title: BC4

city: Ithaca

first: Vimal

last: Selvaraj

address: 204 Morrison Hall

department: Animal Sciences

institute: Cornell University

data_processing:
The quality of raw reads was checked using FastQC before aligning to bovine reference genome (ARS UCD 1.2) using R package STAR.
Differentially expressed genes were identified using R package EdgeR.
Genome_build: ARS UCD 1.2
Supplementary_files_format_and_content: ReadsPerGene.txt files include raw read counts per gene.

organism: Bos taurus

source_name: 7 days old bovine blastocysts

growth_protocol: 50/well mature cumulus oocyte complexes were in vitro fertilized with semen for 8-9 hours in in vitro fertilization medium and embryos that develop to blastocysts after 7 days of insemination were collected for total RNA isolation.

extract_protocol:
Total RNA was isolated using RNAqueous Micro Total RNA isolation kit.
mRNA was captured using poly (A) and cDNA libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina).

treatment_protocol: No treatments.

value: In vitro fertilized bovine blastocysts

value: 7 days


title: ADorSB1

status: Public on Oct 17 2021

type: SRA

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

country: China

institute: Chinese Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
cDNA library was carried out a paired-end sequencing using a HiSeq PE Cluster Kit v4 cBot (Illumina, San Diego, CA, USA) on the Illumina sequencing platform, following the manufacturer’s instructions.
After filtering the low-quality reads, the clean reads were aligned with the garlic genome (GenBank accession: GCA_014155895.2) using hisat2 software
Then, gene expression level was quantified by estimating fragments per kilobase per million reads (FPKM)
Genome_build: GCA_014155895.2
Supplementary_files_format_and_content: the excel file contain the gene name and FPKM value,

molecule: total RNA

organism: Allium sativum

source_name: Chalingzipisuan

growth_protocol: When the flower stems sprout out with one week, the bulbs are generally enlarging, and we collected the bulbs. Then, the enlarging-growth bulbs, together the germinant bulbs (with < 5 cm shoot), and the dormant bulbs were used for sampling.

extract_protocol:
Total RNAs of each sample were extracted using an E.Z.N.A. Plant RNA Kit (OMEGA Bio-Tek, Norcross, GA, USA) according to the protocol of manufacturer.
these RNAs were individually used for performing the construction of cDNA libraries, with a fragment length of 300 bp (± 150 bp), using a NEBNext UltraTM RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) according to the manufacturer’s instructions.

treatment_protocol: The basal and storage clove were separated manually, and then stored immediately at －80 °C until use.

tag: tissue

value: storage clove

tag: developmental stage

value: enlarging growth of bulb


title: KYSE140_RNA_sg_e1_1

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

country: USA

institute: University of Utah

data_processing:
Bowtie2 to align sequencing reads
RSEM to quantify expression for each GENCODE gene
Genome_build: hg19
Supplementary_files_format_and_content: RSEM text file

organism: Homo sapiens

source_name: Esophageal squamous cancer cell line

extract_protocol:
mRNA isolated using NEBNext Poly-A mRNA Magnetic Isolation Module (NEB E7490L)
NEBNext Ultra Directional RNA library prep kit (NEB  E7760S)

tag: cell line

tag: cell type

value: Esophageal squamous cancer cell line

tag: treatment

value: CRISPRi sg-e1#1


title: KYSE140_RNA_sgSOX2_4

value: CRISPR sg-SOX2#4


title: KYSE140_RNA_sgChr22

value: CRISPR sg-Chr2.2


title: ADorLJ1

value: basal clove


title: BC1

state: NY


title: 3565_shDPY30_2_IC

city: La Jolla

first: Deobrat

last: Dixit

address: 10901 N Torrey Pines Rd,

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
FASTQ sequencing reads were trimmed using Trim Galore.
Transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport.
Differential expression analysis was performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Salmon quant files

source_name: Glioblastoma stem cell intracranial xenograft

growth_protocol: Cells were cultured as spheres in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF). Intracranial xenografts were generated by implanting 5000 human derived GSCs into the right cerebral cortex of NSG mice.

extract_protocol:
Cells were collected in TriZol reagent and RNA was extracted using Rneasy Mini kit (Qiagen #74104)
RNA libraries were prepared for sequencing using standard rRNA depletion protocol

treatment_protocol: Transduced cells were selected with 2mg/ml Puromycin for 3 days.

tag: growth conditions

value: Intracranial

tag: genotype

value: knockdown

tag: disease

value: Human glioblastoma


title: 1919_shDPY30_3_IC


title: KYSE140_RNA_sg_NC1

value: CRISPRi sg-NC#1


title: KYSE140_RNA_sgSOX2_3

value: CRISPR sg-SOX2#3


title: KYSE140_RNA_sg_e1_2

value: CRISPRi sg-e1#2


title: BC3


title: 3565_shCONT_2_IC

value: control


title: biPSC_3

data_processing:
The quality of raw reads was checked using FastQC before aligning to bovine reference genome (ARS UCD 1.2) using R package STAR
Differentially expressed genes were identified using R package EdgeR

source_name: induced pluripotent cells from embryonic fibroblasts

growth_protocol: Bovine induced pluripotent cells were grown in GMTi medium supplemented with 1% non-essential amino acids and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated using RNAqueous Micro Total RNA isolation kit.
mRNA was captured using poly (A) and cDNA libraries were prepared using TruSeq stranded total RNA sample preparation kit (Illumina)

treatment_protocol: No treatments

value: Reprogrammed bovine embryonic fibroblasts


title: 3565_shCONT_1_IC


title: SKMES1_sg_e1_1_HiChIP_H3K27ac_A

library_source: genomic

data_processing:
library strategy: HiChIP
HiC-Pro to align sequencing reads
hichipper to identify chromatin loops connecting H3K27ac anchors
Genome_build: hg19
Supplementary_files_format_and_content: mango text file in bedpe format. Rows are interactions (loops). Columns are chromosome1, start1, end1, chromosome2, start2, end2, PETs, the adjusted P-value

molecule: genomic DNA

extract_protocol:
HiChIP protocol (Mumbach et al., 2016, Nature Methods) to enrich DNA fragments that are in proximity with each other
Illumina Tagment DNA Enzyme and Buffer Kit (Illumina 20034197)

value: Lung squamous cancer cell line

value: CRISPRa sg-e1#1

tag: hichip antibody

value: H3K27ac (Active Motif, 39133)


title: 3565_shDPY30_1_IC


title: ADorLJ2

value: enlarging growth of bulb


title: SKMES1_sg_e1_1_HiChIP_H3K27ac_B


title: KYSE140_RNA_sg_NC2

value: Esophageal squamous cancer cell line

value: CRISPRi sg-NC#2


title: 1919_shDPY30_1_IC


title: biPSC_2


title: RERFLCAI_HiChIP_H3K27ac

value: RERFLCAI

value: untreated

value: H3K27ac (Abcam ab4729)


title: BC2

value: In vitro fertilized bovine blastocysts

value: 7 days


title: KYSE140_RNA_DMSO6hrs_A

value: DMSO 6hrs


title: THP1_Input_0.5mil_EtOH_Precipitation_STD_LP

city: Watertown

first: Eric

last: Olson

state: MA

address: 480 Arsenal Street

institute: Syros Pharmaceuticals

data_processing:
Aligned to hg19 using bowtie2-2.0.5/bowtie2 with configuration -p 4 --sensitive
ChIP-seq reads were aligned to the hg19 genome assembly
Genome_build: hg19
Supplementary_files_format_and_content: TDF files(s) represent counts of aligned reads within 1 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

growth_protocol: THP1 cells were purchased from ATCC and cultured according to vendor’s instruction at 37°C in 5% CO2 and in a humidified incubator.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

tag: cancer

value: Acute Myeloid Leukemia

tag: chip antibody

tag: syros chip-seq protocol

value: A (SOP, Greater than 500k cells)


