/mL, 4h


title: 22_MED24 knockout, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R14_C60

description: P1_Mac.txt (matrix)


title: 24_MED24 knockout, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R14_C61

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C58

description: P1_Mac.txt (matrix)


title: 90_MED12 knockout, unstimulated

value: unstimulated


title: Mac1cell_R14_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C48

description: P1_Mac.txt (matrix)


title: 64_MED24 knockout, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R14_C44

description: P1_Mac.txt (matrix)


title: 3_MED12 knockout, TNFa at 30 ng/mL, 4h

value: TNF 1/3k


title: Mac1cell_R14_C40

description: P1_Mac.txt (matrix)


title: 92_MED12 knockout, unstimulated

value: MED12 KO 1.1


title: 77_MED12 knockout, TNFa at 30 ng/mL, 1h


title: 55_MED12 knockout, TNFa at 30 ng/mL, 4h


title: Mac1cell_R14_C49

description: P1_Mac.txt (matrix)


title: 53_MED12 knockout, TNFa at 30 ng/mL, 4h


title: 40_MED12 knockout, unstimulated


title: Mac1cell_R14_C29

description: P1_Mac.txt (matrix)


title: 27_MED12 knockout, TNFa at 30 ng/mL, 1h


title: 79_MED12 knockout, TNFa at 30 ng/mL, 1h


title: Mac1cell_R14_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C2

description: P1_Mac.txt (matrix)


title: 67_MED12 knockout, TNFa at 1 ng/mL, 4h


title: 89_MED12 knockout, TNFa at 1 ng/mL, 1h


title: 4_MED12 knockout, IL-1b at 30 ng/mL, 4h


title: 65_MED12 knockout, TNFa at 1 ng/mL, 4h


title: 15_MED12 knockout, TNFa at 1 ng/mL, 4h


title: Mac1cell_R13_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C23

description: P1_Mac.txt (matrix)


title: 80_MED12 knockout, IL-1b at 30 ng/mL, 1h


title: Mac1cell_R13_C71

description: P1_Mac.txt (matrix)


title: Mac1cell_R14_C18

description: P1_Mac.txt (matrix)


title: 39_MED12 knockout, TNFa at 1 ng/mL, 1h


title: Mac1cell_R13_C5

description: P1_Mac.txt (matrix)


title: Mac1cell_R13_C67

description: P1_Mac.txt (matrix)


title: 28_MED12 knockout, IL-1b at 30 ng/mL, 1h


title: Mac1cell_R13_C8

description: P1_Mac.txt (matrix)


title: 54_MED12 knockout, IL-1b at 30 ng/mL, 4h


title: Mac1cell_R13_C55

description: P1_Mac.txt (matrix)


title: 56_MED12 knockout, IL-1b at 30 ng/mL, 4h


title: 91_MED12 knockout, TNFa at 1 ng/mL, 1h


title: 68_MED12 knockout, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R13_C54

description: P1_Mac.txt (matrix)


title: 16_MED12 knockout, IL-1b at 1 ng/mL, 4h


title: Mac1cell_R14_C0

description: P1_Mac.txt (matrix)


title: Mac1cell_R13_C48

description: P1_Mac.txt (matrix)


title: Mac1cell_R13_C47

description: P1_Mac.txt (matrix)


title: 66_MED12 knockout, IL-1b at 1 ng/mL, 4h


title: 78_MED12 knockout, IL-1b at 30 ng/mL, 1h


title: Mac1cell_R13_C36

description: P1_Mac.txt (matrix)


title: ANG KO Clone5 SA2

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1340 Jefferson Park Ave

department: Department of Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
cutadapt v1.15 (--nextseq-trim=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 15)
STAR aligner v2.5.4
unitas v1.7.3 (–species_miR_only –species homo_sapiens)
Genome_build: hg38
Supplementary_files_format_and_content: unitas tRF count table: tRNA fragments count table grouped by tRF types and parental tRNAs, generated by unitas

source_name: U2OS ANG KO sodium arsenite

growth_protocol: HEK293T and U2OS cells were obtained from ATCC and maintained in HyClone Dulbecco’s High Glucose Modified Eagles Medium (GE #SH30081.01) with 10% FBS.

extract_protocol:
Cells were grown to ~80% confluency and washed briefly twice with ice-cold PBS. Total RNA was extracted by Trizol reagent (Invitrogen #15596018) and purified with column-based Direct-zol RNA Miniprep kit (Zymo Research #R2051).
Small RNA-sequencing libraries were prepared following NEBNext Small RNA library kit (NEB #E7300). Briefly, 1 μg total RNA was ligated with 3’ pre-adenylated adaptors and then 5’ adaptors. After reverse transcription and PCR amplification with indexed-adaptors, each library was size selected on 8% TBE-PAGE gel (Invitrogen #EC6215BOX) to enrich for 15-50 nt insert.

treatment_protocol: For sodium arsenite treatment, U2OS cells were grown to ~80% confluency and replaced with fresh media, supplemented with 1 mM (final concentration in water) sodium arsenite (Sigma #S7400) in CO2 incubator at 37 °C for 1 hour.

value: ANG -/-


title: ANG KO Clone5 SA1


title: Mac1cell_R13_C39

description: P1_Mac.txt (matrix)


title: ANG KO Clone5 ctrl2

source_name: U2OS ANG KO untreated

treatment_protocol: U2OS cells were grown to ~80% confluency and replaced with fresh media, incubated in CO2 incubator at 37 °C for 1 hour.


title: Mac1cell_R13_C34

description: P1_Mac.txt (matrix)


title: ANG KO Clone5 ctrl1


title: Mac1cell_R13_C32

description: P1_Mac.txt (matrix)


title: ANG KO Clone3 SA1


title: ANG KO Clone3 SA2


title: Mac1cell_R13_C30

description: P1_Mac.txt (matrix)


title: ANG KO Clone3 ctrl1


title: ANG KO Clone3 ctrl2


title: Wildtype SA2

source_name: U2OS WT sodium arsenite

value: Wildtype


title: Mac1cell_R13_C20

description: P1_Mac.txt (matrix)


title: Mac1cell_R13_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R13_C11

description: P1_Mac.txt (matrix)


title: Wildtype SA1


title: Wildtype ctrl2

source_name: U2OS WT untreated


title: Mac1cell_R12_C68

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C7

description: P1_Mac.txt (matrix)


title: Wildtype ctrl1


title: Mac1cell_R12_C69

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C71

description: P1_Mac.txt (matrix)


title: ANG overexpression-2

source_name: HEK293T ANG overexpression

treatment_protocol: Transient over-expression of pcDNA3.1-ANG (containing human ANGIOGENIN cDNA sequence corresponding to 147 amino acids, Uniprot #P03950) plasmid was performed with Lipofectamine 2000 (Thermo Fisher #11668027) for 72 hours accordingly to manufacturer’s instructions.

value: ANG overexpression


title: Mac1cell_R12_C67

description: P1_Mac.txt (matrix)


title: ANG overexpression-1


title: EV-2

source_name: HEK293T EV

treatment_protocol: Transient over-expression of control empty pcDNA3.1 plasmid was performed with Lipofectamine 2000 (Thermo Fisher #11668027) for 72 hours accordingly to manufacturer’s instructions.


title: ANG overexpression-3


title: Mac1cell_R12_C66

description: P1_Mac.txt (matrix)


title: EV-3


title: Mac1cell_R13_C28

description: P1_Mac.txt (matrix)


title: Mac1cell_R13_C27

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C56

description: P1_Mac.txt (matrix)


title: EV-1


title: Mac1cell_R12_C65

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C52

description: P1_Mac.txt (matrix)


title: Ad-SREBP2 2 RNA-Seq

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

institute: University of California, San Diego

data_processing:
Base calling and quality scoring were performed by an updated implementation of Real-Time Analysis (RTA), termed RTA v2, on the NextSeq 500 system. bcl2fastq Conversion Software v1.8.4 was used to demultiplex data and convert BCL files to FASTQ file formats.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using tophat v2.0.14 with parameters -p -G -o
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using cufflinks v2.2.1, which assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: HUVEC

growth_protocol: Human umbelical vein endothelial cells (HUVECs) between 6-8 passages were grown to confluence in M199 media supplemented with 15% fetal bovine serum, 5 ng/mL b-endothelial cell growth factor, 4 U/mL haparin, and 100 U/mL penicillin-streptomycin.

extract_protocol:
Total RNA was exracted and purified using the mirVana mRNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were grown to 70% confluency and infected with adenovirus containing SREBP2 (Ad-SREBP2) or empty vector control (Ad-null) for 72 hr.

tag: cell type

value: Umbilical vein endothelial cells

tag: passage


title: Ad-SREBP2 1 RNA-Seq


title: Ad-Null 1 RNA-Seq


title: Mac1cell_R12_C50

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C46

description: P1_Mac.txt (matrix)


title: NICD1_REP3_4 [M6.4]

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
bcl2fastq2 Conversion Software v2.20 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome using STAR version 2.5.0a with parameters --runMode alignReads --runThreadN 12 --readFilesCommand zcat --outStd Log --outSAMunmapped within --outSAMtype BM SortedByCordinate limitGenomeGenerateRAM 40,000,000 --limitIObufferSize 40,000,000 --outWigType wiggle --chimSegmentMin 21
bam files were merge using picard and remove duplicate or PCR product contamination
Raw count from each samples were generated using HT-Seq program with parameters --HTSeq.GenomicArrayOfSets("auto", stranded = True)
Genome_build: hg38
Supplementary_files_format_and_content: tab-limited files with raw counts value

growth_protocol: THLE-2 cell lines, containing empty vector or NICD1 plasmid, were grown in BEGM (BEGM Bullet Kit; CC3170; Lonza/Clonetics Corporation, Walkersville, MD, USA). Additional EGF (5 ng/mL), phosphoethanolamine (70 ng/mL) and 10% fetal bovine serum (FBS) (GIBCO Thermo Fisher Scientific, Waltham, MA, USA) were added to media before use.

