title: Aged, Injured Day 5, replicate 2

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

description: 10x Genomics CellPlex (de-multiplexed)

library_source: transcriptomic single cell

data_processing:
De-multiplexed FASTQ files were generated using the BCL Convert Conversion Software (Illumina, v.3.9.3), and aligned and quantified against the mm10-2020-A reference genome (10x Genomics) using the CellRanger pipeline (v.6.1.2).
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated matrices of genes, cell barcodes, and RNA counts before filtering.

source_name: Skeletal Muscle

growth_protocol: Adult wild type C57BL/6J mice were obtained from Jackson Laboratories (Bar Harbor, ME) at 2-3 months of age. Aged wild type C57BL/6N mice were obtained from the National Institute on Aging at 22-26 months of age. All mice used in this study were male. All animal procedures were conducted in accordance with institutional guidelines approved by the University Committee on Animal Recourses, University of Rochester Medical Center.

extract_protocol:
5 days post injury, the TA muscles were isolated using surgical scissors, minced and digested with Collagenase type II (0.2%) and Dispase II (2.5U/mL) in 10mL of DMEM per muscle. Samples were placed on rocker in a 37˚C incubator for 1 hour and mixed by pipette every 30 minutes. The enzymes within the slurry were then inactivated by addition of 20% heat-inactivated fetal bovine serum (HI-FBS) in Ham’s F10 media. The solution was passed through a 70um cell strainers, centrifuged, washed, and counted. The isolated cells were then stained with Propidium Iodide (PI) and viable cells isolated using fluorescent-activated cell sorting (FACS).
Cells from each mouse were labeled with cellular hash tags using CellPlex reagents (10x Genomics), pooled from two mice according to age (young and aged) into each lane and 10,000-16,000 cells were loaded into the 10x Genomics chromium single cell controller lane. Single cells were then captured in nanoliter-scale gel bead-in-emulsions (GEMs), lysed, RNA captured, and cDNAs prepared using the single cell 3′ v3 Protocol as per manufacturer’s instructions. Each sample was sequenced on a NovaSeq 6000 (Illumina) with 26 bases for read1 and 98x8 bases for read2.

treatment_protocol: Mice received slow-release buprenorphine injection at least 2 hours before surgery. Mice were anesthetized using an isoflurane vaporizer and hindquarter was then carefully shaved and depilation completed with generic Nair hair removal cream prior to skin cleansing with ethanol followed by normal saline. The skin was incised 1 mm posterior and parallel to the femur. The facial plane between the gluteus maximus and the anterior head of the biceps femoris is opened revealing the sciatic nerve. The nerve is crushed for 15 seconds using hemostatic forceps. When the hemostats are re-opened, the entire nerve should be translucent at the crush site. The gluteal musculature is re-opposed, and the skin incision is closed using wound clips. Mice were allowed to recover in their cage placed on a heating pad at 37˚C. For a surgical control (sham), the contralateral sciatic nerve is exposed and mobilized, but left intact.

value: Skeletal Muscle (2,614 cells)

value: Skeletal Muscle

value: 22-26 months


title: HRSWT-HD3

status: Public on Jun 05 2022

type: protein

city: Philadelphia

first: lei

last: guan

state: PA

address: 433 S University Ave.

department: Biology

country: USA

institute: university of pennsylvania

description: healthy donor 3 cd8 T cell treated HRSWT WM9 sEVS

hyb_protocol: Cells were washed by PBS for 3 times before lysis, Samples were probed with antibodies by CSA amplification approach and visualized by DAB colorimetric reaction.

scan_protocol: the array were performed by the protocol from RPPA Core Facility, MD Anderson Cancer Center, Slides were scanned on a flatbed scanner to produce 16-bit tiff image. Spots from tiff images were identified and the density was quantified by Array-Pro Analyzer.

data_processing: Relative protein levels for each sample were determined by interpolation of each dilution curves from the standard curve (supercurve) of the slide (antibody).  Supercurve is constructed by a script in R written by Bioinformatics.  These values (given as Log2 values) are defined as Supercurve Log2 (Raw) value

label: antibody

molecule: protein

organism: Homo sapiens

source_name: cd8 T cells

label_protocol: antibody

growth_protocol: Human CD8 T cells growth T cell culture medium(Thermo) with 10% FBS(Gibco)

extract_protocol: Cells were lysised by Cell Lysis Buffer: 1% Triton X-100, 50mM HEPES, pH 7.4, 150mM NaCl, 1.5mM MgCl2, 1mM EGTA, 100mM NaF, 10mM Na pyrophosphate, 1mM Na3VO4, 10% glycerol, containing freshly added protease and phosphatase inhibitors from Roche Applied Science Cat. # 05056489001 and 04906837001, respectively

treatment_protocol: Human  CD8 T cells were treated with small extracellular vesicles derived from WM9 cells. Human CD8 T cells were stimulated with anti-CD3 and anti-CD28 antibodies for 24 h befor treatment

tag: tissue

value: human blood

tag: donor

value: healthy donor 3

tag: cell type

value: cd8 T cell

tag: agent

value: HRSWT WM9 sEVS


title: HRSWT-HD2

description: healthy donor 2 cd8 T cell treated HRSWT WM9 sEVS

value: healthy donor 2


title: HRSS345A-HD1

description: healthy donor 1 cd8 T cell treated HRSS345A WM9 sEVS

value: healthy donor 1

value: HRSS345A WM9 sEVS


title: Young, Injured Day 5, replicate 2

type: SRA

description: 10x Genomics CellPlex (de-multiplexed)

molecule: total RNA

organism: Mus musculus

value: Skeletal Muscle (2,340 cells)

tag: strain

tag: age

value: 2-3 months


title: Kidney carcinoma cells - A-498, Control-IFNg, rep1

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

description: Sample 4

library_source: transcriptomic

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0, -0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000)
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (version 33; Ensembl version 99)
Assembly: hg38
Supplementary files format and content: FASTQ files have adapters trimmed but were not trimmed for quality using trimmomatic.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

growth_protocol: The ccRCC cell lines 786-O and A498 were purchased from ATCC. They were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Stable 786-O and A498 cell lines expressing Renilla luciferase were generated by transducing cells with LP462-025 lentiviral particles (Genecopia). Briefly, 786-O and A498 cells were transduced with lentiviral particles at a MOI (multiplicity of infection) of 5 in complete media with polybrene at a concentration of 5 μg/mL. Transduced cells were selected with media containing puromycin at a concentration of 4 μg/mL. Renilla Luciferase activity in cells was measured according to the manufacturer protocol.

extract_protocol:
Total RNA from three groups (Cnsi, Cnsi-IFNγ, and PD-L1si IFNγ) for both A498 and 786-O cell lines, was extracted using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol. Quality of the RNA samples was checked using the Agilent Bioanalyzer RNA Nano Chip (Santa Clara, CA) to determine RNA Integrity Number (RIN) ≥ 8.
RNA samples were processed following the Illumina (San Diego, CA) TruSeq Stranded messenger RNA Sample Preparation Kit performed at FDA Core Facility (36). Briefly, poly (A) tailed RNA was purified from 100-200 ng of total RNA, fragmented, and reverse-transcribed into cDNAs. Double strand cDNAs were adenylated at the 3’ ends and individually indexed, followed by limited-cycle (15) amplification.

treatment_protocol: On-Target plus SMARTpool small interfering RNAs (siRNAs) against PD-L1 was purchased from Dharmacon. All siRNA transfections were conducted at a final concentration of 20 nM using Lipofectamine RNAiMAX (Invitrogen) following the manufacturer instructions. Non-targeting pool siRNA was used as a control (Cnsi). Transient silencing experiments had four groups, Cnsi (control scrambled siRNA, untreated), Cnsi IFNγ (IFNγ treated), PD-L1si (PD-L1 siRNA) and PD-L1si IFNγ (PD-L1 siRNA and IFNγ treatment). A498 and 786-O cells were transfected with control (scrambled siRNA) or PD-L1 siRNA, at the end of 24 hours of transfection, select groups were treated with IFNγ (50 ng/mL) for another 24 hours.

tag: disease state

value: clear cell renal cell carcinoma (ccRCC)

value: Kidney carcinoma cells

tag: cell line

tag: sirna

value: Control scrambled siRNA

tag: genotype

value: control

tag: treatment

value: Interferon gamma


title: Aged, Injured Day 5, replicate 1

description: 10x Genomics CellPlex (de-multiplexed)

value: Skeletal Muscle (2,520 cells)


title: Vehicle-HD1

description: healthy donor 1 cd8 T cell treated Vehicle

value: Vehicle


title: Young, Injured Day 5, replicate 1

description: 10x Genomics CellPlex (de-multiplexed)

value: Skeletal Muscle (3,118 cells)

value: Skeletal Muscle


title: prefrontal cortex pre-fecal microbiota transfer [P24]

status: Public on Jun 04 2022

city: Richmond

first: JENNIFER

last: WOLSTENHOLME

state: VA

address: 1217 E Marshall Street, KMSB Rm 536

institute: Virginia Commonwealth University

data_processing:
RNAseq data were aligned to the mouse genome GRCm39 using STAR version 2.7.9a.
Counts were generated from STAR produced BAM files using HTSeq version 0.13.5.
Assembly: GRCm39
Supplementary files format and content: Tab-deliminted text files countaining count values for each sample.

source_name: prefrontal cortex

extract_protocol:
Total RNA was isolated from using STAT60 and the Qiagen mRNEasy kit
Libraries were constructed using the Illumina NEBNext Ultra™ II Directional RNA Library Prep Kit

treatment_protocol: Fecal microbiota samples from a previously published phase 1, double-blind, randomized clinical trial of AUD-related cirrhosis patients were used to colonize germ-free mice. Fecal material was transferred to 10-15-week-old GF C57BL/6 male mice by daily gavage for 3 day. The mice were housed in sterile individually filtered cages for 15 days after which stool was collected and then they underwent the alcohol preference experiment using 2-bottle choice drinking (water and 20% ethanol v/v).

value: prefrontal cortex

value: preFMT


title: prefrontal cortex post-fecal microbiota transfer [P16]

value: postFMT


title: Kidney carcinoma cells - A-498, Control, rep2

description: Sample 2

source_name: Kidney carcinoma cells - A-498, Control


title: prefrontal cortex pre-fecal microbiota transfer [P19]


title: prefrontal cortex pre-fecal microbiota transfer [P21]


title: prefrontal cortex post-fecal microbiota transfer [P17]


title: HRSS345D-HD1

description: healthy donor 1 cd8 T cell treated HRSS345D WM9 sEVS

value: human blood

value: cd8 T cell

value: HRSS345D WM9 sEVS


title: prefrontal cortex pre-fecal microbiota transfer [P22]


title: HRSWT-HD1

description: healthy donor 1 cd8 T cell treated HRSWT WM9 sEVS

value: healthy donor 1

value: HRSWT WM9 sEVS


title: prefrontal cortex pre-fecal microbiota transfer [P23]


title: prefrontal cortex pre-fecal microbiota transfer [P20]


title: WT, rep2

city: shanghai

first: Qianwen

last: Hu

address: 重庆南路280号

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Using HISAT2 RNA-sequencing alignment software, the raw reads were aligned to the mouse reference genome (version mm10). The mapping rate was 96%, on average, across all the samples in the dataset.
The alignment files (bam files) were processed to generate read counts for every gene using HISAT and HTSeq.
The read counts were normalized using the R package DESeq2 and then were centered and scaled for each gene, generating z-scores. P values obtained from multiple tests were adjusted using the Benjamini-Hochberg correction.
Assembly: mm10 (GRCm38)
Supplementary files format and content: genes.readcount.csv: Comma-separated text file containing read count for each gene.

source_name: GC B cell

extract_protocol:
IgD- CD19+CD95+CD38- GC B cells were FACS-sorted and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Bach2+/+ Aicdacre or Bach2fl/fl Aicdacre mice were immunized with SRBC and sacrificed for analysis at day10.