title: 1919_shDPY30_2_IC

value: Intracranial

value: knockdown

value: Human glioblastoma


title: HCC15_HiChIP_H3K27ac

value: Lung squamous cancer cell line


title: KYSE140_RNA_sgAAVS1

value: CRISPR sg-AAVS1


title: LK2_HiChIP_H3K27ac


title: 1919_shCONT_4_IC

value: control


title: SKMES1_sg_NC1_HiChIP_H3K27ac_B

value: CRISPRa sg-NC#1

value: H3K27ac (Active Motif, 39133)


title: GSC-Stat5b-knockdown

type: RNA

city: kyoto

first: Chiami

last: Moyama

address: Misasagi-Nakauchicho 5, Yamashina-ku

country: Japan

institute: Kyoto Pharmaceutical University

hyb_protocol: 100 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray Ver2.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

organism: Mus musculus

source_name: murine glioblastoma stem cell line

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The glioblastoma stem cell line was established with the neurosphere method from SB transposon-mediated de novo murine glioblastomas. The tumor tissues were minced with scalpels and digested with accutase (Innovative Cell Technologies, San Diego, CA, USA) at 37˚C for 20–30 min, and then washed and incubated with serum-free neural stem cell culture medium consisting of Neurobasal Medium supplemented with B27, N2 (Gibco/Thermo Fisher Scientific, Waltham, MA, USA), and 10 ng/ml EGF and bFGF (R&D Systems, Minneapolis, MN, USA). The neurospheres were dissociated by accutase (Innovative Cell Technologies) and maintained in the neural stem cell culture medium at 37°C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted from the cells lysed with Trizol (Thermo Fisher Scientific, Waltham, MA) and purified with the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: Stably Stat5b-knockdown glioblastoma stem cells were established via lentiviral-mediated shRNA. The cells were transducted with lentiviral non-target (control) or Stat5b shRNA.

value: glioblastoma stem cell line


title: JLMG_LowCell_400k

value: H3K27Ac (Abcam, Catalog 4729)

value: SOP (low-cell)


title: SKMES1_sg_NC1_HiChIP_H3K27ac_A


title: GSC-control


title: 1919_shCONT_3_IC


title: H520_HiChIP_H3K27ac

value: untreated

value: H3K27ac (Abcam ab4729)


title: 1919_shCONT_1_IC


title: KYSE140_ARV2hrs_HiChIP_H3K27ac_A

value: Esophageal squamous cancer cell line

value: 0.5uM ARV771 2hrs


title: biPSC_1

value: Reprogrammed bovine embryonic fibroblasts


title: 1919_shCONT_2_IC


title: KYSE140_DMSO2hrs_HiChIP_H3K27ac_A

value: DMSO 2hrs


title: 3565_shDPY30_2_CC

source_name: Glioblastoma stem cell culture

value: Cell culture


title: 3565_shDPY30_1_CC

value: knockdown


title: NJH29_shScr_8A

city: Stanford

first: Sandra

last: Cristea

state: California

address: 265 Campus Drive, G2065

department: Cancer Biology

institute: Stanford University

data_processing:
Alignment to genome: Murine KP1 sample reads (on average, 25 million reads per sample) were mapped to mouse reference genome mm10 with STAR2.5.1b using default settings with an average overall mapping rate of 92% and a 72% average mapping rate to genes. Human NJH29 sample reads (on average, 28 million reads per sample), were mapped to the human reference genome hg19 with STAR2.5.1b using default settings with an average overall mapping rate of 97%, and a 83% average mapping rate to genes.
Manual curation step: Genes that had at least 5 counts in two replicates of two conditions were used for further analysis.
Differentially expressed genes: Differentially expressed genes were obtained using DEseq2
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: excel file (xlsx) including counts, FPM, log2Foldchanges and p values for all genes used for further analysis after curation stage, for both KP1 and NJH29 samples, in different sheets.

source_name: hSCLC NJH29 with shScr replicate #1

growth_protocol: Before infection with shRNA constructs, mSCLC KP1 cells and hSCLC NJH29 cells were grown in RPMI-1640 media supplemented with 10% bovine growth serum (BGS) (Fisher Scientific) and penicillin-streptomycin-glutamine (Gibco). After infection with respective lentiviral shRNA constructs in triplicate, the cells were subjected to 4 days of puromycin (ThermoFisher cat # A1113803) selection (2µg/mL for mSCLC cells and 2.5µg/mL for hSCLC cells), then allowed to recover for 1-2 days without puromycin, and expanded for 3-4 days in 2% serum RPMI media.

extract_protocol:
RNA extraction was performed using the RNeasy mini kit (Qiagen 74104).
RNASeq libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina RS-122-2101) using 1 ug of RNA from each sample, once knockdowns of all samples were confirmed by quantitative PCR analysis, and RNA integrity was checked by BioAnalyzer (Agilent), (RIN>9).
For mSCLC KP1 cells, 3 independently-transfected instances of each hairpin cell line (2 hairpins against MEK5, 2 against ERK5, as well as 2 control hairpins, shGFP and shScr) were barcoded for multiiplexing, pooled and sequenced in a single run of the NextSeq500, generating on average of 20 million paired-end (2x75) uniquely mapped reads per sample. One of the triplicates of KP1-shErk5-2 was excluded from the analysis due low uniquely mapped reads (0.68 million) compared to the other samples, and is therefore not present in this submission). For hSCLC NJH29 cells, 3 independently-transfected instances of each hairpin cell line (2 hairpins against Mek5 and 2 controls hairpins, shGFP and shScr) were barcoded for multiiplexing, pooled and sequenced in a separate NextSeq500 run, generating on average 25 million paired-end (2x75) uniquely mapped reads per sample.

value: human small cell lung cancer-derived cell line

tag: strain


title: NJH29_shScr_8B

source_name: hSCLC NJH29 with shScr replicate #2


title: NJH29_shScr_8C

source_name: hSCLC NJH29 with shScr replicate #3


title: KYSE140_DMSO2hrs_HiChIP_H3K27ac_B


title: NJH29_shGFP_7C

source_name: hSCLC NJH29 with shGFP replicate #3


title: NJH29_shGFP_7B

source_name: hSCLC NJH29 with shGFP replicate #2


title: TT_HiChIP_H3K27ac

value: TT


title: THP1_6H_FLAVO_rep3

description: Gene expression data from THP1 cells treated with FLAVO for 6 hours

hyb_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities

data_processing: Data was processed using the Bioconductor package affy using RMA normalization using the command expresso(raw_data, bgcorrect.method=rma, normalize=TRUE, pmcorrect.method=pmonly, summary.method=medianpolish). This was followed by loess normalization to ERCC spike ins.

label: biotin

extract_protocol: Cells were washed twice with cold PBS before dissolved in trizol. Total RNA isolation was performed following mirVana miRNA isolation kit total RNA extraction protocol.