extract_protocol:
Total RNA samples were extracted from THLE-2 cells that has stably transduced to express GFP or Notch1 intracellular domain (NICD1) using an RNeasy Mini Kit (Qiagen, USA). RNA samples were assessed for quality using an Agilent 2100 Bioanalyzer (Agilent, USA) and quantified using a Qubit 3.0 fluorometer (Life Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Immortalized human hepatocyte cell line

tag: genotype/variation


title: Mac1cell_R12_C40

description: P1_Mac.txt (matrix)


title: NICD1_REP3_2 [M6.2]


title: Mac1cell_R12_C43

description: P1_Mac.txt (matrix)


title: Ad-Null 2 RNA-Seq


title: Mac1cell_R12_C37

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C58

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C36

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C19

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C32

description: P1_Mac.txt (matrix)


title: NICD1_REP2_3 [M5.3]


title: Mac1cell_R12_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C1

description: P1_Mac.txt (matrix)


title: Mac1cell_R12_C10

description: P1_Mac.txt (matrix)


title: NICD1_REP3_1 [M6.1]


title: NICD1_REP2_1 [M5.1]


title: Mac1cell_R11_C57

description: P1_Mac.txt (matrix)


title: NICD1_REP1_2 [M4.2]


title: Empty_Vector_REP3_4 [M3.4]

value: empty vector control


title: NICD1_REP1_4 [M4.4]


title: NICD1_REP3_3 [M6.3]


title: NICD1_REP1_3 [M4.3]


title: Mac1cell_R11_C67

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP3_3 [M3.3]


title: NICD1_REP1_1 [M4.1]


title: NICD1_REP2_4 [M5.4]


title: NICD1_REP2_2 [M5.2]


title: Mac1cell_R11_C55

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C61

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP3_1 [M3.1]


title: Mac1cell_R11_C37

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP2_2 [M2.2]


title: Empty_Vector_REP3_2 [M3.2]


title: Empty_Vector_REP2_1 [M2.1]


title: Mac1cell_R11_C43

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C28

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP2_4 [M2.4]


title: Empty_Vector_REP1_4 [M1.4]


title: Empty_Vector_REP1_2 [M1.2]


title: Mac1cell_R11_C25

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C42

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP2_3 [M2.3]


title: Mac1cell_R11_C22

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C18

description: P1_Mac.txt (matrix)


title: XL6 QKI-B-transHEK-HS repA

city: Freiburg

first: Daniel

last: Maticzka

state: BW

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: University of Freiburg

description: 3'-tag: TTAGCC

data_processing:
Adapters were trimmed using Flexbar (v2.5).
Libraries were demultiplexed using bctools (https://github.com/dmaticzka/bctools, v0.2.0) and Flexbar (v2.5).
Possible readthroughs into the barcoded regions were removed by clipping 13 nt from the 3'-ends of first mate reads.
Reads were mapped to reference genome hg19 using bowtie2 (v2.2.6) with parameters --very-sensitive --end-to-end --no-mixed --no-discordant --maxins 500.
Alignments of uniquely mapped reads were extracted and used to determine crosslinking events as previously described (Ilik, I. A. et al. Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila. Mol. Cell 51, 156–173 (2013)) with bctools (https://github.com/dmaticzka/bctools, v0.2.0).
Genome_build: hg19
Supplementary_files_format_and_content: bed files containing coordinates of crosslinking event alignments with id of a representative read in name column and number of merged PCR-duplicates in score column. bigWig profiles of crosslinking event alignments for each strand.

source_name: Flp-In T-REx 293

extract_protocol:
Cells are crosslinked with 0.15mJ/cm2 UV-C irradiation, lysed with 1xNLB and homogenized by waterbath-sonication. Target protein of interest is pulled-down with paramagnetic beads that bind to polyhistidines, and later to biotinylated proteins.
After a brief RNAseI-digestion, RNA 3'-ends are healed with T4 PNK. Custom-made, barcoded adapters are ligated using T4 RNA Ligase 1 or T4 RNA Ligase 2KQ (if pre-adenylated adapters are used) for 1 hr at 25˚C. Custom FLASH adapters contained two barcodes and random nucleotides adjacent to the 3'-adapters according to the pattern NNBBNTTTTTTNN (N: random tag nucleotide, T: tag nucleotide, B: RY-space tag nucleotide). Random tags are used to merge PCR-duplicates, regular tags are used to specify the pulldown condition, and semi-random RY-space tags are used to distinguish the biological replicates (RR: replicate A, YY: replicate B, R: purine, Y: pyrimidine). Excess adapters are washed away, negative controls (IgG) are mixed with experimental controls and RNA is isolated with Proteinase K treatment and column purification. Isolated RNA is reverse-transcribed and RNaseH-treated. cDNA is column-purified and circularized with CircLigase for 2-16hrs. Circularized cDNA is directly PCR amplified, quantified with Qubit / Bioanalyzer and sequenced on Illumina NextSeq 500 in paired-end mode.

value: Flp-In T-REx 293

tag: purification (ab or affinity)


title: Mac1cell_R11_C30

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C34

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C14

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP1_3 [M1.3]


title: Mac1cell_R11_C54

description: P1_Mac.txt (matrix)


title: Mac1cell_R11_C26

description: P1_Mac.txt (matrix)


title: XL6 GFP-transHEK-HS repB

description: 3'-tag: GTGGAA


title: XL6 QKI-B-transHEK-HS repB

description: 3'-tag: TTAGCC


title: XL6 GFP-transHEK-HS repA

description: 3'-tag: GTGGAA


title: Mac1cell_R11_C45

description: P1_Mac.txt (matrix)


title: XL6 QKI-A-transHEK-HS repB

description: 3'-tag: CAAGTG


title: Mac1cell_R11_C11

description: P1_Mac.txt (matrix)


title: Empty_Vector_REP1_1 [M1.1]


title: XL6 QKI-A-transHEK-HS repA

description: 3'-tag: CAAGTG


title: Mac1cell_R10_C55

description: P1_Mac.txt (matrix)


title: siH19 rep3 (USMC)

city: New Haven

first: Ying

last: Jiang

address: 310 Cedar Street

institute: Department of Obstetrics, Gynecology & Reproductive Sciences

description:
USMC_counts_data.txt
USMC_siCon_vs_siH19_sig_diff_pooled.txt

data_processing:
RTA 2.4.11 software was used for basecalling
Alignments were made using Tophat v2.1.1,  read counts for each gene were estimated using featureCounts v1.5.0
Differential expression of genes between siCon and siH19 samples was determined using DESeq2 v1.14.1 (within R v3.3.3)
Genes that have significant differentiatial expression between siCon and siH19 triplicates (q Value <0.1) were presented in the processed data file
Genome_build: hg38
Supplementary_files_format_and_content: [USMC_counts_data.txt] Tab-delimited text file includes counts.
[USMC_siCon_vs_siH19_sig_diff_pooled.txt] Tab-delimited text file includes log2 fold change of relative gene expression levels between siCon and siH19 conditions.

source_name: UtSMC (Lonza, Cat: CC-2562)

growth_protocol: USMC cells purchased from Lonza were maintained in smooth muscle cell basal medium supplemented with growth supplements including hEGF, Insulin, hFGF-B, FBS and GA-1000. The smooth muscle cell basal medium and the growth supplements were included in the Clonetics™ SmGM™-2 BulletKit™ (CC-3182) from Lonza.

extract_protocol:
Total RNA was harvested using PureLink RNA Mini Kit.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fragments were adenylated and then ligated to indexing   adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.

treatment_protocol: Cells were transfected with either control siRNA or H19 siRNA. 48h later, cells were harvested for RNA extraction.

value: Uterine Smooth Muscle Cell (USMC)

tag: sirna

value: H19 knockdown


title: siH19 rep2 (USMC)


title: Mac1cell_R11_C10

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C6

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C56

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C43

description: P1_Mac.txt (matrix)


title: siCon rep3 (USMC)

value: siControl

value: control


title: Mac1cell_R10_C7

description: P1_Mac.txt (matrix)

value: Retina


title: siCon rep1 (USMC)


title: Mac1cell_R10_C52

description: P1_Mac.txt (matrix)


title: siCon rep2 (USMC)


title: CHO cells, NDST-3_EXP

first: Nathan

middle: E

last: Lewis

state: CA

address: 9500 Gilman Dr

institute: UCSD

data_processing:
The RNA libraries were mapped to the CHO genome (C_griseus_v1.0) using STAR aligner (v. 2.5.4b )
Alignments were processed to quantify gene expression counts with HTSeq-count (v. 0.7.2)
Genes with very low expression (with a cutoff of one count in at least two samples) were excluded from further downstream analysis
To comply with intellectual property requirements, the sequencing data were processed to exclude unmapped reads. This results in less than 5% reduction in available reads.
Genome_build: C_griseus_v1.0
Supplementary_files_format_and_content: comma-separated values (CSV) file of raw counts in matrix format, with sample names denoted by columns and genes by row

organism: Cricetulus griseus

source_name: Chinese hamster ovary (CHO) cells

extract_protocol:
Cell cultures were re-suspended in RLT buffer (Qiagen) and kept at −80 °C until RNA was extracted using the RNeasy kit (Qiagen) and on-column DNAse digestion.
Library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: RS-122-2103), according to manufacturer’s protocol

value: CHO-S cell line

tag: growth phase

value: Exponential phase


title: CHO cells, NDST-2_STA

value: Stationary phase


title: Mac1cell_R10_C38

description: P1_Mac.txt (matrix)


title: CHO cells, NDST-1_STA


title: Mac1cell_R10_C41

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C36

description: P1_Mac.txt (matrix)


title: CHO cells, A1-2_STA

value: amplified progeny of cell line of antibody-producing CHO DG44


title: CHO cells, A1-1_STA


title: CHO cells, A1-3_EXP


title: CHO cells, NDST-1_EXP


title: CHO cells, A1-1_EXP


title: CHO cells, A1-3_STA


title: Mac1cell_R10_C47

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C33

description: P1_Mac.txt (matrix)


title: CHO cells, NDST-2_EXP


title: CHO cells, A04_STA

value: antibody-producing CHO DG44 cell line


title: Mac1cell_R10_C28

description: P1_Mac.txt (matrix)


title: siH19 rep1 (USMC)


title: Mac1cell_R10_C31

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C30

description: P1_Mac.txt (matrix)


title: CHO cells, NDST-3_STA


title: CHO cells, A02_STA


title: CHO cells, A03_STA


title: CHO cells, A1-2_EXP


title: Mac1cell_R10_C51

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C19

description: P1_Mac.txt (matrix)


title: CHO cells, A01_STA


title: CHO cells, A04_EXP_Duplicate


title: CHO cells, A04_EXP


title: Mac1cell_R10_C18

description: P1_Mac.txt (matrix)


title: Mac1cell_R10_C13

description: P1_Mac.txt (matrix)


title: Mac1cell_R0_C9

description: P1_Mac.txt (matrix)


title: CHO cells, A01_EXP_RLT


title: CHO cells, A03_EXP


title: CHO cells, A02_EXP


title: Mac1cell_R0_C69

description: P1_Mac.txt (matrix)


title: CHO cells, A02_EXP_RLT


title: S16: Msr Quadruple Knockout  4-4826

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Illumina CASAVA software was used for basecalling which was coverted to fastq files using the bcl2fastq software.
quality controls of paired-end reads were assessed using FastQC tools
Adapter sequences and low-quality bases were trimmed using Cutadapt Alignment was performed by using HISAT2
Uniquely mapped paired-end reads were used for subsequent FeatureCounts for gene level abundance estimation
Limma-voom was employed for DEA
Genome_build: mm10
Supplementary_files_format_and_content: count matrix, raw count

organism: Mus musculus

source_name: Heart

growth_protocol: Animals were raised in an NIH animal facility following their standard animal protocol

extract_protocol:
Heart and liver were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.  Qiagen Rneasy Plus mini kit (Cat No./ID: 74104) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero following the manufacturer instruction.
RNA-seq were performed on Illumina Hiseq 3000 with paired end 75 bp sequencing and obtained about 75 million reads per sample.