value: spleen

value: CD19+ IgD- CD95+ CD38- GC B cells

value: Bach2+/+ Aicdacre

value: SRBC immunization


title: prefrontal cortex post-fecal microbiota transfer [P18]


title: prefrontal cortex post-fecal microbiota transfer [P14]


title: Kidney carcinoma cells - A-498, Control, rep1

description: Sample 1

value: clear cell renal cell carcinoma (ccRCC)

value: Kidney carcinoma cells

value: Control scrambled siRNA

value: control


title: liver pre-fecal microbiota transfer [L35]

source_name: liver

value: liver


title: liver pre-fecal microbiota transfer [L36]


title: liver pre-fecal microbiota transfer [L33]


title: prefrontal cortex post-fecal microbiota transfer [P15]

value: prefrontal cortex


title: liver pre-fecal microbiota transfer [L34]

value: preFMT


title: liver pre-fecal microbiota transfer [L32]


title: liver pre-fecal microbiota transfer [L31]


title: liver post-fecal microbiota transfer [L29]

value: postFMT


title: liver post-fecal microbiota transfer [L26]


title: prefrontal cortex post-fecal microbiota transfer [P13]


title: liver post-fecal microbiota transfer [L27]


title: liver post-fecal microbiota transfer [L25]


title: intestinal mucosa post-fecal microbiota transfer [I4]

source_name: intestinal mucosa

value: intestine

value: post-FMT


title: intestinal mucosa pre-fecal microbiota transfer [I12]

value: pre-FMT


title: intestinal mucosa pre-fecal microbiota transfer [I7]


title: intestinal mucosa pre-fecal microbiota transfer [I8]


title: intestinal mucosa pre-fecal microbiota transfer [I10]


title: intestinal mucosa post-fecal microbiota transfer [I2]


title: intestinal mucosa post-fecal microbiota transfer [I5]


title: intestinal mucosa post-fecal microbiota transfer [I6]


title: dual

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

data_processing:
mRNA and sgRNA counts were obtained from Cell Ranger 4.0.0 software (10x Genomics).
To assign guides to cells, we used a Poisson-Gaussian mixture model as previously described (Replogle et al., 2020).
Only cells bearing a single Dolcetto sgRNA or a single dual-guide guide B sgRNA were used for downstream calculation of CRISPRi efficacy.
Assembly: GRCh38
Supplementary files format and content: Detected cell in MEX format: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/gex-outputs

source_name: chronic myelogenous leukemia

growth_protocol: K562 cells were grown in RPMI 1640 medium with 25 mM HEPES, 2 mM l-glutamine, 2 g/L NaHCO3 (Gibco) supplemented with 10% (v/v) standard fetal bovine serum (FBS, VWR), 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mM l-glutamine (Gibco).

extract_protocol:
On day 7 post-transduction, cells were prepared for single-cell RNA-sequencing as detailed in the 10x Genomics Single Cell Protocols Cell Preparation Guide (10x Genomics, CG00053 Rev C) and separated into droplet emulsions using the Chromium Controller (10x Genomics) with Chromium Single-Cell 3′ Gel Beads v3.1 (10x Genomics, PN-1000121 and PN-1000120) across 12 lanes/gemgroups with the goal of recovering ~15,000 cells per GEM group before filtering.
Sequencing libraries were prepared following the 10x Genomics Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry) with Feature Barcoding technology for CRISPR Screening (CG000205; Rev C).
10x Genomics 3' v3.1

treatment_protocol:
CRISPRi K562 cells expressing dCas9-KOX1 KRAB (Gilbert et al., 2014) were spinfected (1000g) with polybrene (8 ug/ml) with lentivirus from both libraries in parallel.
On day 3 post-transduction, an infection rate of 5% was measured for both screens, and infected cells were sorted by FACS (BD FACS Aria).

value: chronic myelogenous leukemia

value: CRISPRi

value: day 7 post-transduction


title: dolcetto


title: liver post-fecal microbiota transfer [L30]


title: RBPMS KO 48h 2

city: Cologne

first: Leo

last: Kurian

address: Robert-Kochstr. 21

country: Germany

institute: University of Cologne

data_processing:
Data was processed according to the Rsubread package Release (3.15)
Differential gene expression was analysed DESeq2, Bioconductor version: Release (3.15)
Assembly: hg38
Supplementary files format and content: tab-delimited text filesinclude TPM values for each Sample

growth_protocol: Cells were cultivated in FTDA medium (Frank et al. (2012))

extract_protocol:
RNA was isolated using Quick-RNA MiniPrep Kit™  (Zymo)
The kit used was the illumina TruSeq stranded mRNA

treatment_protocol: For mesoderm induction cells were treated with 1.5 ng/ml BMP4 (R&D) and 1.5 µM CHIR (Tocris)

value: human embryonic stem cells

value: RBPMS KO

value: mesoderm induction


title: WT 48h 3

value: WT


title: WT 48h 2


title: RBPMS KO 48h 1


title: WT 48h 1


title: liver post-fecal microbiota transfer [L28]


title: RBPMS KO 6h 3


title: intestinal mucosa pre-fecal microbiota transfer [I11]


title: RBPMS KO 6h 1


title: intestinal mucosa post-fecal microbiota transfer [I3]


title: RBPMS KO 6h 2


title: intestinal mucosa pre-fecal microbiota transfer [I9]


title: intestinal mucosa post-fecal microbiota transfer [I1]


title: WT 6h 2


title: NK_Xkr8 KO_Mouse3

city: pittsburgh

first: Yinan

last: Gong

address: 5117 Centre Ave, lab 2.19

institute: Hillman Cancer Center

data_processing:
Align fastq file to MM10 transcriptome with Partek Flow TMAP - 5.0.0
Sum counts from transcripts by gene symbol
Assembly: mm10
Supplementary files format and content: text files include RPKM values for each Sample

source_name: Sorted NKs

growth_protocol: subcu MC38 tumors grown on the C57BL6 mice for 16 days. Tumors were dissected and macrophages or NKs were isolated by FACS

extract_protocol:
No RNA extraction process
Smartseq (Takara) or Truseq (illumina) with rRNA depletion
mRNA library constructed from sorted macrophages or NK cells

treatment_protocol: No further treatment

value: Sorted NKs


title: NK_Xkr8 KO_Mouse2


title: NK_Xkr8 KO_Mouse4


title: RBPMS KO 3h 3


title: RBPMS KO 3h 2


title: NK_Xkr8 KO_Mouse1


title: WT 6h 1


title: NK_WT_Mouse4


title: RBPMS KO 48h 3


title: NK_WT_Mouse2


title: NK_WT_Mouse3


title: RBPMS KO 3h 1


title: NK_WT_Mouse1


title: WT 3h 2


title: WT 3h 1


title: MAC_Tmem30a KO_Mouse4

source_name: Sorted macrophages

value: Sorted macrophages


title: WT 3h 3


title: MAC_Tmem30a KO_Mouse2


title: MAC_Tmem30a KO_Mouse3


title: RBPMS KO 0h 2

value: control


title: RBPMS KO 0h 3


title: WT 6h 3


title: MAC_Tmem30a KO_Mouse1


title: MAC_WT_Mouse3


title: RBPMS KO 0h 1


title: WT 0h 3


title: MAC_WT_Mouse2


title: WT 0h 2


title: MAC_WT_Mouse1


title: WT 0h 1


title: T cells that were transduced with SAM library and infected with HIV and enriched for HIV resistant cells 1

city: La jolla

first: Qiong

last: Zhang

state: California

address: 9500 Gilman Dr.

department: Pediatrics

institute: UCSD

data_processing:
Library strategy: CRISPR library sequencing
Sequencing reads were de-multiplexed and adapters trimmed using cutadapt leaving only the 20bp sgRNA spacer sequences.
The sgRNA spacer sequences were then mapped to the Hum_GeCKOv2_Alib library using bowtie allowing a maximum of one mismatch and allowing only uniquely aligning reads. Only sgRNA spacers with multiple reads were analyzed (sgRNA spacer with only a single read were filtered out).
Normalized read counts were obtained by normalizing to total read count per sample (normalized reads per sgRNA = reads per sgRNA/total reads for all sgRNAs in sample x 106+1). Normalized reads were used for input in STARS software following instruction (Doench et al., 2016).
Supplementary_files_format_and_content: sam files were generated after triming the linker and aligned the sgRNA  was to the CRISPR library. The read counts was normalized to total read and an excel was generated at this stage

source_name: HIV permissive CD4 T cell lines

growth_protocol: MT4 T cells were cultured in RPMI containing 10% fetal bovine serum (FBS) and 50 µM β-mercaptoethanol (Sigma).

extract_protocol:
genomic DNA was extracted from cells using the Qiangen genomic extraction kit
The sgRNA library readout was performed using a two-step nested PCR process in which PCR1 amplifies the lentiviral sequence containing the 20bp sgRNA cassette followed by PCR2 which added illumina sequencing adapters and barcodes. 10 μg genomic DNA was used per PCR1 reaction. A total of 200 μg genomic DNA was applied to PCR1 reactions to maintain full library representation. PCR2 was performed with one reaction per 104 constructs (7 reactions per sample). After pooling PCR1 product, 10 μL of pooled PCR1 product was used for each PCR2 reaction. PCR products were purified and sequenced on Illumina NextSeq.

treatment_protocol: For HIV infection group, a total of 60 million cells were infected at MOI = 1 for 4 days, and then added GCV (250 μg/ml) to treat the cells for 3 days to ensure depletion of HIV infected cells. Surviving cells are sorted out using viable cell separation kit. The cells was then expanded for 1 weeks in the presence of GCV. Expanded cells were re-infected with HIV at an MOI of 1 for 4 days, treated with GCV for 3 days and sorted for surviving HIV resistant cells. These cells were collected for sequencing.

value: MT4 T cells

tag: hiv infection

value: infected


title: T cells that were transduced with SAM library and not infected with HIV 1

value: not infected


title: T cells that were transduced with SAM library and infected with HIV and enriched for HIV resistant cells 2


title: T cells that were transduced with SAM library and not infected with HIV 2


title: SKNMC_eKD2_S2

city: PHILADELPHIA

first: Irfan

last: Asangani

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with normaxia samples as controls
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each sample

source_name: SK-N-MC

growth_protocol: SK-NM-C and RD-ES (ATCC) cells were maintained in RPMI-1640 media (Sigma) supplemented with 10% FBS (Sigma), 1%Pen/Strep (Sigma) and 1%L-Glutamine (Sigma).  Cells were grown at 37°C in a 5% CO 2 incubator.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RD-ES and SK-N-MC cells were infected with Lenti-dCas9-KRAB targeting at the GGAA site (eKD2) or empty lenti-dcas9-KRAB (cas9 control) at a MOI of 10. Cells were selected with puromycin at 1μg/ml for three days to obtain stably knock-down cells. Cells within 5 passages after puromycin selection were used for all the experiments.

value: Ewing’s Sarcoma

value: SK-N-MC


title: SKNMC_cas9_S1


title: SKNMC_cas9_S2


title: SKNMC_eKD2_S1


title: RDES_eKD2_S2

source_name: RD-ES

value: RD-ES


title: RDES_eKD2_S1


title: CRC-N2 (circRNA-seq)

city: Nanjing

first: Bing

last: Yao

state: Jiangsu

address: Longmian Road 101

department: Department of Medical Genetics

institute: Nanjing Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequence using fastq software
Trimmed sequence reads were mapped to GRCh38.p13 using STAR software
Read count extraction was performed using CIRI2 software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes count values for each Sample

source_name: colorectal cancer (intestine)

extract_protocol:
TRIzol Reagent extract total RNA
Stranded Total RNA Library

value: colorectal cancer (CRC)

value: colorectal cancer (intestine)


title: CRC-N3 (circRNA-seq)


title: CRC-N1 (circRNA-seq)


title: adjacent normal tissue-C3 (circRNA-seq)

source_name: adjacent normal tissue (intestine)

value: adjacent normal tissue (intestine)


title: adjacent normal tissue-C2 (circRNA-seq)


title: TM-512

city: Foshan

first: Dan

last: Zhou

address: Shiwan Street, Chancheng District, Foshan City

institute: Center, First People's  Hospital of Foshan

data_processing:
Raw files obtained by sequencing with Illumina high-throughput sequencers
The original file is an image file, and after base calling and Bcl2Fastq transformation, the original sequenced sequence (sequenced reads) in FASTQ (fq for short) format can be obtained
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Cells in co-culture were extracted and single cell whole transcriptome sequencing libraries were constructed using the BD platform R hapsody reverse transcription kit and BD R hapsody whole transcriptome amplification kit
RNA libraries were prepared for sequencing using standard BD RhapsodyTM Single cell 3’ whole transcriptome amplification (WTA) with sample multiplexing kit (SMK) protocol

value: multiplexed samples


title: adjacent normal tissue-C1 (circRNA-seq)


title: adjacent normal tissue-C4 (circRNA-seq)


title: TM-568


title: RDES_cas9_S2


title: CRC-N4 (circRNA-seq)


title: SKNMC_eKD2_Hypoxia_S2

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with normaxia samples as controls
Genome_build: hg19
Supplementary_files_format_and_content: Cuffnorm FPKM values for each sample

growth_protocol: SK-N-MC cells were infected with Lenti-dCas9-KRAB targeting at the GGAA site (eKD) or empty lenti-dcas9-KRAB (cas9 control) at a MOI of 10. Cells were selected with puromycin at 1μg/ml for three days to obtain stably knock-down cells. Cells within 5 passages after puromycin selection were used for all the experiments.

treatment_protocol: cas9 control and the stable LOXHD1 knockdown (eKD1) SKNMC cells were incubated in normal or hypoxia chamber of 1% of O2, 5% CO2 at 37°C for the 16 hrs.