treatment_protocol: Cells were treated with SY-1365 100nM, NVP2 25nM, Flavopiridol 200nM, JQ1 250nM or DMSO vehicle treatment for 2 or 6hrs. Total RNA was extracted at the timepoint with trizol

tag: disease state

value: Acute Myeloid Leukemia

value: AML cell line  THP-1

tag: agent

value: FLAVO

tag: time

value: 6 hours


title: KYSE70_HiChIP_H3K27ac


title: 3565_shCONT_2_CC

value: control

value: Human glioblastoma


title: THP1_6H_FLAVO_rep1

scan_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities

source_name: THP1 cells treated with FLAVO for 6 hours


title: NJH29_shMek5_3C

source_name: hSCLC NJH29 with shMek5 hairpin #2 replicate #3


title: THP1_6H_FLAVO_rep2

label_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities


title: THP1_6H_NVP2_rep3

description: Gene expression data from THP1 cells treated with NVP2 for 6 hours


title: THP1_6H_NVP2_rep1

source_name: THP1 cells treated with NVP2 for 6 hours


title: KYSE140_HiChIP_H3K27ac_B


title: THP1_6H_JQ1_rep3

description: Gene expression data from THP1 cells treated with JQ1 for 6 hours

source_name: THP1 cells treated with JQ1 for 6 hours


title: 1919_shDPY30_CC


title: KYSE140_HiChIP_H3K27ac_A


title: 3565_shCONT_1_CC


title: NJH29_shGFP_7A

source_name: hSCLC NJH29 with shGFP replicate #1


title: NJH29_shMek5_3B

source_name: hSCLC NJH29 with shMek5 hairpin #2 replicate #2


title: NJH29_shMek5_3A

source_name: hSCLC NJH29 with shMek5 hairpin #2 replicate #1


title: KYSE140_CTCF

data_processing:
Bowtie2 to align sequencing reads
MACS2 to identify ChIP-seq peaks and calculate Signal Per Million Reads (SPMR)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (bw)

extract_protocol:
Chromatin immunoprecipitation using antibodies to enrich DNA fragments
NEBNext DNA Ultra II library prep kit (E7645S)

value: CTCF (Cell Signaling, 2899)


title: KYSE140_SOX2

value: untreated

value: SOX2 (R&D Systems, AF2018)


title: 3565 TC

data_processing:
ChIP-seq reads were trimmed using Trim Galore v0.4.3 and cutadapt 1.14.
Reads were aligned to the hg19 human genome with BWA-MEM v0.7.17.
BAM files were processed using SAMtools and PCR duplicates were removed with PicardTools.
H3K4me3 peaks were called using MACS2 (v2.1.1) using a ChIP input file as a control using default settings.
BIGWIG track coverage files were generated from merged BAM files using the DeepTools (v2.4.1) bamCoverage command with RPKM normalization .
Genome_build: hg19
Supplementary_files_format_and_content: BigWig .

source_name: Patient derived glioblastoma stem cell

extract_protocol:
Cells were fixed with 1% formaldehyde at room temperature for 10 minutes, and the reaction was subsequently quenched with 0.125 M glycine. Then, the cells were washed with cold PBS and suspended with lysis buffer supplemented with Protease Inhibitor Cocktail II. Chromatin was sonicated to obtain DNA fragments with an average length of 200-500 bp by a Bioruptor Pico sonication device (Diagenode) followed by centrifugation for clearing. The soluble fraction of sheared chromatin was diluted 10-fold with ChIP dilution buffer and incubated with 5L H3K4me3 antibody (Cat# 39159, Active Motif) conjugated to EZ-Magna ChIP A/G magnetic beads overnight at 4°C with rotation. Chromatin-captured beads were washed once with low salt wash buffer, once with high salt wash buffer, once with LiCl wash buffer and once with TE buffer for 10 min each by rotation at 4°C. Beads were resuspended in elution buffer and the supernatant was removed by magnet. Proteinase K was added to the eluted DNA followed by incubation at 62°C for 4 hours and 95°C for 10 minutes with shaking. Reverse-crosslinked DNA was purified by using purification columns and quantified by using PicoGreen 628 (Invitrogen).
Eluted DNA was used for sequencing library preparation or quantitative PCR (qPCR). Sequencing libraries were prepared using ThruPLEX® NGS Library Preparation Kits (Rubicon Genomics, R400427) according to manufacturer’s instruction. Following library amplification, DNA fragments were agarose gel (1.0%) size selected (<1 kb), analyzed using a Bioanalyzer (Agilent Technologies).
Libraries were sequenced at Genewiz by using Illumina HiSeq 2500 2x150-bp paired-end reads.

tag: sample type

value: Tissue culture

tag: antibody


title: NJH29_shMek5_1C

source_name: hSCLC NJH29 with shMek5 hairpin #1 replicate #3


title: 387 TC


title: THP1_6H_JQ1_rep2


title: GSC23 TC


title: NJH29_shMek5_1B

source_name: hSCLC NJH29 with shMek5 hairpin #1 replicate #2


title: NJH29_shMek5_1A

source_name: hSCLC NJH29 with shMek5 hairpin #1 replicate #1


title: KYSE140_ARV2hrs_BRD4_A

value: Esophageal squamous cancer cell line

value: 0.5uM ARV771 2hrs


title: 1919_shCONT_CC

source_name: Glioblastoma stem cell culture


title: KP1_shScr_6C

source_name: mSCLC KP1 with shScr replicate #3

value: murine small cell lung cancer-derived cell line


title: THP1_6H_1365_rep2

description: Gene expression data from THP1 cells treated with SY-1365 for 6 hours


title: THP1_6H_1365_rep3

source_name: THP1 cells treated with SY-1365 for 6 hours


title: 387 IC

value: Intracranial


title: KYSE140_DMSO2hrs_BRD4_A

value: DMSO 2hrs


title: KP1_shScr_6A

source_name: mSCLC KP1 with shScr replicate #1


title: THP1_6H_1365_rep1


title: THP1_6H_DMSO_rep3

description: Gene expression data from THP1 cells treated with DMSO for 6 hours

value: DMSO


title: THP1_6H_DMSO_rep2

source_name: THP1 cells treated with DMSO for 6 hours


title: THP1_6H_JQ1_rep1


title: 3565 IC


title: KYSE140_ARV2hrs_BRD4_B


title: THP1_6H_NVP2_rep2


title: KP1_shScr_6B

source_name: mSCLC KP1 with shScr replicate #2


title: IN528TC


title: THP1_6H_DMSO_rep1


title: 1919 TC


title: KP1_shGFP_5C

source_name: mSCLC KP1 with shGFP replicate #3


title: KP1_shGFP_5A

source_name: mSCLC KP1 with shGFP replicate #1


title: IN528 IC


title: HSC4_sg_NC1_BRD4

value: Head and neck squamous cancer cell line

value: CRISPRi sg-NC#1


title: HSC4_sg_e1_1_BRD4

value: CRISPRi sg-e1#1


title: KP1_shGFP_5B

source_name: mSCLC KP1 with shGFP replicate #2


title: THP1_2H_FLAVO_rep3

description: Gene expression data from THP1 cells treated with FLAVO for 2 hours

value: Acute Myeloid Leukemia

value: AML cell line  THP-1

value: FLAVO

value: 2 hours


title: KYSE140_DMSO2hrs_BRD4_B


title: 1919 IC


title: H520_sg_e1_1_BRD4

value: Lung squamous cancer cell line


title: LK2_sg_e1_1_BRD4


title: KP1_shMek5_4B

source_name: mSCLC KP1 with shMek5 hairpin #2 replicate #2


title: KP1_shMek5_4A

source_name: mSCLC KP1 with shMek5 hairpin #2 replicate #1


title: THP1_2H_FLAVO_rep2

source_name: THP1 cells treated with FLAVO for 2 hours


title: KP1_shMek5_4C

source_name: mSCLC KP1 with shMek5 hairpin #2 replicate #3


title: THP1_2H_NVP2_rep3

description: Gene expression data from THP1 cells treated with NVP2 for 2 hours


title: LK2_sg_NC1_BRD4


title: IN528 Input

source_name: Patient derived glioblastoma stem cell

value: Input


title: GSC23 IC


title: 387 Input


title: KYSE140_sg_e1_1_BRD4


title: KP1_shMek5_3C

source_name: mSCLC KP1 with shMek5 hairpin #1 replicate #3


title: H520_sg_NC1_BRD4


title: KYSE140_sg_e1_2_BRD4

value: CRISPRi sg-e1#2


title: 3565 Input


title: KYSE140_sg_NC2_BRD4

value: CRISPRi sg-NC#2


title: 1919 Input


title: GSC23 Input


title: KP1_shMek5_3A

source_name: mSCLC KP1 with shMek5 hairpin #1 replicate #1


title: KYSE140_ARV2hrs_HiChIP_H3K27ac_B

value: Esophageal squamous cancer cell line

value: H3K27ac (Abcam ab4729)