treatment_protocol: No treatment

tag: strain

tag: age

value: 3-6 months old

value: Msr Quadruple Knockout

tag: gender

value: Female


title: S15: Msr Quadruple Knockout  3-4825


title: A thaliana, dcl1, IL, rep1

city: Norwich

first: Tamas

last: Dalmay

address: Earlham Road

department: School of Biological Sciences

country: United Kingdom

institute: University of East Anglia

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 5' HD signatures, for the HD samples, were trimmed and the files were converted from redundant to non-redundant format [Beckers et al 2017]
the reads were mapped to the reference genomes, allowing 0, 1 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the abundance of the genes was calculated as the algebraic sum of the abundances of incident reads
the abundances of the genes were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change, offset = 20
Genome_build: TAIR 10
Supplementary_files_format_and_content: csv, raw gene abundances

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: the plants were grown in Panasonic Plant  Chambers set at 25 and 18°C ( day and night, respectively) with 16 hours of light

extract_protocol:
The total RNA from leaf tissue was extracted using Tri-reagent and mRNA was purified using Dynabeads
Illumina compatible method using standard Illumina adapters or High definition (HD) adapters [Sorefan et al 2012, Xu et al 2015]

treatment_protocol: no specific treatment

tag: adapters

value: IL adapters


title: Mac1cell_R0_C8

description: P1_Mac.txt (matrix)

tag: sample


title: A thaliana, dcl1, HD, rep2

value: HD adapters


title: Mac1cell_R0_C68

description: P1_Mac.txt (matrix)

tag: tissue


title: A thaliana, dcl1, IL, rep2


title: A thaliana, dcl1, HD, rep1


title: Mac1cell_R0_C65

description: P1_Mac.txt (matrix)


title: S9: Wild Type 1-4755

value: WT


title: S12: Wild Type 4-4812


title: S14: Msr Quadruple Knockout  2-4735


title: S11: Wild Type 3-4811


title: S7: Msr Quadruple Knockout  3-4825

source_name: Liver


title: CHO cells, A01_EXP

tag: cell line


title: A thaliana, wt, IL, rep2

value: wt


title: Mac1cell_R10_C17

description: P1_Mac.txt (matrix)


title: CHO cells, A03_EXP_Duplicate


title: A thaliana, wt, IL, rep1


title: Mac1cell_R0_C58

description: P1_Mac.txt (matrix)


title: S8: Msr Quadruple Knockout  4-4826

tag: genotype


title: Mac1cell_R0_C56

description: P1_Mac.txt (matrix)


title: S5: Msr Quadruple Knockout 1-4732


title: A thaliana, wt, HD, rep2


title: S3: Wild Type 3-4811


title: Mac1cell_R0_C52

description: P1_Mac.txt (matrix)


title: S4: Wild Type 4-4812


title: A thaliana, wt, HD, rep1


title: S2: Wild Type 2-4757


title: S13: Msr Quadruple Knockout 1-4732


title: S10: Wild Type 2-4757


title: Mac1cell_R0_C49

description: P1_Mac.txt (matrix)


title: Mac1cell_R0_C41

description: P1_Mac.txt (matrix)


title: S1: Wild Type 1-4755


title: Mac1cell_R0_C40

description: P1_Mac.txt (matrix)


title: Mac1cell_R0_C38

description: P1_Mac.txt (matrix)


title: Mac1cell_R0_C35

description: P1_Mac.txt (matrix)


title: E. coli-infected Mkp-1 knockout mouse (#7)

city: Chicago

first: Irina

last: Buhimschi

state: IL

address: 820 S. Wood St.

department: Department of Obstetrics & Gynecology

institute: University of Illinois at Chicago College of Medicine

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
1cbfd481cc6bf5b18f8ff7065d233f86 = md5sum of raw file for processed data file: H_MKP1KO_7_1.count.txt
b44805b049759522517241f9ef47d13a = md5sum of raw file for processed data file: H_MKP1KO_7_2.count.txt

data_processing:
RNA-seq reads were subjected to low quality read and adapter trimming using Trim Galore version 0.4.0.
RNA-seq reads were mapped to the University of California Santa Cruz mm10 Mus musculus genome assembly using TopHat2 version 2.1.0.
Raw read counts were generated using HTseq version 0.6.0.
Genome_build: mm10 (UCSC)
Supplementary_files_format_and_content: Tab-delimited text file of raw (non-normalized) mapped reads. Read counts were provided separately for each technical replicate, thus there are two processed data files for each sample.

extract_protocol:
Total RNA was extracted from frozen liver tissues using Trizol reagent (Thermo Fisher Scientific, Waltham, MA), solubilized in UltraPure RNase/DNase-free water (Thermo Fisher Scientific), and quantified by using NanoDrop ND-1000 spectrophotometer (Marshall Scientific, Hampton, NH).
For RNA-seq analyses, 1 µg total RNA was used as starting material. First, cytoplasmic and mitochondrial ribosomal RNAs were depleted using a NEBNext rRNA Depletion Kit (New England Biolabs, Ipswich, MA), according to the manufacture’s recommendations. The RNA library was prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs). Briefly, RNA was fragmented, and cDNA was synthesized using random primers. The resulting double-strand cDNA was then subject to end-repair, adapter ligation, and PCR amplification to generate the library. Each library was sequenced in duplicate (two RNA-seq files per specimen).

treatment_protocol: All mice were housed with a 12 h alternating light-dark cycle at room temperature, and had free access to standard chow diet and water throughout the study. Mkp-1-/- and Mkp-1+/+ mice were infected with E. coli i.v., or injected with PBS. Briefly, E. coli (O55:B5, ATCC 12014), purchased from American Type Culture Collection (Manassas, VA), was grown in Luria broth at 37̊ °C for 18 h. The bacteria were pelleted by centrifugation, washed three times with phosphate-buffered saline (PBS), and finally suspended in PBS. E. coli was injected to the tail veins of mice at 2.5×107 CFU/g body weight. E. coli-infected or PBS-injected mice were euthanized 24 h later by pentobarbital over dose. The liver of each mouse was excised with a small piece preserved in formalin for histological assessment and the rest of the liver snap-frozen in liquid nitrogen prior to storage at -80°C.

value: Liver

tag: infection status

value: E. coli-infected


title: E. coli-infected Mkp-1 knockout mouse (#2)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
2408a511ca86e4b2120ccb20b27da563 = md5sum of raw file for processed data file: H_MKP1KO_2_1.count.txt
ec148a13e32453453f06c9c95a0f943a = md5sum of raw file for processed data file: H_MKP1KO_2_2.count.txt


title: Mac1cell_R0_C33

description: P1_Mac.txt (matrix)


title: E. coli-infected wildtype mouse (#10)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
3d348b0784f1dbe172ee0799d3768043 = md5sum of raw file for processed data file: H_WT_10_1.count.txt
51b9f66c748bd7df50f1c81df6063f2c = md5sum of raw file for processed data file: H_WT_10_2.count.txt

value: Wildtype


title: E. coli-infected wildtype mouse (#3)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
087df1490fbdc2993ce47d3131db5a94 = md5sum of raw file for processed data file: H_WT_3_1.count.txt
16cbf98b2e4f7512943f9d1c7321d90b = md5sum of raw file for processed data file: H_WT_3_2.count.txt


title: E. coli-infected Mkp-1 knockout mouse (#6)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
2eaa1d5be4dbfa494f471bf0c9c6c11b = md5sum of raw file for processed data file: H_MKP1KO_6_1.count.txt
cbea4af60da1a4e954e5576884a8a82f = md5sum of raw file for processed data file: H_MKP1KO_6_2.count.txt


title: Uninfected Mkp-1 knockout mouse (#9)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
8a0b4882a46b70dc1a41458c25f398dd = md5sum of raw file for processed data file: C_MKP1KO_9_1.count.txt
5683bab2e2f367e9d698e3229d60b304 = md5sum of raw file for processed data file: C_MKP1KO_9_2.count.txt

value: Uninfected


title: Mac1cell_R0_C32

description: P1_Mac.txt (matrix)

value: Retina


title: S6: Msr Quadruple Knockout  2-4735


title: E. coli-infected Mkp-1 knockout mouse (#8)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
778619d8efec44a78d7b9e48d395fcef = md5sum of raw file for processed data file: H_MKP1KO_8_1.count.txt
b5c37d42a5e7019c95fddc686fa8ca53 = md5sum of raw file for processed data file: H_MKP1KO_8_2.count.txt


title: Uninfected Mkp-1 knockout mouse (#3)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
188d117e85ca066db90320c98e854fa9 = md5sum of raw file for processed data file: C_MKP1KO_3_1.count.txt
fa1e3a109d24897f799553ddc51c8a1f = md5sum of raw file for processed data file: C_MKP1KO_3_2.count.txt


title: Uninfected Mkp-1 knockout mouse (#10)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
d70b54a7b37d7c2ab26adf171f5a80a5 = md5sum of raw file for processed data file: C_MKP1KO_10_1.count.txt
5a451d37fac381ce1a4c2e4b26378a01 = md5sum of raw file for processed data file: C_MKP1KO_10_2.count.txt


title: Input_DNA_JMJD3-control_rep2

city: Urbana

first: Jongsook

middle: Kim

last: Kemper

state: Illinois

address: 524 Burrill Hall  407 S. Goodwin Ave

department: Department of Molecular & Integrative Physiology

institute: University of Illinois at Champaign-Urbana

description:
input DNA in mouse primary liver cells (control treatment); biological replicate 2
JK2_ACTTGAAT

library_source: genomic

data_processing:
Samples containing 18 ng of DNA were used for genomic sequencing with the Illumina/Solexa Genome Analyzer II (Biotechnology Center, University of Illinois at UrbanaChampaign)
Raw sequencing reads were processed using the AQUAS pipeline (https://github.com/kundajelab/chipseq_pipeline, git commit version id: 910ba91b9e9ba51f51497b39134c8e737a5184a5).
The project-specific parameters were ‘-type histone -species mm10 –use_pooled_ctl’. Other parameters were default values given by the AQUAS pipeline.
In the AQUAS pipeline, reads were mapped to the mouse reference genome (mm10) using bwa (version 0.7.13).
Post-alignment filtering was done by Samtools (version 1.2) and Picard (version 1.126).
Peak calling was done by MACS (5) (version 2.1.0). The final overlapped peaks across replicates reported by AQUAS were determined as the bona fide H3K27-me3 enriched regions.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files and peaks files were generated by the AQUAS pipeline. The values of bigWig files represent either the -log10 of the p-value signals (containing 'pval.signal' in the name of the file) or the fold-enrichment signals  (containing 'fc.signal' in the name of the file). The peak files are in the narrowpeaks format (http://genome.ucsc.edu/FAQ/FAQformat.html#format12)

molecule: genomic DNA

growth_protocol: Male JMJD3 floxed mice were feed to 8 week-old.