value: Ewing's Sarcoma

value: hypoxia

tag: genetic variation

value: LOXHD1 enhancer knockdown


title: TM-536


title: adjacent normal tissue-C5 (circRNA-seq)


title: adjacent normal tissue-C6 (circRNA-seq)


title: CRC-N6 (circRNA-seq)


title: adjacent normal tissue-N6 (miRNA-seq)

data_processing:
Sequence reads were trimmed for adaptor sequence and low-quality sequence using fastq software
Trimmed sequence reads were mapped to GRCh38.p13 using bowtie software
Read count extraction  were performed using miRDeep2  software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes count values for each Sample


title: PC-9 cells - shRBM10#2 2

first: Wei

last: Wu

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

description: RBM10 KD #2

data_processing:
fastq files were used to align with hg19 genome using STAR aligner (v2.4)
transcript expression levels ere quantified using RSEM (v1.2.29)
differentially expressed isoforms between RBM10 KD and control groups were analysis in R using edgeR package.
Assembly: hg19
Supplementary files format and content: isoform expression in txt files

source_name: Lung cancer cells

growth_protocol: 10%FBS RPMI

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

treatment_protocol: no treatment

tag: transfection


title: PC-9 cells - shRBM10#1 2

description: RBM10 KD #1


title: PC-9 cells - shRBM10#2 1

description: RBM10 KD #2


title: CRC-C6 (miRNA-seq)


title: adjacent normal tissue-N5 (miRNA-seq)


title: SKNMC_eKD1_Hypoxia_S2


title: PC-9 cells - shRBM10#1 1

description: RBM10 KD #1


title: CRC-C5 (miRNA-seq)


title: RDES_cas9_S1


title: adjacent normal tissue-N2 (miRNA-seq)


title: PC-9 cells - shScr 1

description: Control

value: shScr


title: SKNMC_Ctrl_Hypoxia_S2


title: SKNMC_Ctrl_Hypoxia_S1


title: CRC-C4 (miRNA-seq)


title: CRC-C2 (miRNA-seq)


title: adjacent normal tissue-N1 (miRNA-seq)


title: adjacent normal tissue-N4 (miRNA-seq)


title: CRC-N5 (circRNA-seq)


title: SKNMC_Ctrl_normoxia_S2

value: normoxia


title: CRC-C1 (miRNA-seq)


title: DoxoR 4

city: Barcelona

first: Carolina

middle: Pimenta

last: Lopes

address: Carrer Feixa Llarga S/N

country: Spain

institute: Univesity of Barcelona

data_processing:
Reads were mapped against the mouse reference genome (GRCh38) with STAR/2.5.3a using the ENCODE parameters for long RNA.
Genes were quantified with RSEM/1.3.0 using the genecode annotation M23.
Quality control of the mapping and quantification steps was performed with 'gtfstats' from GEM-Tools 1.7.1.
Assembly: GRCh38
Supplementary files format and content: COUNTS_genes_VENTURAFRA_01, formato txt, raw counts

source_name: Tibiae and Femur without Bone Marrow

extract_protocol:
Bones were cleaned of soft tissue, and the distal and proximal epiphyses were excised. Bone marrow was removed by centrifugation at >20 000 g for 15 seconds at 4 °C. TRIsure was added to marrow-free bones, which were then flash frozen in liquid nitrogen and stored in -80 °C. For RNA isolation, both tibiae and femurs from each mouse were subjected to 1 cycle of 45 seconds at full speed using a Polytron (Kinematic PT). Total RNA was separated from bone minerals, DNA and protein by phenol-chloroform extraction. The RNA-containing fraction was then purified using the RNeasy Mini Kit (Qiagen) and treated with DNase I (RNase-Free DNase Set, Qiagen). DNA-free RNA samples were quantified with the Qubit® RNA BR Assay kit (Thermo Fisher Scientific), and RNA integrity was estimated with the Agilent RNA 6000 Pico Bioanalyzer 2100 Assay (Agilent).
The RNASeq libraries were prepared with the KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations. Briefly, 500 ng of total RNA was used for enrichment of the poly-A fraction with oligo-dT magnetic beads, following mRNA fragmentation. Strand specificity was achieved during the second-strand synthesis performed in the presence of dUTP instead of dTTP. The blunt-ended double stranded cDNA was 3´adenylated, and Illumina platform-compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles. The size and quality of the libraries were assessed in a High-Sensitivity DNA Bioanalyzer assay (Agilent).

treatment_protocol: 15-week-old wildtype C57BL/6 male mice were randomly assigned to Control (4) or DoxoR (4) groups. At day 0, mice were injected intraperitoneally with vehicle (saline solution) or 10 mg/kg doxorubicin (Cell Signaling). 30 days post-treatment mice were euthanized and long bones of the hindlimbs were prepared for high-quality RNA isolation.

value: Tibiae and Femur without Bone Marrow

tag: Sex

value: male

value: WT

value: Single dose DoxoR 10mg/kg i.p at day 0


title: SKNMC_eKD2_Hypoxia_S1


title: DoxoR 3


title: SKNMC_Ctrl_normoxia_S1


title: DoxoR 2


title: SKNMC_eKD1_Hypoxia_S1


title: DoxoR 1


title: SKNMC_eKD2_K4me3

description: k4me3 chip

library_source: genomic

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Enrichment peaks were calculated using MACS2
For ChIP-seq data, the bam files were converted to bigwig tracks using bamcoverage from deeptools
Genome_build: hg19
Supplementary_files_format_and_content: bigwig tracks for each sample

molecule: genomic DNA

growth_protocol: Ewing sarcoma cell lines RD-ES (obtained from CLS), SK-N-MC, CHLA-10, CADO-ES, prostate cancer cell lines LNCaP, 22RV1, and osteosarcoma U2OS cell lines (obtained from ATCC) were maintained in RPMI-1640 media (Gibco, 11875093) supplemented with 10% FBS (HYC, SH30910.03) and 1% penicillin-streptomycin (Invitrogen, 15140122). All cells were grown at 37°C in a 5% CO2 incubator.

extract_protocol:
ChIP was performed using iDeal ChIP-seq Kit for Transcription Factors (Diagenode, C01010170) according to manufacturer's protocol. In brief, SK-N-MC and RD-ES cells of the control and knockdown groups were trypsinized, washed, and crosslinked with 1% formaldehyde in culture medium for 10 min at room temperature. Cross-linking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Chromatin equivalent to 5×106 cells was isolated and incubated with 5 μg antibody overnight at 4 °C (H3-acetyl K27, H3K4me3, and IgG (Diagenode). ChIP DNA was isolated by washing and reversal of cross-linking. The eluted DNA was used for SYBRgreen qPCR.
10ng of the ChIP DNA was used for ChIP sequencing library preparation following the protocol of TruSeq ChIP library preparation kit (Illumina, IP-202-1012). Briefly, A single “A” nucleotide was added to the 3’ ends of the blunt-ended ChIP DNA fragments and then ligated to a unique adapter. The ligation products were purified and selected at the size of 250-300bp by 4% NuSieve agarose gel (Lonza) electrophoresis. Size selected DNA was purified and PCR-amplified and quantitated with the Bioanalyzer 2100 (Agilent). Libraries were pooled and ran on Nextseq500 platform (Illumina Inc.) with high throughput single-end reads of 75 bases (Cat.TG-160-2005).

treatment_protocol: sgRNAs targeting adjacent to the LOXHD1 GGAA microsatellites were designed with the following website: https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design. For the enhancer region knockout, we inserted two pairs of sgRNAs into lentiCRISPR v2 (Plasmid #52961) backbone. For LOXHD1 repression, two independent sgRNAs were cloned into a lentiviral backbone expressing sgRNA and dCas9-KRAB (Plasmid #71236).

tag: chip antibody


title: MAC INF 3

type: RNA

city: Leuven

first: Johan

last: Van Weyenbergh

state: VL BR

address: Herestraat 49

department: Microbiology, Immunity and Transplantation

country: Belgium

institute: KU Leuven

description: nCounter digital transcriptomics

hyb_protocol: Hybridization for 24h at 65°C

scan_protocol: Nanostring MAX digital analyzer

data_processing: Results were sequentially corrected for background (negative control probes),  technical variation (positive control probes) and RNA content (housekeeping genes) using nSolver 4.0  (NanoString)

source_name: Macrophages infected

label_protocol: Cell lysates were hybridized to unique capture/reporter pairs (50 bp each) targeting 784 transcripts (734 murine transcripts and 20 housekeeping genes present in the Nanostring Myeloid/Innate   Immunity Panel, complemented with 20 murine and 10 Leishmania spp. transcripts from a customized panel) as well as 6 positive and 8 negative control probes (all from NanoString).

growth_protocol: For efficient depletion of mature  lineage-positive hematopoietic cells and to specifically isolate the preferred lineage-negative cells (i.e. undifferentiated progenitor cells), the Direct Lineage Cell Depletion Kit (Miltenyi Biotec) was employed according to manufacturer’s instructions. To obtain BM-derived macrophages (BMDM), cells were centrifuged at 500×g for 10 min at 4°C,  resuspended in Roswell Park Memorial Institute (RPMI) medium (Gibco®) and divided over Petri dishes  (Starstedt) supplemented with BM medium [RPMI 1640 medium with 10% (v/v) iFCS, 1% non-essential  amino acids (NEAA), 1% sodium pyruvate, 1% L-glutamine, 50 U/mL penicillin, 50 μg/mL streptomycin (all  from Gibco®) and 15% L929 supernatant with M-CSF]. Following a 6-day incubation at 37°C with 5% CO2,  the macrophages were collected by replacing the BM medium with ice cold dissociation buffer [PBS with  1% 0.5 M ethylenediaminetetraacetic acid (EDTA) and 2% 1 M 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid (HEPES)]. After detachment, the macrophage cell suspension was centrifuged at 500×g for 10 min and resuspended in RPMI medium. The number of macrophages was counted in PBS using a KOVA®counting chamber. Cells were seeded in a 96-well plate (3×104 530 cells/well) or a 24-well plate.  (1×106 531 cells/well) and incubated for 24 h at 37°C with 5% CO2 to allow adherence of the BMDMs.

extract_protocol: Cell lysates (from approximately 10,000 LT-HSC or macrophages, triplicates for both infected and uninfected conditions) for nCounter (NanoString) analysis were prepared using RNeasy Lysis buffer (RLT   buffer, Qiagen).

treatment_protocol: For in vitro infections, cell monolayers were co-cultured with stationary-phase promastigotes of L. infantum or  L. donovani at a multiplicity of infection (MOI) of 5 for a minimum of 24h at 37°C with 5% CO2.

value: BALB/c

value: Macrophages

tag: infection status

value: infected


title: PC-9 cells - shScr 2

description: Control


title: MAC INF 2

description: nCounter digital transcriptomics


title: MAC 2

description: nCounter digital transcriptomics

source_name: Macrophages

value: uninfected


title: MAC 3

description: nCounter digital transcriptomics


title: SKNMC_eKD2_K27ac

description: k27ac chip

tag: tissue

value: SK-N-MC


title: SKNMC_cas9_K4me3

description: k4me3 chip

value: control


title: CTRL 4

value: Vehicle


title: CTRL 3


title: T-cells, ORP4LKI-3

city: Guangzhou

first: Wenbin

last: Zhong

address: No.601, West Huangpu Avenue

institute: Jinan University

data_processing:
Illumina Casava1.8 software used for basecalling.
Use the FANse3 ultra-high-precision sequence alignment algorithm to compare the reads which obtained by sequencing each sample with the reference sequence (reference library: Mouse RefSeq-RNA mm10 2017-03-25).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text file (reporting read count, rpkm)

source_name: Primary T-cells

extract_protocol:
RNA was extracted following the Trizol reagent (Invitrogen) manual. RNA was precipitated in 1:1 isopropanol (v/v) and 1 μL glycogen at -20°C overnight.
mRNA library was constructed using VAHTS mRNA-seq V3 Library Prep Kit (Cellagen Technology, San Diego, CA) following the manufacturer’s instructions.