title: KP1_shErk5_2B

source_name: mSCLC KP1 with shErk5 hairpin #2 replicate #2

value: murine small cell lung cancer-derived cell line


title: THP1_2H_FLAVO_rep1


title: KYSE140_sg_NC1_BRD4


title: THP1_2H_JQ1_rep3

description: Gene expression data from THP1 cells treated with JQ1 for 2 hours

source_name: THP1 cells treated with JQ1 for 2 hours


title: THP1_2H_NVP2_rep1

source_name: THP1 cells treated with NVP2 for 2 hours


title: THP1_2H_NVP2_rep2


title: THP1_2H_JQ1_rep2


title: THP1_2H_JQ1_rep1


title: KYSE140_ARV2hrs_H3K27ac_B

value: 0.5uM ARV771 2hrs


title: hepatocellular carcinoma, 6A (miRNAseq)

city: zhongshan

first: yongyan

last: pei

address: Long life water, wuguishan street, zhongshan city

department: School of Pharmaceutical and Chemical Engineering

institute: Guangdong Pharmaceutical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of transcripts per million (TPM) 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.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene tpm values for every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every sample

source_name: hepatocellular carcinoma

extract_protocol:
Samples tissues were immediately frozen in liquid nitrogen or stored at − 80 ° C after the surgery.Total RNA of tissue was extracted using the RNeasy Mini Kit (Qiagen, USA) according to the manufacturer’s protocol. Then the extracted RNA was qualitatively controlled and quantified by Nanodrop.
The RNA library was constructed using TruSeq RNA sample preparation kit and TruSeq Small RNA (Illumina, USA). After purification, the library was quantified with Qubit 8000 (Life Technologies, USA) and verified with Agilent 2100 (Agilent Technologies, USA) to confirm the fragment size

tag: tissue

value: hepatocellular carcinoma


title: KP1_shErk5_2A

source_name: mSCLC KP1 with shErk5 hairpin #2 replicate #1


title: KP1_shMek5_3B

source_name: mSCLC KP1 with shMek5 hairpin #1 replicate #2


title: adjacent tissue, 6B (miRNAseq)

source_name: adjacent tissue

value: adjacent tissue


title: THP1_2H_1365_rep3

description: Gene expression data from THP1 cells treated with SY-1365 for 2 hours

tag: cell line


title: KP1_shErk5_1C

source_name: mSCLC KP1 with shErk5 hairpin #1 replicate #3

tag: cell type


title: THP1_2H_1365_rep2

source_name: THP1 cells treated with SY-1365 for 2 hours


title: KYSE140_DMSO2hrs_H3K27ac_A

tag: treatment

value: DMSO 2hrs


title: KYSE140_DMSO2hrs_H3K27ac_B


title: hepatocellular carcinoma, 5A (miRNAseq)


title: hepatocellular carcinoma, 1A (miRNAseq)


title: KYSE140_ARV2hrs_H3K27ac_A


title: adjacent tissue, 5B (miRNAseq)


title: THP1_2H_1365_rep1


title: KP1_shErk5_1A

source_name: mSCLC KP1 with shErk5 hairpin #1 replicate #1


title: KYSE140_H3K27ac

value: untreated


title: adjacent tissue, 1B (miRNAseq)


title: KP1_shErk5_1B

source_name: mSCLC KP1 with shErk5 hairpin #1 replicate #2


title: THP1_2H_DMSO_rep3

description: Gene expression data from THP1 cells treated with DMSO for 2 hours

value: DMSO


title: THP1_2H_DMSO_rep1

source_name: THP1 cells treated with DMSO for 2 hours

value: Acute Myeloid Leukemia


title: THP1_2H_DMSO_rep2

value: AML cell line  THP-1


title: HT29_ORF_POP7_2215

status: Public on Oct 16 2021

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

country: Canada

institute: Montreal Heart Institute

hyb_protocol: Samples were blocked with Agilent blocking reagent and incubated for 17h at 65C in the Agilent Microarray Hybridization oven

scan_protocol: Agilent SureScan Microarray scanner

data_processing:
We used Limma v3.26.9 and sva v3.18.0 packages (Bioconductor v3.1-3.2) to load the fluorescence intensity files and handle the data into R V3.2.0. Arrays failing Agilent quality control according to the Agilent Feature Extraction software were flagged.  Manual quality control of each array was also performed.
Quality control was performed within each batch of arrays. Fluorescence signal was processed to remove local background (bakgroundCorrect, method “normexp”) and then normalized using cyclic loess algorithm.
Batch effects were then corrected using ComBat for known batches and sva for unknown systematic artefacts (both from sva library v3.18.0). Given the experiment was performed in three parts (E1-E4 & P7, E5-E11, E14-E15), the batches from each part were combined first and then combined together.
To reduce impact of residual background, noise and batch effects on very low expression values, the fluorescence intensity values were truncated at 8, and translated down by the same amount.
Duplicated probes were combined, and repeated samples removed. The truncating threshold was determined based on the distribution of negative control probes and detected vs non-detected signals. Data provided includes only samples included in the final dataset.

source_name: HT-29 POP7 transduction, UniqueID 2215

label_protocol: Agilent One-Color Microarray-Based Exon Analysis Low Input Quick Amp WT Labeling kit using Cyanine 3-CTP label.

growth_protocol: The colorectal adenocarcinoma cell line HT-29 (ATCC HTB-38) was maintained at confluence between 20% and 80% at all times in McCoy’s 5A (Wisent, 317-010CL) 10% FBS. All experiments described herein were performed in cell at passages below 25.

extract_protocol:
The RNeasy Plus Mini kit (#74036, Qiagen Inc Canada) according to manufacturer’s protocol.
The RNA samples were quantified, and quality controlled using an Agilent RNA 6000 Nano kit (Agilent, Cat No./ID 5067-1511) on 2100 Bioanalyzer system.
Number (RIN) below 8 were discarded; RIN values were routinely in the range of 9.2-10

treatment_protocol:
ORFs for IBD gene candidates were cloned into a GATEWAY® compatible polycistronic lentiviral expression vector, pLVX-EF1a-IRES-PURO/eGFP expressing an enhanced green fluorescent protein (eGFP) and puromycin N-acetyl-transferase fusion protein.
Proliferative HT-29 cells at 50% confluency in 12 well plate (Corning) were transduced in triplicate with the different ORFs (multiplicity of infection) MOI of 40-100 with 8µg/ml of polybrene (Sigma, Cat: H-9268).
Twenty-four hours post-transduction, media was changed and 3ug/ml puromycin (Millipore Sigma) was added.
The appearance and confluence of the cultures were recorded daily, and cells were grown for an average of 8 days (with a range of 5-27 days) to select successfully transduced cells and reach confluence before RNA extraction.
Transduction of the whole set of IBD gene candidate ORFs was performed in batches of about 15 ORFs, each done in triplicate, and including an empty vector control.