extract_protocol:
Finely minced liver tissue was incubated in PBS containing 1% formaldehyde for 10 min, and then, glycine was added.The samples were resuspended in hypotonic buffer and lysed by homogenization. Nuclei were pelleted and sonicated. The chromatin sample was precleared and immunoprecipitated by binding to Protein G agarose with the H3K27-me3 (Abcam) antibody, the beads were washed, chromatin was eluted, and DNA was isolated.
ChIP assays were performaed using H3K27-me3 antibody (Ab6002) . Two sets of input and immunoprecipitated samples from 2 mices were used respectively. Libraries were prepared accoding to standard Illumina protocols.

treatment_protocol: For liver-specific downregulation of Jmjd3, 8 week-old male Jmjd3 floxed mice were injected with AAV-TBG-Cre or -GFP (1.0 to 2.0 X 1011 active viral particles), and 12 weeks later the mice were fasted for 16 h.

value: Primary liver cells

tag: treatment

value: JMJD3-control (treated with control AAV-GFP)


title: E. coli-infected wildtype mouse (#5)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
854c2015b5459f409c23ac0a3724e75d = md5sum of raw file for processed data file: H_WT_5_1.count.txt
af5edf31dfd5e3119631096ed2a44159 = md5sum of raw file for processed data file: H_WT_5_2.count.txt


title: Mac1cell_R0_C30

description: P1_Mac.txt (matrix)


title: Uninfected wildtype mouse (#9)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
cd38aab581a1c4f697de142662d053ed = md5sum of raw file for processed data file: C_WT_9_1.count.txt
dfc2381da28a326c0bafcad691d2e236 = md5sum of raw file for processed data file: C_WT_9_2.count.txt


title: E0771-HML2 cells, biological rep1

type: RNA

city: Edinburgh

first: Takanori

last: Kitamura

state: State...

address: 47 Little France Crescent

institute: University of Edinburgh

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 ºC on GeneChip Mouse Genome 430 2.0 Array (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using   Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Selected population of E0771 cancer cells with high metastatic potential

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA.

growth_protocol: Cancer cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Invitrogen) including 10% (v/v) Fetal Bovine Serum (FBS, Sigma) and 1% (v/v) Penicillin/Streptomycin (Sigma) at 37 ºC for 3 days.

extract_protocol: Total RNA was extracted by the Trizol extraction method according to the manufacturer's instructions.

treatment_protocol: Cells in tissue culture dishes were rinsed with PBS, and directly lysed with the Trizol solution (GibcoBRL).

value: Mammary tumor


title: E0771 parental cells, biological rep2

source_name: Parental E0771 cancer cells, non selected


title: E0771 parental cells, biological rep3


title: E0771-HML2 cells, biological rep2


title: E. coli-infected wildtype mouse (#9)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
74c1a4008e4c5b5896a3f9a8a18431b1 = md5sum of raw file for processed data file: H_WT_9_1.count.txt
40b5606353655c15f5314f3f840030dc = md5sum of raw file for processed data file: H_WT_9_2.count.txt


title: Input_DNA_JMJD3-control_rep1

description:
input DNA in mouse primary liver cells (control treatment); biological replicate 1
JK1_TGACCAAT


title: E0771-HML2 cells, biological rep3


title: Uninfected wildtype mouse (#2)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
16db9eb1489e5378ec01d14814c6796f = md5sum of raw file for processed data file: C_WT_2_1.count.txt
c1cbea9453b905ab74ba6a7c6e95a081 = md5sum of raw file for processed data file: C_WT_2_2.count.txt


title: Mac1cell_R0_C28

description: P1_Mac.txt (matrix)

source_name: retina


title: Uninfected wildtype mouse (#6)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
b36d4b7c19eafd7659f7f22a7e13e3e9 = md5sum of raw file for processed data file: C_WT_6_1.count.txt
e56bd3cb9f86087cdf45f2988ce94d12 = md5sum of raw file for processed data file: C_WT_6_2.count.txt


title: Uninfected wildtype mouse (#1)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
047d82aeedbd73df00ccce9d913180e1 = md5sum of raw file for processed data file: C_WT_1_1.count.txt
94c3bb011be296cc5ffa9ff9eec6857b = md5sum of raw file for processed data file: C_WT_1_2.count.txt


title: Uninfected Mkp-1 knockout mouse (#7)

description:
The library was sequenced twice, producing two technical replicates. Both raw files are included for each sample, each represented as a separate SRR. Read counts are provided separately for each technical replicate.
f4de33eab54434e13e1781170618e59d = md5sum of raw file for processed data file: C_MKP1KO_7_1.count.txt
ed331a31a4f858d97235afc89bf22b23 = md5sum of raw file for processed data file: C_MKP1KO_7_2.count.txt


title: Mac1cell_R0_C27

description: P1_Mac.txt (matrix)


title: Input_DNA_JMJD3-floxed_rep2

description:
input DNA in mouse primary liver cells with JMJD3 downregulated; biological replicate 2
JK4_GGCTACAT

value: JMJD3-floxed (liver-specific JMJD3 knockdown by AAV-TBG-Cre)


title: Hs_PU1_moDC_ST_ChIPSeq

city: Oviedo

first: Laura

last: Gutiérrez

state: Asturias

address: Avenida de Roma S/N

country: Spain

institute: ISPA - University of Oviedo

data_processing:
peaks were called using  macs version 1.4.1 20110622 with the following settings: bandwidth 125 and a lower and upper M-fold cutoff of 8 and 30 respectively.
Genome_build: GRCh37 (hg19) (human moDC) or mm9 (mouse BMDC)
Supplementary_files_format_and_content: annotated peaks.txt

source_name: human inflammatory DC immature

growth_protocol: Monocytes, isolated with CD14 magnetic beads (Miltenyi Biotech), were cultured at a density of 0.5x10E6 cells/ml in RPMI-1640 supplemented with 10% FCS, 1% Pen/Strep, in the presence of 10 ng/ml GM-CSF and 10 ng/ml IL-4.

extract_protocol:
After crosslinking the chromatin of 2x10E8 cell lysates, sonicated nuclei and PU.1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: At day 7, BMDC were stimulated or not with 500 ng/ml LPS, and collected at day 10.

tag: culture type

value: monocyte derived DC

value: dendritic cells (DC)

tag: treatment and collection date

value: no LPS added, collection day 10

tag: culture conditions

value: GM-CSF + IL4

tag: antibody

value: PU.1 (T-21, Santa Cruz)


title: Hs_PU1_moDC_LPS_ChIPSeq

source_name: human inflammatory DC LPS stimulated

tag: cell type

value: LPS added at day 7, collection day 10


title: Mac1cell_R0_C26

description: P1_Mac.txt (matrix)


title: H3K27me3_ChIP-Seq_JMJD3-control_rep2

description:
H3K27me3 ChIP-Seq in mouse primary liver cells (control treatment); biological replicate 2
JK6_ATGTCAGA

tag: chip antibody

value: H3K27-me3 antibody (Ab6002)


title: H3K27me3_ChIP-Seq_JMJD3-control_rep1

description:
H3K27me3 ChIP-Seq in mouse primary liver cells (control treatment); biological replicate 1
JK5_AGTCAACA


title: Mac1cell_R0_C24

description: P1_Mac.txt (matrix)


title: Mac1cell_R0_C25

description: P1_Mac.txt (matrix)


title: H3K27me3_ChIP-Seq_JMJD3-floxed_rep2

description:
H3K27me3 pulldowned ChIP-Seq in mouse primary liver cells with JMJD3 downregulated; biological replicate 2
JK8_GTGGCCTT


title: Mac1cell_R0_C23

description: P1_Mac.txt (matrix)


title: Input_DNA_JMJD3-floxed_rep1

description:
input DNA in mouse primary liver cells with JMJD3 downregulated; biological replicate 1
JK3_TAGCTTAT


title: Mac1cell_R0_C17

description: P1_Mac.txt (matrix)


title: Mac1cell_R0_C16

description: P1_Mac.txt (matrix)


title: H3K27me3_ChIP-Seq_JMJD3-floxed_rep1

description:
H3K27me3 pulldowned ChIP-Seq in mouse primary liver cells with JMJD3 downregulated; biological replicate 1
JK7_GTGAAACG


title: non_involved_lung_tissue_patient_173 200762720010_I_Expression

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Primary microarray data were collected using BeadStudio v3 software package. Raw data were log2-transformed and normalized using the robust spline normalization method, implemented in the lumi R/Bioconductor package. Batch effects were removed using ComBat function implemented in the sva R/Bioconductor package.

source_name: Non-involved (apparently normal) lung parenchyma

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies).

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

tag: Sex

value: M

tag: smoking status

value: ever-smoker

tag: batch


title: non_involved_lung_tissue_patient_172 200762720010_H_Expression

value: F

tag: age

value: never-smoker


title: ELF4 siRNA treated replicate 3

city: Austin

first: Vishy

last: Iyer

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
Reads were aligned to the human genome (UCSC version hg19) using TopHat. FeatureCounts was then used to count reads mapping to genes and differential gene expression analysis was performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Normalized gene counts in CSV format

growth_protocol: BE-(2)-C neuroblastoma cells were grown in DMEM/F12 (GIBCO) supplemented with 10% Fetal Bovine Serum (GIBCO) and 1% Pen/Strep (GIBCO).

extract_protocol:
RNA was isolated with Trizol.
RNA-seq experiments were performed on poly-A selected mRNA.

treatment_protocol: Cells were treated with either siControl or siELF4 siRNAs.

value: neuroblastoma cells

value: ELF4 siRNA


title: ELF4 siRNA treated replicate 2


title: non_involved_lung_tissue_patient_176 200762720010_L_Expression


title: E0771 parental cells, biological rep1

tag: strain


title: non_involved_lung_tissue_patient_174 200762720010_J_Expression


title: non_involved_lung_tissue_patient_170 200762720010_E_Expression


title: non_involved_lung_tissue_patient_175 200762720010_K_Expression


title: knockdown_1

city: Boston

first: Stefan

last: Haemmig

address: 77 Avenue Louis Pasteur, NRB-742

institute: Brigham and Women Hospital / Harvard Medical School

description: Sample 4

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized counts

source_name: Human Umbilical Vein Cells

growth_protocol: Human Umbilical Vein Cells  (HUVECs) were grown in complete EGM-2 medium for two passages. Transfectoin of gapmeRs (25nM) towards SNHG12 (n=3) or negative control (n=3) was performed using Lipofectamine 2000 based on manufacturers protocol.