value: Primary T-cells

value: 15 months

value: ORP4L knock-in


title: T-cells, ORP4LKI-2


title: T-cells, ORP4LKI-4


title: CTRL 2


title: RDES_eKD2_K4me3

description: k4me3 chip

value: Ewing's Sarcoma

value: RD-ES


title: MAC 1

description: nCounter digital transcriptomics


title: SKNMC_cas9_K27ac

description: k27ac chip


title: T-cells, ORP4LKI-1


title: LT INF 3

description: nCounter digital transcriptomics

source_name: LT-HSC infected

value: LT-HSC


title: RDES_eKD2_K27ac

description: k27ac chip


title: T-cells, WT-3


title: LT 3

description: nCounter digital transcriptomics

source_name: LT-HSC


title: MAC INF 1

description: nCounter digital transcriptomics


title: LT INF 2

description: nCounter digital transcriptomics


title: CTRL 1

value: Tibiae and Femur without Bone Marrow


title: RDES_cas9_K4me3

description: k4me3 chip


title: T-cells, WT-2


title: input

city: Wuhan

first: Wen-Cheng

last: Liu

address: Bayi Road

department: College of Life Sciences

institute: Wuhan University

data_processing:
Raw reads were filtered first to remove low-quality or adaptor sequences by SOAPnuke with parameters: filter -l 5 -q 0.5 -n 0.1 -Q 2 -5 1 -c 50.
Cleaned reads were mapped to the reference genome of XXX (NCBI/UCSC/GenBank/XXX: XXXX) using SOAPaligner/SOAP2 (version: 2.2.5), whose parameters is -v 2 -s 35.
Genome_build: TAIR10 (http://www.arabidopsis.org/download/index-auto.jsp?dir=%2Fdownload_files%2FSequences%2FAraport11_blastsets)
Supplementary_files_format_and_content: wig file

organism: Arabidopsis thaliana

source_name: whole seedlings of Arabidopsis

growth_protocol: Wild-type Arabidopsis was grown on 1/2 MS medium for 7 days

extract_protocol:
The 7-d-old wild-type seedlings grown on 1/2 MS medium were fixed in 1% formaldehyde for 15 min at room temperature under a vacuum. Fixed tissues were ground into a fine powder in liquid nitrogen and the nuclei were isolated. The chromatin released from the nuclei was sonicated into 100–500 bp fragments. One third of the resulting DNA fragments were used as an input, with the remaining two thirds used for immunoprecipitation with or without an anti-ENO2 antibody, respectively. The immunoprecipitated DNA fragments were used to perform ChIP-seq experiment."
The DNA is combined with End Repair Mix, and incubate at 20 for 30 min. Purify the end-repaired DNA with QIAquick PCR Purification Kit(Qiagen)then add A-Tailing Mix, incubate at 37 for 30 min. Combine the purified Adenylate 3'Ends DNA, Adapter and Ligation Mix, incubate the ligation reaction at 20 for 15 min. Purify the Adapterligated DNA with the QIAquick PCR Purification Kit. Several rounds of PCR amplification with PCR Primer Cocktail and PCR Master Mix are performed to enrich the Adapter-ligated DNA fragments. Then the PCR products are selected (about 100-300bp, including adaptor sequence) by running a 2% agarose gel to recover the target fragments. Purify the gel with QIAquick Gel Extraction kit (QIAGEN). The final library is quantitated in two ways: Determine the average molecule length and sample integrity as well as purity using the Agilent 2100 bioanalyzer instrument (Agilent DNA 1000 Reagents) and quantify the library by real-time quantitative PCR (QPCR). The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were formatted as the final library. Library was qualified by Qubit ssDNA kit. The sequencing will be performed with the BGISEQ-500 sequencing system,featuring combinatorial probe-anchor synthesis (cPAS) and DNA Nanoballs (DNB)technology for superior data quality (BGI-Shenzhen, China).
The Qualified libraries will amplify on cBot to generate the cluster on the flowcell (TruSeq PE Cluster Kit V3–cBot–HSIllumina). And the amplified flowcell will be sequenced pair end on the HiSeq 2000 System (TruSeq SBS KIT-HS V3, Illumina)

treatment_protocol: Plants were grown at 22°C under a 16-/8-h light/dark photoperiod on a 1/2 MS medium containing 0.8% agar.

tag: tissues

value: whole seedlings

tag: developemntal stage


title: RDES_cas9_K27ac

description: k27ac chip


title: anti-ENO2 antibody

value: 7-d-old wild-type seedlings grown on 1/2 MS medium


title: LT 1

description: nCounter digital transcriptomics

tag: cell type


title: T-cells, WT-1

tag: strain

value: WT


title: LT INF 1

description: nCounter digital transcriptomics

value: BALB/c


title: LT 2

description: nCounter digital transcriptomics


title: 2011728- 11

status: Public on Jun 03 2022

city: Bethesda

first: Douglas Scott

last: Merrell

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95922.gif

hyb_protocol: not provided

scan_protocol: Scanner Model: G2505B

data_processing: VALUE is log(REDsignal/GREENsignal)

source_name: 825 ng of amplified human cell cDNA (pooled reference)

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: common pooled reference

source_name: 825 ng of amplified human cell cDNA (test)

tag: time

value: 4 h

value: irradiated CD34


title: 20110215- 11

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95949.gif

tag: cell line

value: irradiated HUVEC + irradiated Jurkat


title: 20110913- 15

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95967.gif

value: 1 h

value: non-irradiated HUVEC + non-irradiated Jurkat


title: 20110913- 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95966.gif

value: irradiated HUVEC


title: 20110518- 16

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95943.gif

value: BMEC


title: 20110714- 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95946.gif


title: 20110728- 1A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95923.gif

value: non-irradiated CD34 + non-irradiated BMEC


title: 20110913- 11

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95961.gif

value: non-irradiated Jurkat + irradiated HUVEC


title: 20110215- 14

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95951.gif


title: 20110913- 10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95959.gif

value: irradiated Jurkat + non-irradiated HUVEC


title: 20110913- 9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95958.gif

value: non-irradiated Jurkat + non-irradiated HUVEC


title: 2011728- 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95936.gif


title: 20110913- 19

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95968.gif


title: 20110913- 8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95957.gif

value: irradiated Jurkat + irradiated HUVEC


title: 20110913- 14

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95952.gif


title: 20110518- 11

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95932.gif


title: 20110913- 18

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95954.gif


title: 20110518- 1A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95928.gif


title: 20110627- 8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95947.gif


title: 20110215-7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95965.gif


title: 20110714- 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95919.gif


title: 20110913- 16

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95953.gif


title: 20110714- 9

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95972.gif


title: 20110215- 12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95950.gif


title: 20110913- 12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95962.gif

value: irradiated Jurkat


title: 20110518- 17

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95944.gif


title: 20110215- 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95934.gif


title: 20110913- 20

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95969.gif


title: 20110518- 1B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95929.gif


title: 20110627- 10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95948.gif

value: irradiated HUVEC + non-irradiated Jurkat


title: Ddx3xb mutant+ddx3xb△N 4h ribo-seq rep2 [ribosomes_4h_KO_ddx3xb△N2]

city: Beijing

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

data_processing:
Low-quality bases were trimmed and filtered by cutadapt (V 1.13) and Trimmomatic (V 0.36). Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads.
The remaining reads were mapped to zebrafish genome (Zv9) using TopHat (v2.1.1) with ‘‘–bowtie1’’. The expression levels of mRNAs were evaluated by Cufflinks v2.2.1 with ‘‘-p x -u -G’’. Translation efficiency of each mRNA was calculated by the ratio of RPFs and mean expression of mRNA input replicates.
Genome_build: Zv9
Supplementary_files_format_and_content: txt

organism: Danio rerio

source_name: Ddx3xb mutant+ddx3xb△N 4h ribo-seq

extract_protocol:
Generally, Zebrafish embryos were incubated in 100 mg/ml cycloheximide in E3 buffer (5 mM NaCl, 0.17 mM KCl, 0.33 mM CaCl2, 0.33 mM MgSO4) for 5 min at room temperature. Then embryos were then transferred into 600 ul of ice-cold lysis buffer. Clarify the lysate by centrifugation for 10 min at 20,000g after Triturate the cells ten times through a 26-G needle, and recover the soluble supernatant. Add 6 ul of RNase I (100 U µl−1) to 600ul lysate. Incubate for 45 min at room temperature with gentle mixing. Add 10.0 µl of SUPERase·In (Life Technologies, AM2694) RNase inhibitor to stop nuclease digestion. Meanwhile, MicroSpin S-400 HR columns (GE Healthcare, 27-5140-01) were equilibrated with 3 ml of mammalian polysome buffer by gravity flow and emptied by centrifugation at 600g for 4 min. We then immediately loaded 100 µl of the digested lysate on the column and eluted the column by centrifugation at 600g for 2 min. We extracted RNA from the flow-through (approximately 125 µl) using Trizol LS (Life Technologies, 10296-010).
We  removed ribosomal RNA fragments using the RiboZero Kit (Illumina, MRZH11124) and separated them on a 17% denaturing urea-PAGE gel (National Diagnostics, EC-829). The size range from 27 nt to 30 nt was cut out, and the RNA fragments were subjected to library generation using Smarter smRNA-Seq kit (Clontech Laboratories Inc).

value: zebrafish embryos

tag: age

value: 4 hpf


title: Ddx3xb mutant+ddx3xbFL 4h ribo-seq rep1 [ribosomes_4h_KO_ddx3xbFL1]

source_name: Ddx3xb mutant+ddx3xbFL 4h ribo-seq

tag: genotype


title: Ddx3xb mutant+ddx3xbFL 4h ribo-seq rep2 [ribosomes_4h_KO_ddx3xbFL2]


title: Ddx3xb mutant injected with ddx3xb△N 6h rna-seq rep2 [RNAseq_6h_KO_ddx3xb△N2]

data_processing:
Low-quality bases were trimmed and filtered by cutadapt (V 1.13) and Trimmomatic (V 0.36)
Processed reads were mapped to zebrafish genome (Zv9) from Ensembl annotation using hisat2 (V 2.0.5) with default parameters. After mapping quality (≥ 20) filtering using SAMtools (V1.9), read counts and corresponding RPKM were calculated. The final RPKM of each transcript is the average of RPKMs in replicates.
Genome_build: Zv9
Supplementary_files_format_and_content: rpkm for samples

source_name: Ddx3xb mutant injected with ddx3xb△N 6h

extract_protocol:
Total RNA was isolated from zebrafish embryos at different time points with TRIzol reagent and mRNA was further purified using Dynabeads mRNA purification kit (Ambion, 61006). Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.
Fragmented mRNA was used for library construction using the KAPA Stranded mRNA-Seq Kit (KAPA, K8401) according to the manufacturer’s protocol.

value: 6 hpf


title: Ddx3xb mutant injected with ddx3xb△N 6h rna-seq rep1 [RNAseq_6h_KO_ddx3xb△N1]


title: Ddx3xb mutant injected with ddx3xb△N 4h rna-seq rep2 [RNAseq_4h_KO_ddx3xb△N2]

source_name: Ddx3xb mutant injected with ddx3xb△N 4h


title: Ddx3xb mutant injected with ddx3xb△N 4h rna-seq rep1 [RNAseq_4h_KO_ddx3xb△N1]


title: Ddx3xb mutant injected with ddx3xbFL 6h rna-seq rep2 [RNAseq_6h_KO_ddx3xbFL2]

source_name: Ddx3xb mutant injected with ddx3xbFL 6h


title: Ddx3xb mutant injected with ddx3xb△N 2h rna-seq rep1 [RNAseq_2h_KO_ddx3xb△N1]

source_name: Ddx3xb mutant injected with ddx3xb△N 2h

value: 2 hpf


title: Ddx3xb mutant+ddx3xb△N 4h ribo-seq rep1 [ribosomes_4h_KO_ddx3xb△N1]


title: Ddx3xb mutant injected with ddx3xbFL 4h rna-seq rep2 [RNAseq_4h_KO_ddx3xbFL2]

source_name: Ddx3xb mutant injected with ddx3xbFL 4h


title: Ddx3xb mutant injected with ddx3xbFL 4h rna-seq rep1 [RNAseq_4h_KO_ddx3xbFL1]


title: Ddx3xb mutant injected with ddx3xbFL 2h rna-seq rep2 [RNAseq_2h_KO_ddx3xbFL2]

source_name: Ddx3xb mutant injected with ddx3xbFL 2h


title: 20110913- 2A

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95927.gif

value: common pooled reference

value: irradiated CD34


title: ribosomes 4h KO rep1

description: Ddx3xb mutant 4h ribo-seq rep1

source_name: Ddx3xb mutant 4h ribo-seq rep1


title: ribosomes 4h WT rep2

description: control 4h ribo-seq rep2

source_name: control 4h ribo-seq rep2

value: wild type


title: Ddx3xb mutant injected with ddx3xbFL 2h rna-seq rep1 [RNAseq_2h_KO_ddx3xbFL1]


title: 20110714- 8

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95971.gif

value: 4 h

value: non-irradiated BMEC + non-irradiated CD34+


title: ribosomes 4h WT rep1

description: control 4h ribo-seq rep1

source_name: control 4h ribo-seq rep1


title: Ddx3xb mutant injected with ddx3xb△N 2h rna-seq rep2 [RNAseq_2h_KO_ddx3xb△N2]