tag: orf

tag: uniqueid

tag: arraybatch

tag: transductiondate


title: HT29_ORF_GPR35_2185

source_name: HT-29 GPR35 transduction, UniqueID 2185


title: HT29_ORF_ADO_2173

source_name: HT-29 ADO transduction, UniqueID 2173

value: ADO


title: HT29_ORF_PPM1G_2217

source_name: HT-29 PPM1G transduction, UniqueID 2217


title: HT29_ORF_ZFP90_2242

source_name: HT-29 ZFP90 transduction, UniqueID 2242


title: HT29_ORF_JAK2_2203

source_name: HT-29 JAK2 transduction, UniqueID 2203


title: HT29_ORF_CISD1_2176

source_name: HT-29 CISD1 transduction, UniqueID 2176


title: HT29_ORF_Empty_2239

source_name: HT-29 Empty transduction, UniqueID 2239

value: Empty


title: HT29_ORF_POP7_2214

source_name: HT-29 POP7 transduction, UniqueID 2214


title: HT29_ORF_PNKD_2211

source_name: HT-29 PNKD transduction, UniqueID 2211

value: PNKD


title: HT29_ORF_TSPAN14_2236

source_name: HT-29 TSPAN14 transduction, UniqueID 2236


title: HT29_ORF_PPM1G_2218

source_name: HT-29 PPM1G transduction, UniqueID 2218


title: HT29_ORF_CISD1_2175

source_name: HT-29 CISD1 transduction, UniqueID 2175


title: HT29_ORF_JAZF1_2205

source_name: HT-29 JAZF1 transduction, UniqueID 2205


title: HT29_ORF_IFIH1_2190

source_name: HT-29 IFIH1 transduction, UniqueID 2190


title: HT29_ORF_ZFP90_2241

source_name: HT-29 ZFP90 transduction, UniqueID 2241


title: HT29_ORF_JAZF1_2206

source_name: HT-29 JAZF1 transduction, UniqueID 2206


title: HT29_ORF_TSPAN14_2235

source_name: HT-29 TSPAN14 transduction, UniqueID 2235


title: HT29_ORF_TSPAN14_2234

source_name: HT-29 TSPAN14 transduction, UniqueID 2234


title: HT29_ORF_MAGI3_2209

source_name: HT-29 MAGI3 transduction, UniqueID 2209


title: HT29_ORF_Empty_2237

source_name: HT-29 Empty transduction, UniqueID 2237


title: HT29_ORF_SBNO2_2225

source_name: HT-29 SBNO2 transduction, UniqueID 2225


title: HT29_ORF_GPR35_2184

source_name: HT-29 GPR35 transduction, UniqueID 2184


title: HT29_ORF_ADO_2172

source_name: HT-29 ADO transduction, UniqueID 2172


title: HT29_ORF_JAK2_2202

source_name: HT-29 JAK2 transduction, UniqueID 2202


title: HT29_ORF_PNKD_2212

source_name: HT-29 PNKD transduction, UniqueID 2212


title: HT29_ORF_ZFP90_2240

source_name: HT-29 ZFP90 transduction, UniqueID 2240


title: HT29_ORF_MAGI3_2208

source_name: HT-29 MAGI3 transduction, UniqueID 2208


title: HT29_ORF_PPM1G_2216

source_name: HT-29 PPM1G transduction, UniqueID 2216


title: HT29_ORF_Empty_2147

source_name: HT-29 Empty transduction, UniqueID 2147


title: HT29_ORF_JAK2_2201

source_name: HT-29 JAK2 transduction, UniqueID 2201


title: HT29_ORF_Empty_2149

source_name: HT-29 Empty transduction, UniqueID 2149


title: HT29_ORF_NOD2_2135

source_name: HT-29 NOD2 transduction, UniqueID 2135


title: HT29_ORF_MAGI3_2207

source_name: HT-29 MAGI3 transduction, UniqueID 2207


title: HT29_ORF_CISD1_2174

source_name: HT-29 CISD1 transduction, UniqueID 2174


title: HT29_ORF_ADO_2171

source_name: HT-29 ADO transduction, UniqueID 2171


title: HT29_ORF_NOD2_2137

source_name: HT-29 NOD2 transduction, UniqueID 2137


title: HT29_ORF_PNKD_2210

source_name: HT-29 PNKD transduction, UniqueID 2210


title: HT29_ORF_ATG16L1_2122_2

source_name: HT-29 ATG16L1 transduction, UniqueID 2122_2


title: HT29_ORF_STAT3_324

source_name: HT-29 STAT3 transduction, UniqueID 324


title: HT29_ORF_ZBTB40_2145

source_name: HT-29 ZBTB40 transduction, UniqueID 2145


title: HT29_ORF_IKZF1_2113_2

source_name: HT-29 IKZF1 transduction, UniqueID 2113_2


title: HT29_ORF_POP7_2213

source_name: HT-29 POP7 transduction, UniqueID 2213


title: HT29_ORF_CDKAL1_2126

source_name: HT-29 CDKAL1 transduction, UniqueID 2126


title: HT29_ORF_JAZF1_2204

source_name: HT-29 JAZF1 transduction, UniqueID 2204


title: HT29_ORF_DUSP16_2177

source_name: HT-29 DUSP16 transduction, UniqueID 2177


title: HT29_ORF_ZBTB40_2146

source_name: HT-29 ZBTB40 transduction, UniqueID 2146


title: HT29_ORF_ERRFI1_54_2

source_name: HT-29 ERRFI1 transduction, UniqueID 54_2


title: HT29_ORF_ZBTB40_2144

source_name: HT-29 ZBTB40 transduction, UniqueID 2144


title: HT29_ORF_RASGRP1_394

source_name: HT-29 RASGRP1 transduction, UniqueID 394


title: HT29_ORF_IKZF1_2112_2

source_name: HT-29 IKZF1 transduction, UniqueID 2112_2


title: HT29_ORF_SYT11_445

source_name: HT-29 SYT11 transduction, UniqueID 445


title: HT29_ORF_Empty_2148

source_name: HT-29 Empty transduction, UniqueID 2148


title: HT29_ORF_SYT11_443

source_name: HT-29 SYT11 transduction, UniqueID 443


title: HT29_ORF_CDKAL1_2127

source_name: HT-29 CDKAL1 transduction, UniqueID 2127


title: HT29_ORF_ETS2_55_2

source_name: HT-29 ETS2 transduction, UniqueID 55_2


title: HT29_ORF_NOD2_2136

source_name: HT-29 NOD2 transduction, UniqueID 2136


title: HT29_ORF_STAT3_323

source_name: HT-29 STAT3 transduction, UniqueID 323


title: HT29_ORF_IKZF1_2111_2

source_name: HT-29 IKZF1 transduction, UniqueID 2111_2


title: HT29_ORF_SYT11_444

source_name: HT-29 SYT11 transduction, UniqueID 444


title: HT29_ORF_ZFP36L1_250_2

source_name: HT-29 ZFP36L1 transduction, UniqueID 250_2


title: HT29_ORF_ERRFI1_53_2

source_name: HT-29 ERRFI1 transduction, UniqueID 53_2


title: HT29_ORF_ETS2_56_2

source_name: HT-29 ETS2 transduction, UniqueID 56_2


title: HT29_ORF_RSPO3_2041

source_name: HT-29 RSPO3 transduction, UniqueID 2041


title: HT29_ORF_UBAC2_2002

source_name: HT-29 UBAC2 transduction, UniqueID 2002


title: HT29_ORF_PSMG1_169

source_name: HT-29 PSMG1 transduction, UniqueID 169


title: HT29_ORF_ZGPAT_467

source_name: HT-29 ZGPAT transduction, UniqueID 467

value: ZGPAT


title: HT29_ORF_TYK2_2116

source_name: HT-29 TYK2 transduction, UniqueID 2116


title: HT29_ORF_ZFP91_258

source_name: HT-29 ZFP91 transduction, UniqueID 258


title: HT29_ORF_KSR1_115

source_name: HT-29 KSR1 transduction, UniqueID 115


title: HT29_ORF_STAT3_322

source_name: HT-29 STAT3 transduction, UniqueID 322


title: HT29_ORF_GPR12_2028