extract_protocol:
Rneasy mini kit plus from Qiagen.
Ribosomal RNA depletion.

treatment_protocol: HUVECs were treated with 250µM H202 for 4hrs before RNA was isolated.

tag: passages

value: H2O2 treated


title: non_involved_lung_tissue_patient_167 200762720010_B_Expression


title: control_3

description: Sample 3

value: no treated


title: knockdown_3

description: Sample 6


title: knockdown_2

description: Sample 5


title: non_involved_lung_tissue_patient_168 200762720010_C_Expression


title: ELF4 siRNA treated replicate 1


title: non_involved_lung_tissue_patient_169 200762720010_D_Expression


title: non_involved_lung_tissue_patient_163 200762720009_J_Expression


title: non_involved_lung_tissue_patient_164 200762720009_K_Expression


title: non_involved_lung_tissue_patient_171 200762720010_G_Expression


title: non_involved_lung_tissue_patient_166 200762720010_A_Expression


title: control_2

description: Sample 2


title: non_involved_lung_tissue_patient_165 200762720009_L_Expression


title: non_involved_lung_tissue_patient_161 200762720009_H_Expression


title: non_involved_lung_tissue_patient_162 200762720009_I_Expression


title: Control siRNA treated replicate 3

value: Control siRNA


title: control_1

description: Sample 1


title: Control siRNA treated replicate 2


title: non_involved_lung_tissue_patient_158 200762720009_D_Expression


title: Control siRNA treated replicate 1


title: 222068_Naive_v1

city: New York City

first: Ramin

last: Herati

state: NY

address: 429 E. 29th Street, room 308

institute: NYU School of Medicine

description: CD4+CD45RA+CD27+ T cells before vaccination

data_processing:
FASTQ files were trimmed using Trimmomatic 0.32.
Trimmed FASTQ files were aligned using STAR 2.5.2a against the HG38 reference genome.
The aligned files were processed using PORT 0.8.5 gene-based normalization (https://github.com/itmat/Normalization).
Variance-stabilizing transformation and differential expression analysis were performed using DESeq2 1.20.0.
Genome_build: HG38
Supplementary_files_format_and_content: Counts data

source_name: Naïve CD4 T cells

extract_protocol:
Peripheral blood mononuclear cells were isolated from patient samples by density centrifugation using Ficoll (GE catalog #17144003), followed by cell sorting on a BD Aria II sorter. Sorted cells were lysed and RNA isolated using the Rneasy Plus Micro kit (Qiagen catalog #74034 ) using the standard protocol.
cDNA was produced and amplified using Clontech SMARTer v3, followed by Nextera XT for library preparation according to standard protocols.

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 0

tag: cohort

value: Elderly


title: ChIP-Seq_HCC1806_H3K27ac

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.1 with the default options.
The bigwig files were generated by using HOMER, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Genome_build: hg19

source_name: breast cancer

growth_protocol: HCC1806 and HCC1937 were cultured in RPMI-1640 medium (Gibco, Grand Island, USA) supplemented with 10 % FBS (Gibco).

extract_protocol:
HCC1806 and HCC1937 cells were cross-linked with 1 % formaldehyde (for H3K27Ac), or cross-linked with disuccinimidyl glutarate, followed by double cross-linked with 1 % formaldehyde (for BRD4).
The libraries were constructed following NEB’s Chip-Seq Sample prep kit. Briefly, Chip DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: no treatment

tag: cell line


title: ChIP-Seq_HCC1806_BRD4


title: ChIP-Seq_HCC1937_H3K27ac


title: non_involved_lung_tissue_patient_157 200762720009_C_Expression


title: 222068_Naive_v2

description: CD4+CD45RA+CD27+ T cells one week after vaccination

value: Post-vaccine day 7


title: non_involved_lung_tissue_patient_160 200762720009_G_Expression


title: 222068_LoLo_v1

description: CD4+CXCR5+PD1+ICOS-CD38- T cells before vaccination

source_name: Quiescent Tfh


title: ChIP-Seq_HCC1937_BRD4


title: non_involved_lung_tissue_patient_153 200796230052_J_Expression


title: 222068_HiHi_v1

description: CD4+CXCR5+PD1+ICOS+CD38+ T cells before vaccination

source_name: Activated Tfh


title: non_involved_lung_tissue_patient_156 200762720009_B_Expression


title: non_involved_lung_tissue_patient_150 200796230052_F_Expression


title: 222068_HiHi_v2

description: CD4+CXCR5+PD1+ICOS+CD38+ T cells one week after vaccination


title: non_involved_lung_tissue_patient_152 200796230052_I_Expression


title: non_involved_lung_tissue_patient_154 200796230052_K_Expression


title: non_involved_lung_tissue_patient_149 200796230052_E_Expression


title: 222067_Naive_v2


title: non_involved_lung_tissue_patient_146 200796230043_L_Expression


title: non_involved_lung_tissue_patient_148 200796230052_D_Expression


title: non_involved_lung_tissue_patient_151 200796230052_H_Expression


title: non_involved_lung_tissue_patient_155 200762720009_A_Expression


title: 222068_LoLo_v2

description: CD4+CXCR5+PD1+ICOS-CD38- T cells one week after vaccination


title: non_involved_lung_tissue_patient_159 200762720009_F_Expression


title: non_involved_lung_tissue_patient_145 200796230043_J_Expression


title: CIT siRNA R1881 biol rep3

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

description:
RawCounts.csv
SBS-RS012

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using HTSeq v0.6.1 using intersect-strict option
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: CIT siRNA R1881

extract_protocol: RNA Libraries are prepared using the Illumina NextSeqTruSeq RNA Exome protocol and kit reagents.

value: LNCaP prostate cancer cells

tag: transfection

value: CIT siRNA

tag: treatment

tag: biological replicate


title: CIT siRNA R1881 biol rep1

description:
RawCounts.csv
SBS-RS010


title: CIT siRNA R1881 biol rep2

description:
RawCounts.csv
SBS-RS011


title: CIT siRNA vehicle biol rep3

description:
RawCounts.csv
SBS-RS009

source_name: CIT siRNA vehicle

value: ETOH


title: non_involved_lung_tissue_patient_147 200796230052_B_Expression


title: 222067_LoLo_v2


title: 222067_LoLo_v1


title: 222067_Naive_v1


title: non_involved_lung_tissue_patient_144 200796230043_I_Expression


title: 222067_HiHi_v2


title: CIT siRNA vehicle biol rep2

description:
RawCounts.csv
SBS-RS008


title: non_involved_lung_tissue_patient_142 200796230043_G_Expression


title: non_involved_lung_tissue_patient_141 200796230043_F_Expression


title: CIT siRNA vehicle biol rep1

description:
RawCounts.csv
SBS-RS007


title: 222067_HiHi_v1


title: control siRNA R1881 biol rep3

description:
RawCounts.csv
SBS-RS006

source_name: control siRNA R1881

value: control (OTPC) siRNA


title: 222065_Naive_v2


title: non_involved_lung_tissue_patient_138 200796230043_A_Expression


title: non_involved_lung_tissue_patient_143 200796230043_H_Expression

value: M


title: non_involved_lung_tissue_patient_137 200796200066_L_Expression


title: non_involved_lung_tissue_patient_136 200796200066_K_Expression

value: ever-smoker


title: non_involved_lung_tissue_patient_140 200796230043_D_Expression

value: F


title: non_involved_lung_tissue_patient_134 200796200066_H_Expression


title: non_involved_lung_tissue_patient_133 200796200066_G_Expression


title: control siRNA R1881 biol rep1

description:
RawCounts.csv
SBS-RS004


title: non_involved_lung_tissue_patient_135 200796200066_J_Expression


title: non_involved_lung_tissue_patient_130 200796200066_B_Expression

value: never-smoker


title: 222065_LoLo_v2


title: control siRNA vehicle biol rep3

description:
RawCounts.csv
SBS-RS003

source_name: control siRNA vehicle


title: non_involved_lung_tissue_patient_129 200796200046_K_Expression


title: control siRNA vehicle biol rep2

description:
RawCounts.csv
SBS-RS002


title: 222065_HiHi_v2


title: control siRNA vehicle biol rep1

description:
RawCounts.csv
SBS-RS001


title: 222065_LoLo_v1


title: 222065_HiHi_v1


title: 222062_Naive_v2


title: A1023C20: Input-EGF-2

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

data_processing:
Raw sequencing reads were first aligned with the bowtie2 software (v2.2.9) on the Drosophila Melanogaster (dmel-R6,21) reference genome to extract reads coming from spike-in chromatin. Remaining reads were then aligned on the Human hg38 reference genome using bowtie2 very-sensitive mode. PCR duplicates were removed from aligned data using Picard tools, and genome-browser tracks files were generated using the Deeptools suite (v3.1.0) and the bamCoverage function. In order to validate the overall H3K9me2 profile, large genomic domains were called with the EPIC software  (v0.2.9, https://github.com/biocore-ntnu/epic, --window-size 500 --gaps-allowed 5 --false-discovery-rate-cutoff 0.01), and LOCKs were defined as previously proposed (McDonald et al. 2017).
Raw sequencing reads were first aligned with the bowtie2 software (v2.2.9) on the Drosophila Melanogaster (dmel-R6,21) reference genome to extract reads coming from spike-in chromatin. Remaining reads were then aligned on the Human hg38 reference genome using bowtie2 very-sensitive mode. PCR duplicates were removed from aligned data using Picard tools, and genome-browser tracks files were generated using the Deeptools suite (v3.1.0) and the bamCoverage function. Input samples per condition have been merged in a single coverage WIG file.
In order to validate the overall H3K9me2 profile, large genomic domains were called with the EPIC software [3] (v0.2.9, https://github.com/biocore-ntnu/epic, --window-size 500 --gaps-allowed 5 --false-discovery-rate-cutoff 0.01), and LOCKs were defined as previously proposed (McDonald et al. 2017).
Counts of aligned reads per human gene have been generated using the FeatureCounts software [4] and the gene coordinates extracted from the GENCODE annotation file (v26). Genes with less than 10 reads were discarded from the analysis. The raw count table was then normalized using the TMM method from the edgeR R package [5] (v3,22,3), and the limma voom (v3.36.3)  functions were applied to detect genes with differential binding between untreated and EGF samples. Finally, genes with an adjusted pvalue < 0,05 and a log2 fold-change > 0,3 were called significant.
Genome_build: hg38
Supplementary_files_format_and_content: wig file of ChIP signal

source_name: Basal breast cancer  cells

growth_protocol: MDA-MB-468 cells grown in 145 mm2 dishes until ~ 70% confluence were treated with EGF (100 ng mL-1) for 72h in biological triplicate and untreated cells were used as an appropriate control.