title: 20110728- 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95973.gif

value: BMEC


title: 2011728- 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95937.gif

value: 1 h

value: non-irradiated BMEC + irradiated CD34+


title: RNAseq_6h_ddx3xb-/-_rep2

description: Ddx3xb mutant 6h rna-seq rep2

source_name: Ddx3xb mutant 6h rna-seq rep2


title: 20110714- 12

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95921.gif

value: non-irradiated CD34 + non-irradiated BMEC


title: 20110518- 1C

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95930.gif

value: irradiated CD34 + non-irradiated BMEC


title: 20110215- 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95933.gif


title: ribosomes 4h KO rep2

description: Ddx3xb mutant 4hribo-seq rep2

source_name: Ddx3xb mutant 4hribo-seq rep2


title: 20110518- 14

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95941.gif


title: 20110518-5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95964.gif


title: RNAseq_4h_ddx3xb-/-_rep1

description: Ddx3xb mutant 4h rna-seq rep1

source_name: Ddx3xb mutant 4h rna-seq rep1


title: RNAseq_2h_ddx3xb-/-_rep1

description: Ddx3xb mutant 2h rna-seq rep1

source_name: Ddx3xb mutant 2h rna-seq rep1


title: 20110728- 1D

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95926.gif

source_name: 825 ng of amplified human cell cDNA (pooled reference)


title: 20110714- 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95920.gif

source_name: 825 ng of amplified human cell cDNA (test)


title: RNAseq_6h_ddx3xb+/+_rep2

description: control 6h rna-seq rep2

source_name: control 6h rna-seq rep2


title: 20110728- 1C

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95925.gif


title: 20110913- 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95956.gif

value: non-irradiated BMEC


title: 20110215- 1

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95945.gif


title: RNAseq_4h_ddx3xb+/+_rep2

description: control 4h rna-seq rep2

source_name: control 4h rna-seq rep2


title: RNAseq_6h_ddx3xb+/+_rep1

description: control 6h rna-seq rep1

source_name: control 6h rna-seq rep1


title: RNAseq_4h_ddx3xb+/+_rep1

description: control 4h rna-seq rep1

source_name: control 4h rna-seq rep1


title: RNAseq_2h_ddx3xb+/+_rep2

description: control 2h rna-seq rep2

source_name: control 2h rna-seq rep2


title: RNAseq_2h_ddx3xb+/+_rep1

description: control 2h rna-seq rep1

source_name: control 2h rna-seq rep1


title: RNAseq_4h_ddx3xb-/-_rep2

description: Ddx3xb mutant 4h rna-seq rep2

source_name: Ddx3xb mutant 4h rna-seq rep2


title: RNAseq_6h_ddx3xb_MO_rep1

description: Ddx3xb MO 6h rna seq rep1

source_name: Ddx3xb MO 6h rna seq rep1

value: ddx3xb morphants zebrafish embryos cells


title: Ddx3xb mutant injected with ddx3xbFL 6h rna-seq rep1 [RNAseq_6h_KO_ddx3xbFL1]

source_name: Ddx3xb mutant injected with ddx3xbFL 6h


title: 20110913- 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95955.gif


title: 20110215- 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95963.gif


title: RNAseq_2h_ddx3xb_MO_rep1

description: Ddx3xb MO 2h rna seq rep1

source_name: Ddx3xb MO 2h rna seq rep1


title: 20110627- 3

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95939.gif

value: irradiated BMEC + non-irradiated CD34+


title: RNAseq_6h_ddx3xb_MO_rep2

description: Ddx3xb MO 6h rna seq rep2

source_name: Ddx3xb MO 6h rna seq rep2

value: zebrafish embryos

value: ddx4xb morphants zebrafish embryos cells


title: RNAseq_6h_MO_control_rep2

description: control 6h rna-seq rep2

value: 6 hpf


title: RNAseq_2h_ddx3xb_MO_rep2

description: Ddx3xb MO 2h rna seq rep2

source_name: Ddx3xb MO 2h rna seq rep2

value: 2 hpf


title: 2011728- 5

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95938.gif

value: common pooled reference


title: RNAseq_6h_MO_control_rep1

description: control 6h rna-seq rep1


title: RNAseq_2h_MO_control_rep2

description: control 2h rna-seq rep2


title: RNAseq_6h_ddx3xb-/-_rep1

description: Ddx3xb mutant 6h rna-seq rep1

source_name: Ddx3xb mutant 6h rna-seq rep1


title: rip 4h WT rep1

description: control 4h RIP-seq rep1

data_processing:
low-quality bases were trimmed and filtered by cutadapt (V 1.13) and Trimmomatic (V 0.36). Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads. The remaining reads were mapped to zebrafish genome (Zv9) using TopHat (v2.1.1) with ‘‘–bowtie1’’.
The target binding regions of Ddx3xb were identified using MACS2 software (version 2.0.10) with options ‘–nomodel’ --keep-dup and --gsize=1.4e9, and using RNA seq data as input. A stringent cutoff threshold for P value of 1 × 10−2 was used to obtain target genes of Ddx3xb. The target genes were annotated based on Ensembl (release 79) gene annotation information by applying BEDTools’ intersectBed (version 2.16.2).
Genome_build: Zv9
Supplementary_files_format_and_content: binding peaks for Ddx3xb protein

source_name: control 4h RIP-seq rep1

extract_protocol:
flag-ddx3xb mRNA injected embryos were collected at 2 hpf or 4 hpf and lysed in NETN lysis buffer (150 mM NaCl, 0.5% NP-40, 50 mM Tris-HCl, pH 7.4). Ddx3xb RIP was carried out following a published protocol, but with some modifications. Lysate was incubated with anti-FLAG M2 Magnetic Beads (Merck, M8823) for 4 h at 4C. RNA was extracted and subjected to library construction using the SMARTer smRNA-Seq kit (Clontech, 635031).
RNA was extracted and subjected to library construction using Smarter smRNA-Seq kit (Clontech Laboratories Inc).

value: 4 hpf


title: rip 4h WT rep2

description: control 4h RIP-seq rep2

source_name: control 4h RIP-seq rep2

value: wild type


title: rip 2h WT rep2

description: control 2h RIP-seq rep2

source_name: control 2h RIP-seq rep2


title: m126_5_Hela_IFN6h

city: Pamplona

first: Puri

last: Fortes

address: Pio XII 55

institute: CIMA/UNAV

description: sequenced with Illumina TRuSeq stranded mRNA kit. Sequences were paired-end, 150 bases long and strand-specific.

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCh38 human assembly using STAR v2.5.3a with default parameters.
featureCounts v1.6.0 software and Gencode v25 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: cervix

extract_protocol:
MaxWell 16 research system from Promega
TRuSeq stranded mRNA kit

treatment_protocol: 1000 units /mL IFNa

value: cervix

value: HeLa

value: cervical cancer

value: WT

tag: treatment

value: IFNa for 6h


title: m126_1_Hela_Ctrl


title: m126_21_pNISR8_IFN6h

value: CRISPR-depleted IRF1-AS1 promoter


title: Input_rep2

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

data_processing:
adapter and bar code sequences were trimmed by cutadapt/1.18 . PCR duplicates were removed using in-house script.
Processed reads were aligned to human hg19 genome and HAV/18f with STAR/2.7.3a
Enriched peaks on HAV genome were analyzed with deeptools/3.2.0
Enrich peaks on cellular RNAs were identified with CLIPper (https://github.com/YeoLab/clipper/wiki/CLIPper-Home)
Peaks were annotated with HOMERv4.11(http://homer.ucsd.edu/homer/).
Genome_build: hg19 and HAV/18f
Supplementary_files_format_and_content: peak text files in bedgraph format

source_name: 293T cell

growth_protocol: 293T cells were maintained in DMEM media with 10%FBS

extract_protocol:
Lysates were sonicated and treated with Rnase I, and protein-RNA complexes were isolated with anti-FLAG magnetic beads.
Libraries were constructed following eCLIP protocol. Briefly, crosslinked RNAs were ligated with a 3' RNA adapter and reverse transcribed. The cDNAs were ligated with a 3' ssDNA adapter with barcode and randomer sequences.  After ligation, DNAs were PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 bp were band isolated from an agarose gel.

treatment_protocol: cells were infected with HAV/18f virus for 3 days and transfected with FLAG-ZCCHC14 for 2 more days

tag: infection

value: HAV(18f strain) 5 days

tag: antibody


title: Input_rep1


title: FLAG-ZCCHC14-CLIP_rep2

value: anti-Flag M2 (Millipore M8823)


title: rip 2h WT rep1

description: control 2h RIP-seq rep1

source_name: control 2h RIP-seq rep1


title: melanoma cells IP HA

city: New York

first: Pietro

last: Berico

state: NY

address: 550 1st Ave

department: Pathology

institute: NYU Langone Health

data_processing:
All quality controls presented in this section have been computed using FASTQC
FastQScreen was used to map a subset of reads (10,000,000) from each sample to selected DNA sequences in order to assess the presence of contamination within the samples.
Peaks detected were annotated using HOMER (http://biowhat.ucsd.edu/homer/ngs/annotation.html) as well as TSS protein enrichment comparison.
As reference coordinates, we used the MACS-determined peaks or the annotated TSS/TTS of human genes as defined by RefSeq database.
Sequence enrichment was performed using RSAT (http://rsat.sb-roscoff.fr) with MACS-determined peaks as reference.
Assembly: hg19
Library strategy: CUT&Tag

source_name: Skin

extract_protocol:
Assays were performed following the manufacturer's instructions (Active motif CUT&Tag-IT™ Assay Kit, #53165, #53160). Briefly, 500 000 cells per condition were used. The cells were washed 2 time before the binding on Concavalin A beads and then incubated overnight with BAHCC1 and HA primary antibodies at the recommended dilution (1:50) or without antibody (negative control). The next day the corresponding secondary antibody, a guinea pig Anti-rabbit antibody was used following a 1:100 dilution in digitonin buffer and incubated at room temperature for 1 hour. The CUT&Tag-IT™ Assembled pA-Tn5 Transposomes were incubated for 1 hour at room temperature before tagmentation. Cells were resuspended in Tagmentation buffer and incubated at 37°C for 1 hour, then the tagmentation process was stopped by addition of EDTA and SDS. Protein digestion was performed by the addition of 80µg/mL of proteinase K and incubated at 55°C for 60 minutes. DNA was retrieved on DNA purification columns provided by the manufacturer.
Library preparation and PCR amplification were done using the Kit primers and purified by 2 successive washes with SPRI beads. Libraries were sequenced on an Illumina HiSeq 4000 sequencer as paired-end 100 base reads.

value: Human melanoma cells

value: no treatment


title: melanoma cells IP neg


title: RNAseq_2h_ddx3xb-/-_rep2

description: Ddx3xb mutant 2h rna-seq rep2

source_name: Ddx3xb mutant 2h rna-seq rep2

value: zebrafish embryos


title: melanoma cells IP BAHCC1


title: m126_17_pNISR8_Ctrl


title: FLAG-ZCCHC14-CLIP_rep1


title: VerapamilHCl_8 24h dose4_2

city: Kyoto

first: Junko

last: Yamane

address: 53, Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Kyoto University

data_processing:
All sequenced reads passed quality filters were extracted to FASTQ format and demultiplexed to individual cells by barcodes using BCL2FASTQ Conversion Software v2.20.0.422.
FASTQ converted reads were then mapped to Ensembl GRCh38 release 100 human cDNA and ncRNA sequences using Bowtie2 v2.2.5 with very-sensitive-local option.
Average counts of 28,652,809 and 28,291,682 reads for each sample at 24 h and 48 h were obtained, respectively.
Only transcription factor-related genes included in the Gene Ontology GO: 0006351 were selected using BioMart (4032 genes).
Following analyses were performed by R ver. 4.0.5 package edgeR.

source_name: human ESCs

growth_protocol: hESCs were cultured using Essential 8 medium in feeder-free culture manner.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN) and performed On-coloum DNase digestion (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hESCs were exposed by 24 different conditions of chemicals.