source_name: HT-29 GPR12 transduction, UniqueID 2028


title: HT29_ORF_SLAIN2_496

source_name: HT-29 SLAIN2 transduction, UniqueID 496


title: HT29_ORF_PTGER4_391

source_name: HT-29 PTGER4 transduction, UniqueID 391


title: HT29_ORF_SLC26A3_204

source_name: HT-29 SLC26A3 transduction, UniqueID 204


title: HT29_ORF_IRF5_2125

source_name: HT-29 IRF5 transduction, UniqueID 2125


title: HT29_ORF_PITX1_2032

source_name: HT-29 PITX1 transduction, UniqueID 2032


title: HT29_ORF_RPL3_2068

source_name: HT-29 RPL3 transduction, UniqueID 2068


title: HT29_ORF_ERRFI1_54

source_name: HT-29 ERRFI1 transduction, UniqueID 54


title: HT29_ORF_MAP3K8_2023_2

source_name: HT-29 MAP3K8 transduction, UniqueID 2023_2


title: HT29_ORF_DLD_48

source_name: HT-29 DLD transduction, UniqueID 48

value: DLD


title: HT29_ORF_IRF1_2119

source_name: HT-29 IRF1 transduction, UniqueID 2119


title: HT29_ORF_KPNA7_2108

source_name: HT-29 KPNA7 transduction, UniqueID 2108


title: HT29_ORF_SBNO2_487

source_name: HT-29 SBNO2 transduction, UniqueID 487


title: HT29_ORF_PEX3_159

source_name: HT-29 PEX3 transduction, UniqueID 159


title: HT29_ORF_FOXD1_2014

source_name: HT-29 FOXD1 transduction, UniqueID 2014


title: HT29_ORF_IPMK_99

source_name: HT-29 IPMK transduction, UniqueID 99

value: IPMK


title: HT29_ORF_CEP72_288

source_name: HT-29 CEP72 transduction, UniqueID 288


title: HT29_ORF_Empty_2238

source_name: HT-29 Empty transduction, UniqueID 2238


title: HT29_ORF_HINT1_454

source_name: HT-29 HINT1 transduction, UniqueID 454


title: HT29_ORF_FIBP_448

source_name: HT-29 FIBP transduction, UniqueID 448

value: FIBP


title: HT29_ORF_ATG16L1_2122

source_name: HT-29 ATG16L1 transduction, UniqueID 2122


title: HT29_ORF_UBQLN4_243

source_name: HT-29 UBQLN4 transduction, UniqueID 243


title: HT29_ORF_MAP3K8_2022_2

source_name: HT-29 MAP3K8 transduction, UniqueID 2022_2


title: HT29_ORF_CARD9_2011

source_name: HT-29 CARD9 transduction, UniqueID 2011


title: HT29_ORF_GPR12_2029

source_name: HT-29 GPR12 transduction, UniqueID 2029


title: HT29_ORF_CHP1_27

source_name: HT-29 CHP1 transduction, UniqueID 27


title: HT29_ORF_NKX2-3_379

source_name: HT-29 NKX2-3 transduction, UniqueID 379


title: HT29_ORF_TMEM258_231

source_name: HT-29 TMEM258 transduction, UniqueID 231


title: HT29_ORF_ASXL1_463

source_name: HT-29 ASXL1 transduction, UniqueID 463


title: HT29_ORF_NFKB1_2083

source_name: HT-29 NFKB1 transduction, UniqueID 2083


title: HT29_ORF_ATG5_2008

source_name: HT-29 ATG5 transduction, UniqueID 2008


title: HT29_ORF_IRGM_2059

source_name: HT-29 IRGM transduction, UniqueID 2059

value: IRGM


title: HT29_ORF_ERAP2_302

source_name: HT-29 ERAP2 transduction, UniqueID 302


title: HT29_ORF_ATG16L1_2120

source_name: HT-29 ATG16L1 transduction, UniqueID 2120


title: HT29_ORF_AIRE_2044

source_name: HT-29 AIRE transduction, UniqueID 2044

value: AIRE


title: HT29_ORF_CARD9_2010

source_name: HT-29 CARD9 transduction, UniqueID 2010


title: HT29_ORF_USP25_2004

source_name: HT-29 USP25 transduction, UniqueID 2004


title: HT29_ORF_HDAC7_451

source_name: HT-29 HDAC7 transduction, UniqueID 451


title: HT29_ORF_MAP3K8_2021_2

source_name: HT-29 MAP3K8 transduction, UniqueID 2021_2


title: HT29_ORF_GPBAR1_472

source_name: HT-29 GPBAR1 transduction, UniqueID 472


title: HT29_ORF_PTPN1_460

source_name: HT-29 PTPN1 transduction, UniqueID 460


title: HT29_ORF_SLAIN2_494

source_name: HT-29 SLAIN2 transduction, UniqueID 494


title: HT29_ORF_TYK2_2115

source_name: HT-29 TYK2 transduction, UniqueID 2115


title: HT29_ORF_PTPN1_459

source_name: HT-29 PTPN1 transduction, UniqueID 459


title: HT29_ORF_KSR1_117

source_name: HT-29 KSR1 transduction, UniqueID 117


title: HT29_ORF_RASGRP1_393

source_name: HT-29 RASGRP1 transduction, UniqueID 393


title: HT29_ORF_IRF1_2118

source_name: HT-29 IRF1 transduction, UniqueID 2118


title: HT29_ORF_NFKB1_2082

source_name: HT-29 NFKB1 transduction, UniqueID 2082


title: HT29_ORF_UBAC2_2001

source_name: HT-29 UBAC2 transduction, UniqueID 2001


title: HT29_ORF_ATG5_2007

source_name: HT-29 ATG5 transduction, UniqueID 2007


title: HT29_ORF_NKX2-3_378

source_name: HT-29 NKX2-3 transduction, UniqueID 378


title: HT29_ORF_IRF5_2124

source_name: HT-29 IRF5 transduction, UniqueID 2124


title: HT29_ORF_RPL3_2067

source_name: HT-29 RPL3 transduction, UniqueID 2067


title: HT29_ORF_AIRE_2043

source_name: HT-29 AIRE transduction, UniqueID 2043


title: HT29_ORF_ERAP2_303

source_name: HT-29 ERAP2 transduction, UniqueID 303


title: HT29_ORF_FOXF1_2080

source_name: HT-29 FOXF1 transduction, UniqueID 2080


title: HT29_ORF_USP25_2005

source_name: HT-29 USP25 transduction, UniqueID 2005


title: HT29_ORF_SLC9A3_406

source_name: HT-29 SLC9A3 transduction, UniqueID 406


title: HT29_ORF_PEX3_158

source_name: HT-29 PEX3 transduction, UniqueID 158


title: HT29_ORF_ERAP2_301

source_name: HT-29 ERAP2 transduction, UniqueID 301


title: HT29_ORF_KPNA7_2109

source_name: HT-29 KPNA7 transduction, UniqueID 2109


title: HT29_ORF_PSMG1_171

source_name: HT-29 PSMG1 transduction, UniqueID 171


title: HT29_ORF_NRBP1_135

source_name: HT-29 NRBP1 transduction, UniqueID 135


title: HT29_ORF_NRBP1_134

source_name: HT-29 NRBP1 transduction, UniqueID 134


title: HT29_ORF_RPL3_2066

source_name: HT-29 RPL3 transduction, UniqueID 2066


title: HT29_ORF_IRGM_2058

source_name: HT-29 IRGM transduction, UniqueID 2058


title: HT29_ORF_FOXF1_2079

source_name: HT-29 FOXF1 transduction, UniqueID 2079


title: HT29_ORF_KPNA7_2110

source_name: HT-29 KPNA7 transduction, UniqueID 2110


title: HT29_ORF_ZGPAT_468

source_name: HT-29 ZGPAT transduction, UniqueID 468


title: HT29_ORF_YDJC_2070

source_name: HT-29 YDJC transduction, UniqueID 2070

value: YDJC


title: HT29_ORF_SLC22A4_400

source_name: HT-29 SLC22A4 transduction, UniqueID 400


title: HT29_ORF_HDAC7_450

source_name: HT-29 HDAC7 transduction, UniqueID 450