extract_protocol:
The pelleted cells were washed twice with ice-cold PBS1x by centrifuging at 500 x g for 5 min at 4°C.  For lysis of crosslinked chromatin, the pellet was resuspended in lysis buffer A (50 mM Tris HCl pH8, 10 mM EDTA, 1% SDS, 50 x protease inhibitor cocktail) at room temperature and incubated for 5 min on rotating wheel. Next, lysate was centrifuged at 300 x g for 10 min at 8°C to prevent SDS precipitation and the supernatant was discarded. For chromatin shearing, the pellet was sheared in buffer B (25 mM Tris HCl pH8, 3 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, 50 x protease inhibitor cocktail) to approximatively 200-600 base-pair average size using the Bioruptor Pico (Diagenode). After centrifugation at 20 000 x g, 4ºC for 15 min, the supernatant containing sheared chromatin was used for immunoprecipitation. 25 µL (10%) of sheared chromatin was used as input DNA to normalize sequencing data. As supplement control for normalization, we used spike-in chromatin Drosophila and spike-in antibody (Active motif). For chromatin immunoprecipitation (1 million cells per ChIP), it was carried out using sheared chromatin and antibody H3K9me2 complexed to Dynal Protein G magnetic beads (Thermo Fisher). Briefly, 6 µL of H3K9me2 antibody was mixed with 1 µg of spike-in antibody. 23 µL of magnetic beads were washed three times in ice-cold buffer C (20 mM Tris HCl pH8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 150 mM NaCl, 50 x protease inhibitor cocktail) and incubated with the mix of H3K9me2 and spike-in antibody for 4h at room temperature on rotating wheel in buffer C (494 µL). After the quick-spin and the removal of supernatant, the beads were resuspended in 100 µL buffer C. Each 50 µL of the latter was incubated with 250 µL of sheared chromatin mixed previously with 50 ng of spike-in chromatin Drosophila (250 µL chromatin of interest: 2,5 µL of spike-in chromatin, v:v) at 4°C on rotating wheel, overnight (~ 16h).  After quick-spin, the supernatant was discarded and the beads were successively washed in buffer C, buffer D (20 mM Tris-HCl pH8, 2 mM EDTA, 0.1% SDS, 1% Triton X-100, 500 mM NaCl), buffer E (10 mM Tris-HCl pH8, 0.25 M LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate, 1 mM EDTA) and buffer F (10 mM Tris-HCl pH8, 1 mM EDTA, 50 mM NaCl).  Finally, input and immunoprecipitated chromatin samples were resuspended in solution containing TE buffer/ 1% SDS, decrosslinked by heating at 65°C overnight and subjected to both RNase A and Proteinase K treatments.
Illumina compatible libraries were prepared from input and immunoprecipitated DNAs using the Illumina TruSeq ChIP library preparation kit according to the manufacturer’s protocol. Briefly, 4 to 10ng of DNA were subjected to subsequent steps of end-repair, dA-tailing and ligation of TruSeq indexed Illumina adapters. After a final PCR amplification step, the 24 resulting barcoded libraries were equimolarly pooled in 2 groups quantified using a qPCR method (KAPA library quantification kit, Roche) before sequencing on the Illumina HiSeq2500 instrument. Each pool was loaded on 1 rapid flow cell (11pM) and sequenced using a single read mode (SR50). This sequencing configuration was set to reach an average of 25 million reads (50-base long) per sample.

treatment_protocol: Cells were harvested by trypsinization. After adding media to stop trypsin, cells were centrifuged at 500 x g for 5 min at room temperature. The pelleted cells were resuspended in media, counted and crosslinked with 37% formaldehyde (final concentration 1%) for 10 min at room temperature. The crosslinking was stopped by addition of 2.5 M glycine (final concentration 0.125 M) for 5 min at room temperature followed by centrifugation at 500 x g for 5 min at 4°C.

value: Basal breast cancer  cells

tag: passages used

value: From  6 to 14

value: none (input)


title: A1014C10: Input-EGF-1


title: 222062_Naive_v1


title: non_involved_lung_tissue_patient_123 200796200046_D_Expression


title: non_involved_lung_tissue_patient_131 200796200066_C_Expression


title: non_involved_lung_tissue_patient_128 200796200046_J_Expression


title: non_involved_lung_tissue_patient_127 200796200046_I_Expression


title: non_involved_lung_tissue_patient_122 200796200046_C_Expression


title: non_involved_lung_tissue_patient_120 200796200046_A_Expression


title: A1023C19: Input-untreated-2


title: non_involved_lung_tissue_patient_118 200796200037_K_Expression


title: 222062_LoLo_v2


title: non_involved_lung_tissue_patient_126 200796200046_G_Expression


title: non_involved_lung_tissue_patient_124 200796200046_E_Expression


title: non_involved_lung_tissue_patient_119 200796200037_L_Expression


title: A1014C01: Input-untreated-1


title: non_involved_lung_tissue_patient_117 200796200037_J_Expression


title: 222062_LoLo_v1


title: non_involved_lung_tissue_patient_132 200796200066_F_Expression


title: non_involved_lung_tissue_patient_121 200796200046_B_Expression


title: A1023C24: H3K9me2_EGF-3

value: H3K9me2 ( cell signaling, Cat # 4658S; Rabbit monoclonal [D85B4])


title: 222062_HiHi_v1


title: non_involved_lung_tissue_patient_116 200796200037_I_Expression


title: non_involved_lung_tissue_patient_125 200796200046_F_Expression


title: non_involved_lung_tissue_patient_115 200796200037_G_Expression


title: A1023C14: H3K9me2_EGF-2


title: non_involved_lung_tissue_patient_111 200796200037_C_Expression


title: non_involved_lung_tissue_patient_112 200796200037_D_Expression


title: non_involved_lung_tissue_patient_114 200796200037_F_Expression


title: 222062_HiHi_v2


title: non_involved_lung_tissue_patient_110 200796200037_B_Expression


title: 222060_Naive_v2


title: 222060_Naive_v1


title: non_involved_lung_tissue_patient_109 200796200037_A_Expression


title: 222060_LoLo_v2


title: non_involved_lung_tissue_patient_113 200796200037_E_Expression


title: A1014C06: H3K9me2_EGF-1


title: A1023C13: H3K9me2_untreated-2


title: 222060_LoLo_v1


title: BY4741_YPD_rep2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  with one mismatch
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using STAR 2.5.3a default settings except AlignIntronMax(2500). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: Saccharomyces cerevisiae  grown in YPD at 30°C.

extract_protocol:
RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (14 cycles). Ampure beads size selected libraries with a length of 300-500 nt were sent for sequencing (llumina NextSeq 500 instrument).

treatment_protocol: Cells were incubated with 0.1 mg/ml final cycloheximide  for 10 minutes prior to harvesting.

tag: genotype

tag: parental strain

value: BY4741(MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0)


title: A1023C23: H3K9me2_untreated-3

tag: chip antibody


title: 222060_HiHi_v2

value: PBMC


title: BY4741_YPD_rep1

value: MATa his3[delta]1 leu2[delta]0 met15[delta]0 ura3[delta]0


title: non_involved_lung_tissue_patient_105 200796200023_H_Expression

tag: Sex


title: non_involved_lung_tissue_patient_106 200796200023_J_Expression

tag: smoking status


title: non_involved_lung_tissue_patient_100 200796200023_A_Expression

tag: batch


title: non_involved_lung_tissue_patient_102 200796200023_E_Expression

tag: age


title: non_involved_lung_tissue_patient_108 200796200023_L_Expression


title: non_involved_lung_tissue_patient_139 200796230043_B_Expression


title: non_involved_lung_tissue_patient_101 200796200023_B_Expression


title: non_involved_lung_tissue_patient_103 200796200023_F_Expression


title: 222060_HiHi_v1

value: Post-vaccine day 0

value: Elderly


title: non_involved_lung_tissue_patient_98 9983140109_K_Expression


title: non_involved_lung_tissue_patient_104 200796200023_G_Expression


title: CHX_rrp6∆_rep2

value: Cycloheximide treatment


title: 222049_Naive_v2

value: Post-vaccine day 7


title: CHX_set2∆_rep2


title: non_involved_lung_tissue_patient_97 9983140109_J_Expression


title: 222049_LoLo_v2


title: CHX_rrp6∆_rep1


title: non_involved_lung_tissue_patient_95 9983140109_G_Expression


title: 222049_Naive_v1


title: CHX_set2∆_rep1


title: non_involved_lung_tissue_patient_96 9983140109_I_Expression


title: 222049_LoLo_v1


title: non_involved_lung_tissue_patient_99 9983140109_L_Expression


title: 222049_HiHi_v2


title: CHX_BY4741_rep2


title: non_involved_lung_tissue_patient_94 9983140109_F_Expression


title: control siRNA R1881 biol rep2

description:
RawCounts.csv
SBS-RS005

value: LNCaP prostate cancer cells


title: non_involved_lung_tissue_patient_93 9983140109_E_Expression


title: non_involved_lung_tissue_patient_92 9983140109_D_Expression


title: non_involved_lung_tissue_patient_91 9983140109_C_Expression


title: non_involved_lung_tissue_patient_90 9983140109_B_Expression


title: 222049_HiHi_v1


title: rrp6∆_rep2

data_processing:
Library strategy: 5'cap-seq
For polyribosomes 5’ cap sequencing reads, random barcodes were first extracted and added to the reads name. The reads were aligned to yeast genome with Novoalign (http://www.novocraft.com) using default setting.
For 5’PSeq each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using STAR 2.5.3a default settings except AlignIntronMax(2500). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand for 5PSeq. For polyribosome 5'cap sequencing both strands are in the same file.