value: human ESCs

value: VerapamilHCl

tag: treatment time

tag: dose


title: VerapamilHCl_17 48h dose3_1


title: VerapamilHCl_10 24h dose5_2


title: VerapamilHCl_7 24h dose4_1


title: VerapamilHCl_9 24h dose5_1


title: VerapamilHCl_15 48h dose2_1


title: VerapamilHCl_18 48h dose3_2


title: VerapamilHCl_24 48h dose6_2


title: VerapamilHCl_12 24h dose6_2


title: VerapamilHCl_20 48h dose4_2


title: VerapamilHCl_16 48h dose2_2


title: VerapamilHCl_19 48h dose4_1


title: VerapamilHCl_11 24h dose6_1


title: VerapamilHCl_22 48h dose5_2


title: VerapamilHCl_14 48h dose1_2


title: VerapamilHCl_6 24h dose3_2


title: VerapamilHCl_5 24h dose3_1


title: VerapamilHCl_2 24h dose1_2


title: VerapamilHCl_3 24h dose2_1


title: VerapamilHCl_4 24h dose2_2


title: VerapamilHCl_1 24h dose1_1


title: ValproicAcid_23 48h dose6_1

value: ValproicAcid


title: ValproicAcid_21 48h dose5_1


title: VerapamilHCl_23 48h dose6_1


title: VerapamilHCl_13 48h dose1_1


title: VerapamilHCl_21 48h dose5_1


title: ValproicAcid_22 48h dose5_2


title: ValproicAcid_20 48h dose4_2


title: 20110728- 1B

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95924.gif

source_name: 825 ng of amplified human cell cDNA (pooled reference)

value: common pooled reference

source_name: 825 ng of amplified human cell cDNA (test)