title: HT29_ORF_GPR12_2027

source_name: HT-29 GPR12 transduction, UniqueID 2027


title: HT29_ORF_CHP1_26

source_name: HT-29 CHP1 transduction, UniqueID 26


title: HT29_ORF_RSPO3_2040

source_name: HT-29 RSPO3 transduction, UniqueID 2040


title: HT29_ORF_UBAC2_2000

source_name: HT-29 UBAC2 transduction, UniqueID 2000


title: HT29_ORF_FOXF1_2078

source_name: HT-29 FOXF1 transduction, UniqueID 2078


title: HT29_ORF_GIGYF1_2026

source_name: HT-29 GIGYF1 transduction, UniqueID 2026


title: HT29_ORF_TTPAL_240

source_name: HT-29 TTPAL transduction, UniqueID 240

value: TTPAL


title: HT29_ORF_ZGPAT_469

source_name: HT-29 ZGPAT transduction, UniqueID 469


title: HT29_ORF_ZFP91_257

source_name: HT-29 ZFP91 transduction, UniqueID 257


title: HT29_ORF_ACTN1_489

source_name: HT-29 ACTN1 transduction, UniqueID 489


title: HT29_ORF_MTMR3_2077

source_name: HT-29 MTMR3 transduction, UniqueID 2077


title: HT29_ORF_GPBAR1_471

source_name: HT-29 GPBAR1 transduction, UniqueID 471


title: HT29_ORF_PSMG1_170

source_name: HT-29 PSMG1 transduction, UniqueID 170


title: HT29_ORF_IRF8_427

source_name: HT-29 IRF8 transduction, UniqueID 427


title: HT29_ORF_SLAIN2_495

source_name: HT-29 SLAIN2 transduction, UniqueID 495


title: HT29_ORF_TYK2_2114

source_name: HT-29 TYK2 transduction, UniqueID 2114


title: HT29_ORF_HINT1_453

source_name: HT-29 HINT1 transduction, UniqueID 453


title: HT29_ORF_CFL1_478

source_name: HT-29 CFL1 transduction, UniqueID 478


title: HT29_ORF_H2AFY_484

source_name: HT-29 H2AFY transduction, UniqueID 484


title: HT29_ORF_ACTN1_490

source_name: HT-29 ACTN1 transduction, UniqueID 490


title: HT29_ORF_NDFIP1_480

source_name: HT-29 NDFIP1 transduction, UniqueID 480


title: HT29_ORF_MTMR3_2076

source_name: HT-29 MTMR3 transduction, UniqueID 2076


title: HT29_ORF_NDFIP1_481

source_name: HT-29 NDFIP1 transduction, UniqueID 481


title: HT29_ORF_DLD_47

source_name: HT-29 DLD transduction, UniqueID 47


title: HT29_ORF_GIGYF1_2025

source_name: HT-29 GIGYF1 transduction, UniqueID 2025


title: HT29_ORF_FIBP_447

source_name: HT-29 FIBP transduction, UniqueID 447


title: HT29_ORF_AHRR_123

source_name: HT-29 AHRR transduction, UniqueID 123

value: AHRR


title: HT29_ORF_UBQLN4_241

source_name: HT-29 UBQLN4 transduction, UniqueID 241


title: HT29_ORF_SLC2A4RG_499

source_name: HT-29 SLC2A4RG transduction, UniqueID 499


title: HT29_ORF_NFKB1_2081

source_name: HT-29 NFKB1 transduction, UniqueID 2081


title: HT29_ORF_PPP5C_456

source_name: HT-29 PPP5C transduction, UniqueID 456


title: HT29_ORF_RORC_184

source_name: HT-29 RORC transduction, UniqueID 184

value: RORC


title: HT29_ORF_IPMK_98

source_name: HT-29 IPMK transduction, UniqueID 98


title: HT29_ORF_PEX3_157

source_name: HT-29 PEX3 transduction, UniqueID 157


title: HT29_ORF_YDJC_2069

source_name: HT-29 YDJC transduction, UniqueID 2069


title: HT29_ORF_ATG5_2006

source_name: HT-29 ATG5 transduction, UniqueID 2006


title: HT29_ORF_DLD_46

source_name: HT-29 DLD transduction, UniqueID 46


title: HT29_ORF_NR5A2_130

source_name: HT-29 NR5A2 transduction, UniqueID 130


title: HT29_ORF_CHP1_25

source_name: HT-29 CHP1 transduction, UniqueID 25


title: HT29_ORF_SLC2A4RG_498

source_name: HT-29 SLC2A4RG transduction, UniqueID 498


title: HT29_ORF_NRBP1_133

source_name: HT-29 NRBP1 transduction, UniqueID 133


title: HT29_ORF_SLC22A4_399

source_name: HT-29 SLC22A4 transduction, UniqueID 399


title: HT29_ORF_MTMR3_2075

source_name: HT-29 MTMR3 transduction, UniqueID 2075


title: HT29_ORF_Empty_2096

source_name: HT-29 Empty transduction, UniqueID 2096


title: HT29_ORF_SLC2A4RG_497

source_name: HT-29 SLC2A4RG transduction, UniqueID 497


title: HT29_ORF_FOXD1_2012

source_name: HT-29 FOXD1 transduction, UniqueID 2012


title: HT29_ORF_ZFP91_256

source_name: HT-29 ZFP91 transduction, UniqueID 256


title: HT29_ORF_TTPAL_239

source_name: HT-29 TTPAL transduction, UniqueID 239


title: HT29_ORF_Empty_2097

source_name: HT-29 Empty transduction, UniqueID 2097


title: HT29_ORF_SLC26A3_203

source_name: HT-29 SLC26A3 transduction, UniqueID 203


title: HT29_ORF_RSPO3_2039

source_name: HT-29 RSPO3 transduction, UniqueID 2039


title: HT29_ORF_Empty_2088

source_name: HT-29 Empty transduction, UniqueID 2088


title: HT29_ORF_SLC2A13_403

source_name: HT-29 SLC2A13 transduction, UniqueID 403


title: HT29_ORF_USP25_2003

source_name: HT-29 USP25 transduction, UniqueID 2003


title: HT29_ORF_CFL1_477

source_name: HT-29 CFL1 transduction, UniqueID 477


title: HT29_ORF_NKX2-3_377

source_name: HT-29 NKX2-3 transduction, UniqueID 377


title: HT29_ORF_PTGER4_390

source_name: HT-29 PTGER4 transduction, UniqueID 390


title: HT29_ORF_H2AFY_483

source_name: HT-29 H2AFY transduction, UniqueID 483


title: HT29_ORF_FOXD1_2013

source_name: HT-29 FOXD1 transduction, UniqueID 2013


title: HT29_ORF_TMEM258_230

source_name: HT-29 TMEM258 transduction, UniqueID 230


title: HT29_ORF_Empty_2087

source_name: HT-29 Empty transduction, UniqueID 2087


title: HT29_ORF_IRF8_426

source_name: HT-29 IRF8 transduction, UniqueID 426


title: HT29_ORF_SBNO2_485

source_name: HT-29 SBNO2 transduction, UniqueID 485


title: HT29_ORF_TAGAP_414

source_name: HT-29 TAGAP transduction, UniqueID 414

value: TAGAP


title: HT29_ORF_SLC2A13_402

source_name: HT-29 SLC2A13 transduction, UniqueID 402


title: HT29_ORF_GIGYF1_2024

source_name: HT-29 GIGYF1 transduction, UniqueID 2024


title: HT29_ORF_ACTN1_488

source_name: HT-29 ACTN1 transduction, UniqueID 488


title: HT29_ORF_NDFIP1_479

source_name: HT-29 NDFIP1 transduction, UniqueID 479


title: HT29_ORF_PITX1_2031

source_name: HT-29 PITX1 transduction, UniqueID 2031


title: HT29_ORF_H2AFY_482

source_name: HT-29 H2AFY transduction, UniqueID 482


title: HT29_ORF_CARD9_2009

source_name: HT-29 CARD9 transduction, UniqueID 2009


title: HT29_ORF_ASXL1_461

source_name: HT-29 ASXL1 transduction, UniqueID 461