extract_protocol:
For polyribosome analysis, cells resuspended on Lysis buffer were transferred to pre-cooled 1.5mL screw-tubes with 300 µL glass beads and supplemented with 100 units of RNAse inhibitor (RNAsin plus, Promega). Cells were lysed using a FastPrep-24 shaker (6.0m/s for 15 seconds, MP biomedicals). Supernatant was recovered after 5 minutes centrifugation at 2300g, and cleared with an additional centrifugation at 5900g. Extracts were supplemented with glycerol (5% final  v/v) and stored at -70C. 10-50% sucrose gradients were prepared with a Gradient Master BIOCOMP (Nycomed Pharma). Sucrose solution contains 20 mM Tris-HCl, pH 8, 140 mM KCl, 5 mM MgCl2 , 0.5 mM DTT, 100 µg/mL cycloheximide and sucrose (from 10 to 50 %). Cleared cell extracts were ultracentifuged at 34400 rpm for 2 hours 40 minutes at 4C using a C-1000 XP centrifuge with SW40 rotor (Beckman Coulter). Gradient UV absorption at 254 nm was measured and selected fractions were selected for 5’cap library preparation (5µg purified RNA per sample). Polyribosome fraction (i.e., 2n+) was compared with the total extract prior to fractionation).    For 5PSeq RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
5’cap polyribosome fractioned libraries was performed as previously described (Pelechano et al. Nat Protocols. 2016  PMID: 26820793). In brief, 10µg total RNA was treated with Calf intestinal alkaline phosphatase (NEB)
to remove 5′P from fragmented and non-capped molecules. After purification, mRNA caps were removed using 3.75 units of Cap-Clip (Biozyme) exposing a 5’P in those molecules previously capped. Samples were ligated overnight at 16ºC with a DNA/RNA oligo (rP5_RND: TTTCCCTACACGACGCTCTTCCGATrCrUrNrNrNrNrNrNrNrN ) using T4 RNA ligase 1 (New England Biolabs). RNA integrity after ligation was assayed by agarose gel electrophoresis and polyA RNA was purified using oligo dT magnetic beads. After this, ligated mRNA was fragmented at 80ºC for 5 min in the presence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc, 30 mM MgOAc). Ligated RNA was subjected to reverse transcription using random hexamers with Superscript II (Life Technologies) with the following program: 10 min at 25ºC, 50 min at 42ºC and heat inactivated for 15 min at 72ºC. Second strand cDNA synthesis was performed by a single PCR cycle (1 min at 98ºC; 2 min at 50ºC and 15 min at 72ºC) using Phusion High-Fidelity PCR Master Mix (New England Biolabs). A biotinilated oligo (BioNotI-P5-PET: [Btn]TATAGCGGCCGCAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTAC ACGACGCTCTTCCGATCT) was added during the generation of the second cDNA strand. Double stranded cDNA was purified using Ampure XP (Beckman Coulter) or HighPrep (Magbio) beads. After the samples were bound to streptavidin coated magnetic beads (M-280 Dynabeads, Life Technologies) and subjected to standard Illumina end-repair, dA addition and adapter ligation was performed as previously described. Libraries were enriched by PCR and sequenced in an Illumina HiSeq 2000 instrument.     5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (14 cycles). Ampure beads size selected libraries with an average length of 451 nt were sent for sequencing (llumina NextSeq 500 instrument).

treatment_protocol: For polyribosome analysis  100 mL of S. cerevisiae cells at OD600 ~1 were treated with cycloheximide for 5 minutes (100 µg/mL, final concentration), harvested by centrifugation and transferred to ice. Pellets were washed with ice-cold lysis buffer and resuspended in 700µL lysis buffer. Lysis buffer contains 20 mM Tris-HCl, pH 8, 140 mM KCl,  5 mM MgCl2 , 0.5 mM DTT, 1% Triton X-100, 100 µg/mL cycloheximide, 500 µg/mL heparin and complete EDTA-free protease inhibitor (1 tablet per 10 mL, Sigma Aldrich).    For 5PSeq cells were shifted for 5 minutes to YP media without glucose (1% yeast extract, 2% peptone) prior to harvesting.


title: 222039_Naive_v2


title: rrp6∆_rep1


title: C09 Pre placebo

city: Jena

first: Amol

last: Kolte

address: Am Klinikum 1

institute: Center for Sepsis Control and Care, University Clinic, Jena

description:
C09 Pre placebo
1842761048_C

hyb_protocol: 1.5 µg cRNA of each sample was hybridized on Human-WG6-V3 BeadChips. Hybridization was performed according to the Gene Expression on Sentrix® Arrays Direct Hybridization System Manual (Illumina Inc.). After 16 h hybridization time at a temperature of 58° C for a volume of 30 µl, label incorporation was performed by staining of hybridized arrays with 1µg/µl Streptavidin-Cy3 (FluoroLink® Cy3, GE Biosciences). Arrays were washed, dried and scanned immediately.

scan_protocol: Arrays were scanned on an Illumina BeadArray Reader (MIAME compliant file). BeadChips were scanned by Gene Expression Module v3.2 according to the protocol of the manufacturer (Revision A). Arrays were readout with the detection system iScan from Illumina.

data_processing: Raw data was pre-processed using GenomeStudio (v 1.9.0). Microarray normalization and statistical analysis were performed using R/Bioconductor (www.r-project.org). Probes with a detection significance P ≤ 0.05 were selected for further analysis. The data was log2 transformed followed by quantile normalization using the lumi package. Probe annotations were processed using lumiHumanIDMapping and lumiHumanAll.db to get HGNC symbols via Illumina nuIDs.

source_name: C09 Pre placebo

label_protocol: Biotinylated probes were prepared from total RNA, using the TargetAmp™-Nano Labeling Kit for Illumina® Expression BeadChip®.

extract_protocol: Blood was drawn on (pre) and 24 h after admission (post) and prepared with PAXgene reagent (PreAnalytix®, Qiagen, Hilden, Germany).

tag: individual

value: Pid C09

tag: timepoint

value: Pre

value: placebo

tag: acth

value: Non responder

tag: survival (28 days)

value: survived

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: high

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: set2∆_rep1

description:
set2Δ::KanMX
BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)

data_processing:
Library strategy: 5P-Seq
Base-calling was done using bcl2fastq v2.20.0.422  with one mismatch
For each read we trimmed the first 8 nt (UMI, unique molecular identifier) and align the rest to S. cerevisiae genome (version R64-1-1) using STAR 2.5.3a default settings except AlignIntronMax(2500). Reads with the same 5’mapping site and UMI were considered PCR duplicates and omitted from the analysis.
Genome_build: S. cerevisiae R64-1-1
Supplementary_files_format_and_content: Bedgraph files for UMI collapsed reads for positive and negative strand

extract_protocol:
RNA was extracted from yeast cells using the hot phenol procedure. The amount of RNA was quantified in a Nanodrop 2000 Spectrophotometer (Thermo Scientific) and RNA integrity was checked by agarose gel electrophoresis.
5PSeq methods was performed as previously described (PMID: 26820793). 6µg of total RNA was used as input. In brief a RNA oligo (rP5_RND) containing an Illumina adaptor and unique molecular identifiers (UMI) was ligated to the intermediates of mRNA co-translation degradation (5’P). Ribosomal RNA was depleted using Ribo-Zero Magnetic Gold Kit (Illumina).Libraries were PCR amplified (14 cycles). Ampure beads size selected libraries with an average length of 451 nt were sent for sequencing (llumina NextSeq 500 instrument).

treatment_protocol: Cells were shifted for 5 minutes to YP media without glucose (1% yeast extract, 2% peptone) prior to harvesting.

value: BY4741(MATa his3delta1 leu2delta0 met15delta0 ura3delta0)


title: C15 Post(24h) placebo

description:
C15 Post(24h) placebo
1848089002_E

source_name: C15 Post(24h) placebo

value: Pid C15

tag: treatment

value: Responder


title: C09 Post(24h) placebo

description:
C09 Post(24h) placebo
1842761048_D

source_name: C09 Post(24h) placebo


title: C15 Pre placebo

description:
C15 Pre placebo
1848089002_D

source_name: C15 Pre placebo


title: 222039_LoLo_v2

tag: tissue

value: PBMC

tag: time point

tag: cohort


title: 222039_Naive_v1

value: Post-vaccine day 0

value: Elderly


title: set2∆_rep2

tag: genotype

tag: parental strain


title: BY4741_wt rep2

description:
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
BY4741(MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0)

source_name: MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: 222039_HiHi_v2

value: Post-vaccine day 7


title: BY4741_wt rep1


title: non_involved_lung_tissue_patient_107 200796200023_K_Expression

source_name: Non-involved (apparently normal) lung parenchyma

tag: Sex

value: F

tag: smoking status

value: never-smoker


title: C12 Post(24h) hydrocortisone

description:
C12 Post(24h) hydrocortisone
1848089002_A

source_name: C12 Post(24h) hydrocortisone

value: Pid C12

value: hydrocortisone

tag: age

value: low


title: C13 Pre placebo

description:
C13 Pre placebo
1848089002_B

source_name: C13 Pre placebo

tag: individual

value: Pid C13

value: Pre

value: placebo

value: died

value: male


title: C12 Pre hydrocortisone

description:
C12 Pre hydrocortisone
1842761018_E

source_name: C12 Pre hydrocortisone

tag: timepoint

value: Non responder

value: survived

value: septic shock

value: blood leukocytes


title: C11 Post(24h) placebo

description:
C11 Post(24h) placebo
1842761018_D

source_name: C11 Post(24h) placebo

value: Pid C11

tag: acth

value: female


title: 222039_HiHi_v1

source_name: Activated Tfh

value: PBMC

value: Post-vaccine day 0

value: Elderly


title: C13 Post(24h) placebo

description:
C13 Post(24h) placebo
1848089002_C

source_name: C13 Post(24h) placebo

value: Responder

tag: survival (28 days)


title: non_involved_lung_tissue_patient_88 9983140102_L_Expression

value: M

value: ever-smoker

tag: batch


title: C11 Pre placebo

description:
C11 Pre placebo
1842761018_C

source_name: C11 Pre placebo

tag: gender

tag: pre-treatment ifng il10 ratio

value: low


title: C10 Pre placebo

description:
C10 Pre placebo
1842761018_A

source_name: C10 Pre placebo

value: Pid C10

value: Pre

tag: disease

tag: cell type


title: C10 Post(24h) placebo

description:
C10 Post(24h) placebo
1842761018_B

source_name: C10 Post(24h) placebo

tag: treatment

value: placebo

value: died


title: C83 Pre hydrocortisone

description:
C83 Pre hydrocortisone
1705168130_E

source_name: C83 Pre hydrocortisone

value: Pid C83

value: hydrocortisone

value: male

value: high


title: C83 Post(24h) hydrocortisone

description:
C83 Post(24h) hydrocortisone
1705168130_F

source_name: C83 Post(24h) hydrocortisone

value: survived

value: septic shock

value: blood leukocytes


title: M98 iPSC clone 4 (E418K)

city: Cambridge

first: Ralitsa

middle: Radostinova

last: Madsen

address: Addenbrookes Treatment Centre, Keith Day Road

department: Metabolic Research Laboratories, Clinical Biochemistry

institute: University of Cambridge

data_processing:
The raw reads were mapped to the human genome build GRCh38 using Spliced Transcripts Alignment to a Reference (STAR) v2.5.
Gene level counts were performed using Spliced Transcripts Alignment to a Reference (STAR) v2.5. The output results of this step are provided as processed data files.
All subsequent data analyses steps were performed in R using RStudio. Briefly, the edgeR package was used to calculate counts per million (CPM) for each gene and sample. Genes were included for further analysis if expressed at CPM > 1 in at least 1/3 of all samples. Sample library size was normalised by the TMM (trimmed mean of M values) method (Robinson and Oshlack, 2010 Genome Biology), followed by differential gene expression analysis with voom(), lmFit() and eBayes() according to the limma analysis pipeline described by Ritchie et al. (2015 Nucleic Acid Research).
Genome_build: GRCh38
Supplementary_files_format_and_content: the standard STAR output:
Column 1: gene ID; Column 2: Counts for unstranded RNAseq; Column 3: Counts for the 1st read strand aligned with RNA; Column 4: Counts for the 2nd strand aligned with RNA (these are the counts that should be used for subsequent analysis of our data because of the strandedness of the kit that was used).