value: 4 h

value: irradiated CD34 + non-irradiated BMEC


title: ValproicAcid_24 48h dose6_2


title: ValproicAcid_18 48h dose3_2


title: ValproicAcid_16 48h dose2_2


title: ValproicAcid_13 48h dose1_1


title: ValproicAcid_15 48h dose2_1


title: ValproicAcid_17 48h dose3_1


title: ValproicAcid_14 48h dose1_2


title: ValproicAcid_19 48h dose4_1


title: 2011728- 2

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95935.gif

value: 1 h

value: non-irradiated BMEC + non-irradiated CD34+


title: RNAseq_2h_MO_control_rep1

description: control 2h rna-seq rep1

source_name: control 2h rna-seq rep1

value: wild type

value: 2 hpf


title: 20110627- 4

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95940.gif

value: non-irradiated BMEC + irradiated CD34+


title: ValproicAcid_7 24h dose4_1


title: Thioacetamide_12 24h dose6_2

value: Thioacetamide


title: ValproicAcid_4 24h dose2_2


title: ValproicAcid_9 24h dose5_1


title: ValproicAcid_3 24h dose2_1


title: ValproicAcid_10 24h dose5_2


title: Thioacetamide_20 48h dose4_2


title: Thioacetamide_19 48h dose4_1


title: Thioacetamide_22 48h dose5_2


title: ValproicAcid_2 24h dose1_2


title: Thioacetamide_16 48h dose2_2


title: ValproicAcid_11 24h dose6_1


title: Thioacetamide_23 48h dose6_1


title: Thioacetamide_15 48h dose2_1


title: ValproicAcid_6 24h dose3_2


title: Thioacetamide_17 48h dose3_1


title: Thioacetamide_13 48h dose1_1


title: Thioacetamide_21 48h dose5_1


title: ValproicAcid_12 24h dose6_2


title: ValproicAcid_1 24h dose1_1


title: ValproicAcid_5 24h dose3_1


title: Thioacetamide_11 24h dose6_1


title: Thioacetamide_14 48h dose1_2


title: ValproicAcid_8 24h dose4_2


title: Thioacetamide_24 48h dose6_2


title: Thioacetamide_18 48h dose3_2


title: Thioacetamide_10 24h dose5_2


title: Thioacetamide_9 24h dose5_1


title: Thioacetamide_7 24h dose4_1


title: Thioacetamide_8 24h dose4_2


title: Sunitinib_11 24h dose6_1

value: Sunitinib


title: Thioacetamide_4 24h dose2_2


title: Sunitinib_21 48h dose5_1


title: Thioacetamide_5 24h dose3_1


title: Thioacetamide_2 24h dose1_2


title: Sunitinib_15 48h dose2_1


title: 20110714- 7

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95970.gif

value: BMEC


title: Sunitinib_13 48h dose1_1


title: Sunitinib_14 48h dose1_2


title: Sunitinib_20 48h dose4_2


title: Sunitinib_18 48h dose3_2


title: Sunitinib_12 24h dose6_2


title: Thioacetamide_1 24h dose1_1


title: Sunitinib_22 48h dose5_2


title: Sunitinib_10 24h dose5_2


title: Sunitinib_16 48h dose2_2


title: Sunitinib_19 48h dose4_1


title: Sunitinib_23 48h dose6_1


title: Thioacetamide_3 24h dose2_1


title: 20110518- 15

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95942.gif


title: Sunitinib_17 48h dose3_1


title: Thioacetamide_6 24h dose3_2


title: Sunitinib_8 24h dose4_2


title: Sunitinib_9 24h dose5_1


title: 20110518- 10

description: Image: http://smd.stanford.edu/MicroArray/gifs/2012-02/95931.gif

value: non-irradiated CD34 + irradiated BMEC


title: Sunitinib_5 24h dose3_1


title: Sunitinib_6 24h dose3_2


title: Sunitinib_2 24h dose1_2


title: MethapyrileneHCl_24 48h dose6_2

value: MethapyrileneHCl


title: MethapyrileneHCl_21 48h dose5_1


title: MethapyrileneHCl_23 48h dose6_1


title: MethapyrileneHCl_20 48h dose4_2


title: Sunitinib_3 24h dose2_1


title: Sunitinib_7 24h dose4_1


title: MethapyrileneHCl_15 48h dose2_1


title: MethapyrileneHCl_9 24h dose5_1


title: MethapyrileneHCl_11 24h dose6_1


title: MethapyrileneHCl_14 48h dose1_2


title: MethapyrileneHCl_8 24h dose4_2


title: Sunitinib_1 24h dose1_1


title: MethapyrileneHCl_16 48h dose2_2


title: MethapyrileneHCl_19 48h dose4_1


title: MethapyrileneHCl_18 48h dose3_2


title: MethapyrileneHCl_13 48h dose1_1


title: MethapyrileneHCl_6 24h dose3_2


title: MethapyrileneHCl_5 24h dose3_1


title: MethapyrileneHCl_12 24h dose6_2


title: MethapyrileneHCl_7 24h dose4_1


title: MethapyrileneHCl_4 24h dose2_2


title: MethapyrileneHCl_3 24h dose2_1


title: MethapyrileneHCl_2 24h dose1_2


title: MethapyrileneHCl_17 48h dose3_1


title: Sunitinib_4 24h dose2_2


title: MethapyrileneHCl_22 48h dose5_2


title: MethapyrileneHCl_1 24h dose1_1


title: MethapyrileneHCl_10 24h dose5_2


title: LithocholicAcid_23 48h dose6_1

value: LithocholicAcid


title: LithocholicAcid_22 48h dose5_2

value: human ESCs


title: LithocholicAcid_21 48h dose5_1


title: LithocholicAcid_20 48h dose4_2


title: LithocholicAcid_19 48h dose4_1


title: LithocholicAcid_18 48h dose3_2


title: LithocholicAcid_15 48h dose2_1


title: LithocholicAcid_14 48h dose1_2


title: LithocholicAcid_13 48h dose1_1


title: LithocholicAcid_16 48h dose2_2


title: LithocholicAcid_7 24h dose4_1


title: LithocholicAcid_9 24h dose5_1


title: LithocholicAcid_5 24h dose3_1


title: LithocholicAcid_17 48h dose3_1


title: LithocholicAcid_10 24h dose5_2


title: LithocholicAcid_11 24h dose6_1


title: LithocholicAcid_6 24h dose3_2


title: LithocholicAcid_4 24h dose2_2


title: LithocholicAcid_8 24h dose4_2


title: LithocholicAcid_3 24h dose2_1


title: LithocholicAcid_2 24h dose1_2


title: Itraconazole_24 48h dose6_2

value: Itraconazole


title: LithocholicAcid_24 48h dose6_2


title: Itraconazole_23 48h dose6_1


title: Itraconazole_21 48h dose5_1


title: Itraconazole_22 48h dose5_2


title: Itraconazole_20 48h dose4_2


title: Itraconazole_18 48h dose3_2


title: LithocholicAcid_12 24h dose6_2


title: Itraconazole_16 48h dose2_2


title: Itraconazole_15 48h dose2_1


title: Itraconazole_14 48h dose1_2


title: Itraconazole_17 48h dose3_1


title: Itraconazole_5 24h dose3_1


title: Itraconazole_4 24h dose2_2


title: Itraconazole_7 24h dose4_1


title: Itraconazole_3 24h dose2_1


title: LithocholicAcid_1 24h dose1_1


title: Itraconazole_6 24h dose3_2


title: Itraconazole_11 24h dose6_1


title: Itraconazole_8 24h dose4_2


title: Itraconazole_2 24h dose1_2


title: Ibprofen_22 48h dose5_2

value: Ibprofen


title: Itraconazole_9 24h dose5_1


title: Ibprofen_23 48h dose6_1


title: Itraconazole_1 24h dose1_1


title: Ibprofen_24 48h dose6_2


title: Ibprofen_21 48h dose5_1


title: Itraconazole_10 24h dose5_2


title: Ibprofen_19 48h dose4_1


title: Itraconazole_19 48h dose4_1


title: Ibprofen_18 48h dose3_2


title: Ibprofen_17 48h dose3_1


title: Ibprofen_20 48h dose4_2


title: Itraconazole_12 24h dose6_2


title: Ibprofen_15 48h dose2_1


title: Itraconazole_13 48h dose1_1


title: Ibprofen_13 48h dose1_1


title: Ibprofen_14 48h dose1_2


title: Ibprofen_11 24h dose6_1


title: Ibprofen_12 24h dose6_2


title: Ibprofen_9 24h dose5_1


title: Ibprofen_8 24h dose4_2


title: Ibprofen_10 24h dose5_2


title: Ibprofen_7 24h dose4_1


title: Ibprofen_4 24h dose2_2


title: Ibprofen_5 24h dose3_1


title: Ibprofen_6 24h dose3_2


title: Ibprofen_3 24h dose2_1


title: Gentamicin_24 48h dose6_2

value: Gentamicin


title: Ibprofen_1 24h dose1_1


title: Ibprofen_16 48h dose2_2


title: Ibprofen_2 24h dose1_2


title: Gentamicin_22 48h dose5_2


title: Gentamicin_20 48h dose4_2


title: Gentamicin_21 48h dose5_1


title: Gentamicin_23 48h dose6_1


title: Gentamicin_18 48h dose3_2


title: Gentamicin_16 48h dose2_2


title: Gentamicin_19 48h dose4_1


title: Gentamicin_12 24h dose6_2


title: Gentamicin_17 48h dose3_1


title: Gentamicin_15 48h dose2_1


title: Gentamicin_14 48h dose1_2


title: Gentamicin_13 48h dose1_1


title: Gentamicin_11 24h dose6_1


title: Gentamicin_10 24h dose5_2


title: Gentamicin_9 24h dose5_1


title: Gentamicin_7 24h dose4_1


title: Gentamicin_8 24h dose4_2


title: Gentamicin_4 24h dose2_2


title: Doxorubicin_24 48h dose6_2

value: Doxorubicin


title: Doxorubicin_23 48h dose6_1


title: Gentamicin_5 24h dose3_1


title: Gentamicin_3 24h dose2_1


title: Doxorubicin_22 48h dose5_2


title: Doxorubicin_21 48h dose5_1


title: Gentamicin_2 24h dose1_2


title: Doxorubicin_18 48h dose3_2


title: Gentamicin_1 24h dose1_1


title: Doxorubicin_15 48h dose2_1


title: Doxorubicin_13 48h dose1_1


title: Doxorubicin_20 48h dose4_2


title: Doxorubicin_16 48h dose2_2


title: Sunitinib_24 48h dose6_2


title: Doxorubicin_12 24h dose6_2


title: Doxorubicin_17 48h dose3_1


title: Doxorubicin_14 48h dose1_2


title: Doxorubicin_11 24h dose6_1


title: Doxorubicin_10 24h dose5_2


title: Doxorubicin_9 24h dose5_1


title: Doxorubicin_6 24h dose3_2


title: Doxorubicin_8 24h dose4_2


title: Doxorubicin_4 24h dose2_2


title: Doxorubicin_5 24h dose3_1


title: Doxorubicin_3 24h dose2_1


title: Doxorubicin_2 24h dose1_2


title: Doxorubicin_7 24h dose4_1


title: Gentamicin_6 24h dose3_2


title: Doxorubicin_19 48h dose4_1


title: Digoxin_24 48h dose6_2

value: Digoxin


title: Digoxin_23 48h dose6_1


title: Digoxin_21 48h dose5_1


title: Digoxin_20 48h dose4_2


title: Digoxin_19 48h dose4_1


title: Digoxin_17 48h dose3_1


title: Digoxin_15 48h dose2_1


title: Digoxin_11 24h dose6_1


title: Digoxin_12 24h dose6_2


title: Digoxin_13 48h dose1_1


title: Digoxin_14 48h dose1_2


title: Digoxin_10 24h dose5_2


title: Digoxin_8 24h dose4_2


title: Digoxin_3 24h dose2_1


title: Digoxin_7 24h dose4_1


title: Digoxin_4 24h dose2_2


title: Digoxin_9 24h dose5_1


title: Digoxin_6 24h dose3_2


title: CyclosporinA_22 48h dose5_2

value: CyclosporinA


title: Digoxin_1 24h dose1_1


title: Digoxin_18 48h dose3_2


title: Doxorubicin_1 24h dose1_1


title: Digoxin_5 24h dose3_1


title: Digoxin_22 48h dose5_2


title: CyclosporinA_21 48h dose5_1


title: CyclosporinA_24 48h dose6_2


title: CyclosporinA_16 48h dose2_2


title: CyclosporinA_17 48h dose3_1


title: Digoxin_16 48h dose2_2


title: CyclosporinA_19 48h dose4_1


title: CyclosporinA_18 48h dose3_2


title: CyclosporinA_15 48h dose2_1


title: CyclosporinA_14 48h dose1_2


title: CyclosporinA_12 24h dose6_2


title: CyclosporinA_11 24h dose6_1


title: CyclosporinA_20 48h dose4_2


title: CyclosporinA_23 48h dose6_1


title: CyclosporinA_10 24h dose5_2


title: CyclosporinA_13 48h dose1_1


title: Digoxin_2 24h dose1_2


title: CyclosporinA_9 24h dose5_1


title: CyclosporinA_8 24h dose4_2


title: CyclosporinA_6 24h dose3_2


title: CyclosporinA_5 24h dose3_1


title: CyclosporinA_4 24h dose2_2


title: Cyclopamine_23 48h dose6_1

value: Cyclopamine


title: CyclosporinA_1 24h dose1_1


title: CyclosporinA_2 24h dose1_2


title: Cyclopamine_24 48h dose6_2


title: CyclosporinA_3 24h dose2_1


title: Cyclopamine_20 48h dose4_2


title: Cyclopamine_21 48h dose5_1


title: Cyclopamine_22 48h dose5_2


title: Cyclopamine_19 48h dose4_1


title: Cyclopamine_17 48h dose3_1


title: Cyclopamine_16 48h dose2_2


title: Cyclopamine_15 48h dose2_1


title: Cyclopamine_14 48h dose1_2


title: Cyclopamine_13 48h dose1_1


title: CyclosporinA_7 24h dose4_1


title: Cyclopamine_12 24h dose6_2


title: Cyclopamine_5 24h dose3_1


title: Cyclopamine_7 24h dose4_1


title: Cyclopamine_9 24h dose5_1


title: Cyclopamine_4 24h dose2_2


title: Cyclopamine_8 24h dose4_2


title: Cyclopamine_6 24h dose3_2


title: Cyclopamine_3 24h dose2_1


title: Cyclopamine_2 24h dose1_2


title: Cisplatin_24 48h dose6_2

value: Cisplatin


title: Cyclopamine_18 48h dose3_2


title: Cyclopamine_1 24h dose1_1


title: Cisplatin_22 48h dose5_2


title: Cisplatin_20 48h dose4_2


title: Cisplatin_21 48h dose5_1


title: Cisplatin_18 48h dose3_2


title: Cisplatin_15 48h dose2_1


title: Cisplatin_14 48h dose1_2


title: Cisplatin_16 48h dose2_2


title: Cisplatin_17 48h dose3_1


title: Cyclopamine_10 24h dose5_2


title: Cisplatin_13 48h dose1_1


title: Cisplatin_23 48h dose6_1


title: Cyclopamine_11 24h dose6_1


title: Cisplatin_12 24h dose6_2


title: Cisplatin_11 24h dose6_1


title: Cisplatin_8 24h dose4_2


title: Cisplatin_10 24h dose5_2


title: Cisplatin_6 24h dose3_2


title: Cisplatin_4 24h dose2_2


title: Cisplatin_2 24h dose1_2


title: Cisplatin_5 24h dose3_1


title: Cisplatin_7 24h dose4_1


title: Cisplatin_3 24h dose2_1


title: Chlorpromazine_24 48h dose6_2

value: Chlorpromazine


title: Cisplatin_1 24h dose1_1


title: Cisplatin_19 48h dose4_1


title: Chlorpromazine_20 48h dose4_2


title: Chlorpromazine_21 48h dose5_1


title: Chlorpromazine_22 48h dose5_2


title: Chlorpromazine_19 48h dose4_1


title: Chlorpromazine_17 48h dose3_1


title: Chlorpromazine_16 48h dose2_2


title: Chlorpromazine_18 48h dose3_2


title: Chlorpromazine_15 48h dose2_1


title: Chlorpromazine_13 48h dose1_1


title: Cisplatin_9 24h dose5_1


title: Chlorpromazine_14 48h dose1_2


title: Chlorpromazine_12 24h dose6_2


title: Chlorpromazine_10 24h dose5_2


title: Chlorpromazine_9 24h dose5_1


title: Chlorpromazine_11 24h dose6_1


title: Chlorpromazine_8 24h dose4_2


title: Chlorpromazine_7 24h dose4_1


title: Chlorpromazine_6 24h dose3_2


title: Chlorpromazine_5 24h dose3_1


title: Chlorpromazine_23 48h dose6_1


title: Chlorpheniramine_23 48h dose6_1

value: Chlorpheniramine


title: Chlorpromazine_4 24h dose2_2


title: Chlorpromazine_2 24h dose1_2


title: Chlorpheniramine_24 48h dose6_2


title: Chlorpromazine_1 24h dose1_1


title: Chlorpheniramine_21 48h dose5_1


title: Chlorpheniramine_19 48h dose4_1


title: Chlorpheniramine_20 48h dose4_2


title: Chlorpheniramine_22 48h dose5_2


title: Chlorpheniramine_18 48h dose3_2


title: Chlorpheniramine_16 48h dose2_2


title: Chlorpheniramine_17 48h dose3_1


title: Chlorpheniramine_11 24h dose6_1


title: Chlorpheniramine_12 24h dose6_2


title: Chlorpheniramine_13 48h dose1_1


title: Chlorpheniramine_15 48h dose2_1


title: Chlorpheniramine_14 48h dose1_2


title: Chlorpromazine_3 24h dose2_1


title: Chlorpheniramine_4 24h dose2_2


title: Chlorpheniramine_9 24h dose5_1


title: Chlorpheniramine_8 24h dose4_2


title: Chlorpheniramine_10 24h dose5_2


title: Chlorpheniramine_7 24h dose4_1


title: Chlorpheniramine_3 24h dose2_1


title: Chlorpheniramine_5 24h dose3_1


title: ButylatedHA_24 48h dose6_2

value: ButylatedHA


title: ButylatedHA_18 48h dose3_2


title: ButylatedHA_19 48h dose4_1


title: Chlorpheniramine_1 24h dose1_1


title: ButylatedHA_23 48h dose6_1


title: ButylatedHA_22 48h dose5_2


title: ButylatedHA_21 48h dose5_1


title: ButylatedHA_17 48h dose3_1


title: ButylatedHA_13 48h dose1_1


title: ButylatedHA_15 48h dose2_1


title: ButylatedHA_16 48h dose2_2


title: Chlorpheniramine_6 24h dose3_2


title: ButylatedHA_14 48h dose1_2


title: ButylatedHA_9 24h dose5_1


title: ButylatedHA_11 24h dose6_1


title: ButylatedHA_7 24h dose4_1


title: Chlorpheniramine_2 24h dose1_2


title: ButylatedHA_12 24h dose6_2


title: ButylatedHA_8 24h dose4_2


title: ButylatedHA_10 24h dose5_2


title: ButylatedHA_5 24h dose3_1


title: ButylatedHA_1 24h dose1_1


title: ButylatedHA_4 24h dose2_2


title: ButylatedHA_2 24h dose1_2


title: ButylatedHA_6 24h dose3_2


title: ButylatedHA_3 24h dose2_1


title: Bucillamine_24 48h dose6_2

value: Bucillamine


title: ButylatedHA_20 48h dose4_2


title: Bucillamine_17 48h dose3_1


title: Bucillamine_22 48h dose5_2


title: Bucillamine_18 48h dose3_2


title: Bucillamine_20 48h dose4_2


title: Bucillamine_23 48h dose6_1


title: Bucillamine_19 48h dose4_1


title: Bucillamine_21 48h dose5_1


title: Bucillamine_15 48h dose2_1


title: Bucillamine_9 24h dose5_1