source_name: M98 iPSC_E418K

growth_protocol: The cells were cultured in 6-well plates coated with hESC-qualified Geltrex (Thermo Fisher Scien- tific # A1413302) diluted 1:100 in DMEM/F12 (Sigma # D6421). Cells were maintained in Essential 8 Flex medium (Thermo Fisher Scientific # A2858501) and passaged every four days when 80-90 % confluent, with split ratios ranging from 1:10 to 1:15. ReLeSR (Stem Cell Technologies # 5872) was used to dissociate the cells non- enzymatically, and 1X RevitaCell (Thermo Fisher Scientific # A2644501) was included during the first 24 hours to promote survival.

extract_protocol:
Cells were washed in DPBS and lysed with QIAzol. The RNA was extracted with the Direct-zol RNA Miniprep Kit (ZymoResearch # R2051) according to the manufacturer's instructions (eluted in 50 μl nuclease-free water). The quality of the RNA was confirmed on an Agilent 2100 Bioanalyzer using the RNA 6000 Nano Kit (Agilent # 5067-1511) according to the manufacturer’s instructions, with all samples pre-diluted to 250-300 ng/μl in nuclease-free water. All samples had high RNA Integrity Number (RIN) scores of 9.9-10.
A total of 1 μg RNA per sample was used as input to prepare indexed, 50-bp-long single-end mRNA libraries with Illumina's TruSeq Stranded mRNA Library Prep Kit (# 20020594) and TruSeq RNA Single Indexes Set A (# 20020492) according to the manufacturer's instructions. The integrity and quantity of the libraries were determined on the Agilent Bioanalyzer using the DNA 12000 Kit (Agilent # 5067-1508).
mRNA sequencing of pooled libraries on an Illumina HiSeq 4000

treatment_protocol: The cells were replenished with fresh Essential 8 Flex medium 3 hours before collection for RNA extraction.

tag: cell line

value: PIK3CA-related overgrowth syndrome (PROS) patient-derived induced pluripotent stem cell (iPSC) line

tag: passage


title: C82 Post(24h) placebo

description:
C82 Post(24h) placebo
1705168130_D

source_name: C82 Post(24h) placebo

value: Pid C82

value: Non responder

value: female


title: 222006_Naive_v2

source_name: Naïve CD4 T cells

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Elderly


title: M98 iPSC clone 3 (E418K)

tag: genotype


title: C79 Post(24h) placebo

description:
C79 Post(24h) placebo
1705168130_B

source_name: C79 Post(24h) placebo

value: Pid C79

tag: age

value: low


title: M98 iPSC clone 2 (E418K)


title: C82 Pre placebo

description:
C82 Pre placebo
1705168130_C

source_name: C82 Pre placebo

tag: individual

value: Pre

value: placebo


title: 222006_Naive_v1

value: Post-vaccine day 0


title: 222006_LoLo_v2

source_name: Quiescent Tfh


title: C79 Pre placebo

description:
C79 Pre placebo
1705168130_A

source_name: C79 Pre placebo

tag: timepoint

value: died

value: male


title: C75 Pre placebo

description:
C75 Pre placebo
1705168126_E

source_name: C75 Pre placebo

value: Pid C75

tag: acth

value: Responder

value: survived

value: high


title: M98 iPSC clone 8.2 (WT)

source_name: M98 iPSC_WT

value: PIK3CA-related overgrowth syndrome (PROS) patient-derived induced pluripotent stem cell (iPSC) line


title: 222006_HiHi_v2


title: C69 Post(24h) placebo

description:
C69 Post(24h) placebo
1705168126_D

source_name: C69 Post(24h) placebo

value: Pid C69

value: Non responder

tag: survival (28 days)

value: septic shock

value: blood leukocytes


title: M98 iPSC clone 8.1 (WT)


title: C75 Post(24h) placebo

description:
C75 Post(24h) placebo
1705168126_F

source_name: C75 Post(24h) placebo

value: female


title: 222006_HiHi_v1

source_name: Activated Tfh

value: PBMC

value: Elderly


title: G11_1758AF_ATGTCA [1758AFAF]

city: New York

first: Alice

middle: V

last: Easton

address: 430 E 29th St

institute: NYU Langone

data_processing:
CEL-Seq
Three lanes of a paired-end 50 Illumina HiSeq 4000 run
Per-read per-lane FASTQ files were generated using the bcl2fastq2 Conversion software (v.2.2.0) to convert per-cycle BCL base call output files produced by the sequencing instrument into the FASTQ format, and the FASTQ files were then further split based on corresponding CEL-seq barcodes for each sample using the CEL-Seq demultiplexer, “bc_demultiplex”.
Bowtie2 (v.2.3.4.1), was used for mapping reads of 264 demultiplexed human CEL-Seq samples to the human reference genome hg19; and the CEL-Seq wrapper for the HTSeq-count script of the Python (v.2.7.15) package, HTSeq, was used to generate the matrix of read counts for annotated genomic features.
This resulted in a final median read depth of 1,707,022 mapped reads per sample, covering a median of 10,210 genes per sample. PCA was performed using 1835 genes with high variance, defined using the varFilter function in the genefilter package with default parameters, which keeps only features with variance inter-quartile range > 0.85. Gene Ontology annotation terms associated with each of the genes were fetched through the R package GO.db
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Orang Asli (indigenous) study village resident_After treatment

extract_protocol:
PAXgene RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject id

tag: subject group

value: M

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not paired)

value: blood


title: C69 Pre placebo

description:
C69 Pre placebo
1705168126_C

source_name: C69 Pre placebo

value: Pre

tag: treatment

value: placebo

tag: gender

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

tag: cell type


title: 111055_Naive_v2

tag: tissue

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: C61 Pre placebo

description:
C61 Pre placebo
1705168119_C

source_name: C61 Pre placebo

tag: individual

value: Pid C61

tag: timepoint

tag: acth

value: survived

tag: age

value: male


title: 111055_Naive_v1

value: Post-vaccine day 0


title: M98 iPSC clone 10 (WT)

tag: cell line

value: PIK3CA-related overgrowth syndrome (PROS) patient-derived induced pluripotent stem cell (iPSC) line

tag: genotype

tag: passage


title: C61 Post(24h) placebo

description:
C61 Post(24h) placebo
1705168119_D

source_name: C61 Post(24h) placebo

value: Non responder

tag: survival (28 days)

value: septic shock

value: blood leukocytes


title: 222006_LoLo_v1

value: PBMC

value: Elderly


title: 222039_LoLo_v1


title: C57 Post(24h) hydrocortisone

description:
C57 Post(24h) hydrocortisone
1705168046_F

source_name: C57 Post(24h) hydrocortisone

value: Pid C57

value: hydrocortisone

value: high


title: D9_1372_GTTTCG [1372]

source_name: Orang Asli (indigenous) study village resident_Before treatment

tag: subject id

tag: subject group

value: F

tag: time point (before or after anthelmintic treatment)

value: Before

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not paired)

value: blood

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

tag: wasting

tag: stunting

value: Significant

tag: underweight

value: Normal


title: 111055_LoLo_v2

tag: tissue

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: C59 Pre placebo

description:
C59 Pre placebo
1705168119_A

source_name: C59 Pre placebo

tag: individual

value: Pid C59

tag: timepoint

value: Pre

tag: treatment

value: placebo

tag: acth

value: Responder

tag: survival (28 days)

value: died

tag: age

tag: gender

value: male

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

tag: cell type


title: C63 Post(24h) hydrocortisone

description:
C63 Post(24h) hydrocortisone
1705168119_F

source_name: C63 Post(24h) hydrocortisone

value: Pid C63

value: hydrocortisone

value: survived

value: septic shock

value: blood leukocytes


title: C52 Pre hydrocortisone

description:
C52 Pre hydrocortisone
1705168046_C

source_name: C52 Pre hydrocortisone

value: Pid C52

value: female


title: H7_103AF_ACTTGA [103AFAF]

tag: subject id

tag: subject group

value: Orang Asli (indigenous) study village resident

value: F

tag: time point (before or after anthelmintic treatment)

value: After

tag: trichuris egg count

tag: ascaris egg count

tag: hookworm infection (yes/no)

tag: treatment responder or not

value: NA (not paired)

value: blood


title: 111055_LoLo_v1

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 0

tag: cohort

value: Young


title: A1014C05: H3K9me2_untreated-1

source_name: Basal breast cancer  cells

tag: cell line

value: Basal breast cancer  cells

tag: passages used

value: From  6 to 14

tag: chip antibody

value: H3K9me2 ( cell signaling, Cat # 4658S; Rabbit monoclonal [D85B4])


title: E8_15104_AGTCAA [15104]

tag: gender

value: Before

tag: age

tag: kilocalories

tag: protein

tag: carbohydrate

tag: cholesterol

tag: tryptophan

tag: threonine

tag: isoleucine

tag: leucine

tag: lysine

tag: methionine

tag: cystine

tag: phenylalanine

tag: tyrosine

tag: valine

tag: histidine

tag: thiamin

tag: riboflavin

tag: niacin

tag: pyridoxine

tag: folate

tag: cobalamin

tag: biotin

tag: pantothenic

tag: iron

tag: magnesium

tag: zinc

tag: copper

tag: manganese

tag: selenium

tag: chromium

tag: molybdenum

tag: fat

tag: fruit

tag: vegetable

value: Overweight

value: Pre-obese

tag: wasting

tag: stunting

tag: underweight


title: C52 Post(24h) hydrocortisone

description:
C52 Post(24h) hydrocortisone
1705168046_D

source_name: C52 Post(24h) hydrocortisone

tag: individual

tag: timepoint

tag: treatment

value: hydrocortisone

tag: acth

value: Responder

tag: survival (28 days)

value: survived

tag: age

tag: gender

tag: pre-treatment ifng il10 ratio

value: low

tag: disease

value: septic shock

tag: cell type

value: blood leukocytes


title: C59 Post(24h) placebo

description:
C59 Post(24h) placebo
1705168119_B

source_name: C59 Post(24h) placebo

value: Pid C59

value: placebo

value: died

value: male


title: 111055_HiHi_v2

tag: tissue

value: PBMC

tag: time point

value: Post-vaccine day 7

tag: cohort

value: Young


title: 111055_HiHi_v1

value: Post-vaccine day 0


title: C63 Pre hydrocortisone

description:
C63 Pre hydrocortisone
1705168119_E

source_name: C63 Pre hydrocortisone

value: Pid C63

value: Pre

value: high