title: Bucillamine_12 24h dose6_2


title: Bucillamine_8 24h dose4_2


title: Bucillamine_11 24h dose6_1


title: Bucillamine_10 24h dose5_2


title: Bucillamine_5 24h dose3_1


title: Bucillamine_6 24h dose3_2


title: Bucillamine_2 24h dose1_2


title: Bucillamine_3 24h dose2_1


title: Bucillamine_7 24h dose4_1


title: Axitinib_21 48h dose5_1

value: Axitinib


title: Axitinib_23 48h dose6_1


title: Bucillamine_1 24h dose1_1


title: Axitinib_22 48h dose5_2


title: Axitinib_19 48h dose4_1


title: Bucillamine_16 48h dose2_2


title: Axitinib_18 48h dose3_2


title: Axitinib_20 48h dose4_2


title: Bucillamine_4 24h dose2_2


title: Axitinib_14 48h dose1_2


title: Axitinib_17 48h dose3_1


title: Axitinib_13 48h dose1_1


title: Bucillamine_14 48h dose1_2


title: Axitinib_16 48h dose2_2


title: Axitinib_15 48h dose2_1


title: Axitinib_11 24h dose6_1


title: Bucillamine_13 48h dose1_1


title: Axitinib_12 24h dose6_2


title: Axitinib_24 48h dose6_2


title: Axitinib_4 24h dose2_2


title: Axitinib_5 24h dose3_1


title: Axitinib_7 24h dose4_1


title: Axitinib_10 24h dose5_2


title: Axitinib_6 24h dose3_2


title: Axitinib_3 24h dose2_1


title: Axitinib_9 24h dose5_1


title: Atorvastatin_24 48h dose6_2

value: Atorvastatin


title: Axitinib_8 24h dose4_2


title: Atorvastatin_20 48h dose4_2


title: Atorvastatin_19 48h dose4_1


title: Atorvastatin_23 48h dose6_1


title: Axitinib_2 24h dose1_2


title: Atorvastatin_18 48h dose3_2


title: Atorvastatin_21 48h dose5_1


title: Atorvastatin_17 48h dose3_1


title: Atorvastatin_16 48h dose2_2


title: Atorvastatin_10 24h dose5_2


title: Atorvastatin_22 48h dose5_2


title: Atorvastatin_13 48h dose1_1


title: Atorvastatin_9 24h dose5_1


title: Atorvastatin_14 48h dose1_2


title: Atorvastatin_12 24h dose6_2


title: Atorvastatin_8 24h dose4_2


title: Atorvastatin_7 24h dose4_1


title: Axitinib_1 24h dose1_1


title: Atorvastatin_4 24h dose2_2


title: Atorvastatin_3 24h dose2_1


title: AmitriptylineHCl_24 48h dose6_2

value: AmitriptylineHCl


title: Atorvastatin_5 24h dose3_1


title: AmitriptylineHCl_23 48h dose6_1


title: AmitriptylineHCl_21 48h dose5_1


title: Atorvastatin_15 48h dose2_1


title: AmitriptylineHCl_22 48h dose5_2


title: AmitriptylineHCl_19 48h dose4_1


title: AmitriptylineHCl_20 48h dose4_2


title: AmitriptylineHCl_16 48h dose2_2


title: AmitriptylineHCl_18 48h dose3_2


title: AmitriptylineHCl_15 48h dose2_1


title: AmitriptylineHCl_10 24h dose5_2


title: AmitriptylineHCl_13 48h dose1_1


title: AmitriptylineHCl_9 24h dose5_1


title: AmitriptylineHCl_5 24h dose3_1


title: AmitriptylineHCl_12 24h dose6_2


title: AmitriptylineHCl_14 48h dose1_2


title: AmitriptylineHCl_7 24h dose4_1


title: AmitriptylineHCl_8 24h dose4_2


title: AmitriptylineHCl_6 24h dose3_2


title: AmitriptylineHCl_4 24h dose2_2


title: AmitriptylineHCl_3 24h dose2_1


title: Atorvastatin_1 24h dose1_1


title: Atorvastatin_2 24h dose1_2


title: AmitriptylineHCl_2 24h dose1_2


title: AmitriptylineHCl_1 24h dose1_1


title: Amiodarone_24 48h dose6_2

value: Amiodarone


title: Amiodarone_23 48h dose6_1

value: human ESCs


title: AmitriptylineHCl_17 48h dose3_1


title: Amiodarone_22 48h dose5_2


title: Amiodarone_21 48h dose5_1


title: Amiodarone_19 48h dose4_1


title: Amiodarone_20 48h dose4_2


title: Amiodarone_18 48h dose3_2


title: Amiodarone_16 48h dose2_2


title: AmitriptylineHCl_11 24h dose6_1


title: Amiodarone_15 48h dose2_1


title: Amiodarone_14 48h dose1_2


title: Amiodarone_11 24h dose6_1


title: Amiodarone_12 24h dose6_2


title: Amiodarone_13 48h dose1_1


title: Amiodarone_8 24h dose4_2


title: Amiodarone_10 24h dose5_2


title: Amiodarone_9 24h dose5_1


title: Amiodarone_7 24h dose4_1


title: Amiodarone_6 24h dose3_2


title: Atorvastatin_6 24h dose3_2


title: Amiodarone_5 24h dose3_1


title: Amiodarone_4 24h dose2_2


title: Amiodarone_3 24h dose2_1


title: Amiodarone_1 24h dose1_1


title: Amiodarone_2 24h dose1_2


title: Acrylamide_24 48h dose6_2

value: Acrylamide


title: Amiodarone_17 48h dose3_1


title: Acrylamide_23 48h dose6_1


title: Acrylamide_22 48h dose5_2


title: Acrylamide_20 48h dose4_2


title: Acrylamide_21 48h dose5_1


title: Acrylamide_19 48h dose4_1


title: Acrylamide_18 48h dose3_2


title: Acrylamide_17 48h dose3_1


title: Acrylamide_13 48h dose1_1


title: Acrylamide_14 48h dose1_2


title: Acrylamide_12 24h dose6_2


title: Acrylamide_16 48h dose2_2


title: Acrylamide_11 24h dose6_1


title: Acrylamide_10 24h dose5_2


title: Acrylamide_8 24h dose4_2


title: Acrylamide_7 24h dose4_1


title: Acrylamide_6 24h dose3_2


title: Acrylamide_9 24h dose5_1


title: Acrylamide_3 24h dose2_1


title: Acrylamide_2 24h dose1_2


title: Acetonylacetone_23 48h dose6_1

value: Acetonylacetone


title: Acrylamide_1 24h dose1_1


title: Acetonylacetone_24 48h dose6_2


title: Acetonylacetone_20 48h dose4_2


title: Acetonylacetone_21 48h dose5_1


title: Acetonylacetone_19 48h dose4_1


title: Acetonylacetone_22 48h dose5_2


title: Acetonylacetone_16 48h dose2_2


title: Acetonylacetone_18 48h dose3_2


title: Acetonylacetone_13 48h dose1_1


title: Acrylamide_15 48h dose2_1


title: Acetonylacetone_17 48h dose3_1


title: Acetonylacetone_12 24h dose6_2


title: Acetonylacetone_11 24h dose6_1


title: Acrylamide_4 24h dose2_2


title: Acetonylacetone_15 48h dose2_1


title: Acetonylacetone_8 24h dose4_2


title: Acetonylacetone_5 24h dose3_1


title: Acetonylacetone_6 24h dose3_2


title: Acetonylacetone_7 24h dose4_1


title: Acetonylacetone_2 24h dose1_2


title: Acetonylacetone_3 24h dose2_1


title: Acrylamide_5 24h dose3_1


title: Acetonylacetone_14 48h dose1_2


title: Acetonylacetone_4 24h dose2_2


title: HEPG2, dFBS+Q, Treated_3

city: ALBANY

first: Anwesha

last: Sarkar

address: 1400 Washington Ave Albany, 1003K

department: Department of Biological Sciences

institute: University at Albany

data_processing:
Data alignment using STAR
Differential gene expression analysis using DESeq2
Comparative analysis
Data processing and visualization using Rstudio
Supplementary files format and content: Differential gene expression in comma-sepated value (csv) file

growth_protocol:
Toxicant: Sodium arsenite (iAs)
Dosage: 0.12mM (Lethal dose-20, LD20)
Cells: HEPG2 cells were grown in normal growth media (NGM), Queuosine depleted media (dFBS) and Queuine-addback media (dFBS+Q).

extract_protocol:
RNA was extracted using Trizol/Chloroform method using manufacturers protocol
The library was constructed using Illumina polyA selection kit following manufacturers protocol

treatment_protocol: The cells were grown overnight in the pre-described three media. Next day, the cells were exposed to LD20 dose of iAs for 2 hours. Post-exposure the media was exchanged with fresh media and further incubated for 6 hours. After 6 hours, RNA was isolated from the cells using Trizol-chloroform method and processed for mRNA sequencing.

value: Hepatocellular carcinoma cells

value: Q-addback

value: Arsenic Treated


title: HEPG2, dFBS, Treated_3

value: Q-depleted


title: HEPG2, dFBS+Q, Untreated_3

value: Untreated


title: HEPG2, dFBS, Untreated_2


title: HEPG2, dFBS+Q, Untreated_2


title: HEPG2, dFBS+Q, Treated_2


title: HEPG2, NGM, Untreated_3

value: Control


title: HEPG2, dFBS, Untreatedv


title: HEPG2, NGM, Treated_3


title: HEPG2, NGM, Untreated_2


title: HEPG2, dFBS, Treated_2


title: Acetonylacetone_9 24h dose5_1


title: HEPG2, NGM, Treated_2


title: Acetonylacetone_10 24h dose5_2


title: HEPG2, dFBS+Q, Treated_1


title: HEPG2, NGM, Treated_1


title: HEPG2, NGM, Untreated_1


title: HEPG2, dFBS, Untreated_1


title: HEPG2, dFBS, Treated_1


title: iPSC GENtoniK Replicate 2

first: Emiliano

last: Hergenreder

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality.
Transcripts were quantified directly from trimmed FASTQ files using Salmon referenced to GENCODE Release 36 transcripts
TPM values from Salmon were used for differential expression analysis using DESeq2
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: DESeq2 results (csv files)

source_name: iPSC-cortical neurons

growth_protocol: hPSC-derived cortical neurons were plated at a density of 150,000/cm2 on poly-L-ornithine and laminin-coated 6-well plates, and maintained in Neurobasal medium supplemented with B27 and GlutaMAX.

extract_protocol:
Directly lysed in Trizol reagent. RNA was isolated using Zymo RNA miniprep kit.
RNA was sent to GENEWIZ for sequencing. Standard Illumina protocols were used for library preparation.

treatment_protocol: Treatment was initiated 7 days after plating and maintained for 7 days. Cells were collected 7 days after treatment withdrawal and washout.

value: iPSC-cortical neurons

value: 1 uM GSK2869552, 1 uM EPZ5676, 1 uM NMDA, 1 uM Bay K 8644


title: Acetonylacetone_1 24h dose1_1


title: iPSC GENtoniK Replicate 3


title: iPSC DMSO Replicate 3

value: DMSO


title: iPSC DMSO Replicate 1


title: RNA-seq_GENtoniK Replicate 3

source_name: hESC-cortical neurons

growth_protocol: hESC-derived cortical neurons were plated at a density of 150,000/cm2 on poly-L-ornithine and laminin-coated 6-well plates, and maintained in Neurobasal medium supplemented with B27 and GlutaMAX.

value: hESC-cortical neurons


title: RNA-seq_GENtoniK Replicate 2


title: iPSC GENtoniK Replicate 1


title: HEPG2, dFBS+Q, Untreated_1


title: RNA-seq_NK Replicate 3

value: 1 uM NMDA, 1 uM Bay K 8644


title: RNA-seq_GENtoniK Replicate 1


title: RNA-seq_NK Replicate 2


title: RNA-seq_DMSO Replicate 2


title: RNA-seq_GE Replicate 2


title: RNA-seq_GE Replicate 1


title: RNA-seq_DMSO Replicate 1


title: RNA-seq_DMSO Replicate 3


title: ControlIGG_Rep3

data_processing:
Library strategy: CUT&RUN
Sequenced reads were trimmed for adaptor and low-quality sequence, then mapped to Hg38  genome assembly using Bowtie2 default parameters
BAM files were filtered for unmapped and upaired reads
Peaks were called using MACS: lower mfold (5), upper mfold (50), band width (180), minimum FDR (0.05). Broad peaks were called for H3K79me2 with broad region cutoff (0.1)
Genome_build: Hg38
Supplementary_files_format_and_content: Peak text files (csv)

source_name: hESC-derived cortical neurons

growth_protocol: hESC-derived cortical neurons were plated at a density of 150,000/cm2 on poly-L-ornithine and laminin-coated 6-well plates, and maintained in Neurobasal medium supplemented with B27 and GlutaMAX

extract_protocol:
Standard CUT&RUN protocol, 100,000 cells were used per antibody, all antibodies used at 1 to 100 dilution, phenol chloroform extraction
Samples were sent to MSKCC Integrated Genome Operations (IGO). Libraries were prepared using standard Illumina protocols

value: hESC-derived cortical neurons

value: Mouse IGG (ab46540)


title: RNA-seq_GE Replicate 3


title: RNA-seq_NK Replicate 1


title: ControlIGG_Rep2


title: H3K4me2_Rep3

value: H3K4me2 (Upstate 07-03)


title: H3K4me2_Rep2


title: H3K4me2_Rep1


title: H3K79me2_Rep2

value: H3K79me2 (Active Motif 39143)


title: H3K79me2_Rep3


title: H3K79me2_Rep1


title: GFP-negative

city: Shanghai

first: Xiaojuan

last: Fan

address: 320 Yue Yang Road

institute: CAS-MPG Partner Institute of Computational Biology

description: sequencing libraries were generated by using RT-PCR

data_processing:
More than 20 million reads were obtained from cells with different levels of GFP fluorescence, generating 10-nt sequences from each cell fraction. The inserted 10-nt sequences were recovered when the flanking sequences have exact match to the minigene reporter (24-nt upstream sequences and 30-nt downstream sequences were used for comparison).
Each inserted 10-mer was extended into a 14-mer by appending 2-nt of the vector sequence at each end to allow for cases in which IRES activity derived from sequences overlapping the vector.  The resulting 14-nt sequences were broken into overlapping hexamers and the occurrences of different hexamers were counted from sequences recovered in cells with mid-high fluorescence vs. no fluorescence.
The enrichment score of each 6-mer between two datasets was calculated using Z-test
Genome_build: None
Supplementary_files_format_and_content: Matrix table with Z-score of all hexamers

source_name: HEK293T cell

growth_protocol: 293T human embryonic kidney cell line was cultured in DMEM (high glucose) medium containing 10% fetal bovine serum (FBS, Hyclone)

extract_protocol:
The RNAs were isolated with TRIzol reagent following the manufacturer’s instructions.
The Amplicon sequencing libraries were generated through RT-PCR using mutiplexed PCR primers (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTTCGGCATGGACGAGCTGTACAAG and CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGCCGGTGGTGCAGATGAACTTCAG) NNNNNN is the sample barcode.

treatment_protocol: To transient transfect plasmids into cells, 2μg of mini-gene reporters were transfected into cells in 6 well plate, using lipofectamine 3000 (Invitrogen) according to the manufacturer’s instruction. After 48 h, cells were collected for further analysis of RNA and protein levels. Then cells were collected for FACS sorting using BD FACSAria II.

value: HEK293T cell

tag: group

value: GFP-negative


title: GFP-low

value: GFP-low


title: Atorvastatin_11 24h dose6_1

value: human ESCs

value: Atorvastatin


title: iPSC DMSO Replicate 2


title: GCN2 mutant YAA-All rep 3

city: Cologne

first: Dennis

middle: Said

last: Gadalla

state: NRW

address: Joseph-Stelzmann-Straße 26

department: Systems Biology

institute: CECAD Research Center

description:
processed files column: GCN2_YAAa.Rep_3
GCN2_AA 24

data_processing:
Raw reads were mapped to BDGP6.32 ENSEMBL build 103 using kallisto (v0.46.2). Genes counts were quantified in the same step.
Differential gene expression was calculated using DESeq2 (v1.24.0) in R (v3.6.3).
All steps were automated by utilizing the FLASKI RNA-Seq analysis pipeline (v fb00137)
Assembly: BDGP6.32 of ENSEMBL build 103
Supplementary files format and content: DESeq2 normalized abundances, RPKM, differential expression results of all samples: comma separated file
Supplementary files format and content: DESeq2 differential expression results files for treatment vs control: comma separated files

organism: Drosophila melanogaster

source_name: Head and thorax

growth_protocol: Flies were maintained in culture bottles at 25 °C on a 12:12 h light:dark cycle at constant humidity (65%) on indicated diets.

extract_protocol:
Total RNA was extracted from head and thorax of 25 frozen flies using standard Trizol-Chloroform based protocol (Invitrogen). DNase treatment was done with RNase free DNase kit (Qiagen). 2 μg RNA in a total of 20 μl was sent for sequencing.
Libraries for sequencing were generated using the polyA purification method.

treatment_protocol: Once mated female flies per genotype were kept for 3 days on the Yaa, -R, -M, and -All diets and were then snap-frozen in liquid nitrogen.

value: Head and thorax

value: GCN2 null

value: All-deprived food for 3 days

tag: Sex

value: female


title: GCN2 mutant YAA-All rep 2

description:
processed files column: GCN2_YAAa.Rep_2
GCN2_AA 23

tag: tissue


title: GFP-high

value: GFP-high