title: HT29_ORF_PPP5C_455

source_name: HT-29 PPP5C transduction, UniqueID 455


title: HT29_ORF_PTPN1_458

source_name: HT-29 PTPN1 transduction, UniqueID 458


title: HT29_ORF_ASXL1_462

source_name: HT-29 ASXL1 transduction, UniqueID 462


title: HT29_ORF_CFL1_476

source_name: HT-29 CFL1 transduction, UniqueID 476


title: HT29_ORF_HDAC7_449

source_name: HT-29 HDAC7 transduction, UniqueID 449


title: HT29_ORF_SLC9A3_405

source_name: HT-29 SLC9A3 transduction, UniqueID 405


title: HT29_ORF_PITX1_2030

source_name: HT-29 PITX1 transduction, UniqueID 2030


title: HT29_ORF_UBQLN4_242

source_name: HT-29 UBQLN4 transduction, UniqueID 242


title: HT29_ORF_FIBP_446

source_name: HT-29 FIBP transduction, UniqueID 446


title: HT29_ORF_KSR1_116

source_name: HT-29 KSR1 transduction, UniqueID 116


title: HT29_ORF_IPMK_97

source_name: HT-29 IPMK transduction, UniqueID 97


title: HT29_ORF_IRF8_425

source_name: HT-29 IRF8 transduction, UniqueID 425


title: HT29_ORF_SLC9A3_404

source_name: HT-29 SLC9A3 transduction, UniqueID 404


title: HT29_ORF_SLC2A13_401

source_name: HT-29 SLC2A13 transduction, UniqueID 401


title: HT29_ORF_TAGAP_413

source_name: HT-29 TAGAP transduction, UniqueID 413


title: HT29_ORF_TTPAL_238

source_name: HT-29 TTPAL transduction, UniqueID 238


title: HT29_ORF_TMEM258_229

source_name: HT-29 TMEM258 transduction, UniqueID 229


title: HT29_ORF_GPBAR1_470

source_name: HT-29 GPBAR1 transduction, UniqueID 470


title: HT29_ORF_SLC22A4_398

source_name: HT-29 SLC22A4 transduction, UniqueID 398


title: HT29_ORF_HINT1_452

source_name: HT-29 HINT1 transduction, UniqueID 452


title: HT29_ORF_CEP72_287

source_name: HT-29 CEP72 transduction, UniqueID 287


title: HT29_ORF_IRGM_2057

source_name: HT-29 IRGM transduction, UniqueID 2057


title: HT29_ORF_SLC26A3_202

source_name: HT-29 SLC26A3 transduction, UniqueID 202


title: HT29_ORF_RASGRP1_392

source_name: HT-29 RASGRP1 transduction, UniqueID 392


title: HT29_ORF_AHRR_122

source_name: HT-29 AHRR transduction, UniqueID 122


title: HT29_ORF_DENND1B_237

source_name: HT-29 DENND1B transduction, UniqueID 237


title: HT29_ORF_CLN3_345

source_name: HT-29 CLN3 transduction, UniqueID 345


title: HT29_ORF_SLC22A5_201

source_name: HT-29 SLC22A5 transduction, UniqueID 201


title: HT29_ORF_GNA12_76

source_name: HT-29 GNA12 transduction, UniqueID 76


title: HT29_ORF_ITLN1_312

source_name: HT-29 ITLN1 transduction, UniqueID 312


title: HT29_ORF_MMP24_376

source_name: HT-29 MMP24 transduction, UniqueID 376


title: HT29_ORF_AHRR_121

source_name: HT-29 AHRR transduction, UniqueID 121


title: HT29_ORF_PTGER4_389

source_name: HT-29 PTGER4 transduction, UniqueID 389


title: HT29_ORF_LRRK2_318

source_name: HT-29 LRRK2 transduction, UniqueID 318


title: HT29_ORF_RPS6KA4_189

source_name: HT-29 RPS6KA4 transduction, UniqueID 189


title: HT29_ORF_GIPC2_75

source_name: HT-29 GIPC2 transduction, UniqueID 75


title: HT29_ORF_RTEL1_2086

source_name: HT-29 RTEL1 transduction, UniqueID 2086


title: HT29_ORF_POFUT1_162

source_name: HT-29 POFUT1 transduction, UniqueID 162


title: HT29_ORF_CEP72_286

source_name: HT-29 CEP72 transduction, UniqueID 286


title: HT29_ORF_MMP24_375

source_name: HT-29 MMP24 transduction, UniqueID 375


title: HT29_ORF_ZMIZ1_424

source_name: HT-29 ZMIZ1 transduction, UniqueID 424


title: HT29_ORF_LRRK2_317

source_name: HT-29 LRRK2 transduction, UniqueID 317


title: HT29_ORF_DENND1B_236

source_name: HT-29 DENND1B transduction, UniqueID 236


title: HT29_ORF_LRRC32_120

source_name: HT-29 LRRC32 transduction, UniqueID 120


title: HT29_ORF_RTEL1_2085

source_name: HT-29 RTEL1 transduction, UniqueID 2085


title: HT29_ORF_KIF21B_105

source_name: HT-29 KIF21B transduction, UniqueID 105


title: HT29_ORF_CLN3_344

source_name: HT-29 CLN3 transduction, UniqueID 344


title: HT29_ORF_SLC22A5_200

source_name: HT-29 SLC22A5 transduction, UniqueID 200


title: HT29_ORF_AIRE_2042

source_name: HT-29 AIRE transduction, UniqueID 2042


title: HT29_ORF_GIPC2_74

source_name: HT-29 GIPC2 transduction, UniqueID 74


title: HT29_ORF_LRRC32_119

source_name: HT-29 LRRC32 transduction, UniqueID 119


title: HT29_ORF_POFUT1_161

source_name: HT-29 POFUT1 transduction, UniqueID 161


title: Bur-0_ambient_CO2, replicate 2

city: Iizuka

first: Kousuke

last: Hanada

state: Fukuoka

address: 680-4 Kawazu

department: Department of Bioscience and Bioinformatics

institute: Kyushu Institute Technology

description: Gene expression in Bur-0

hyb_protocol: Hybridization was performed using the in situ Hybridization Kit Plus.

scan_protocol: Microarrays were scanned using an Agilent G2505 B Microarray Scanner. Microarray images were analyzed and data extracted using Feature Extraction 9.1 software (Agilent Technologies).

data_processing: The microarray signal intensities were processed using the Bioconductor (www.bioconductor.org) package in the R software environment (www.r-project.org, version 3.5.2).

organism: Arabidopsis thaliana

source_name: seedling, 38DAY, Bur-0, ambient CO2 condition, replicate 2

label_protocol: cRNA amplification and fluorescence labelling with Cy3 were performed using the Agilent One-Color Low RNA Input Linear Amplification Kit (Agilent Technologies, Tokyo, Japan).

growth_protocol: A. thaliana were grown under ambient and elevated CO2 conditions (800 μmol mol-1) for 38 days and harvested for the analysis. The ambient CO2 condition was mostly kept as 380–400 μmol mol-1. Growth temperature and humidity were set to 20 °C and 60 %. The photoperiod was 10 h day-1 (130 μmol m-2 s-1 for a total of 9 h and 660 μmol m-2 s-1 for 1 h in the midphotoperiod). Metal-halide lamps (MF400L-J2/BU-PS; Mitsubishi/Osram, Yokohama, Japan) were used as the growth light sources.

extract_protocol: In each condition, total RNA was prepared using TRIzol reagent (Life Technologies Japan, Tokyo, Japan) and 800 ng RNA was used for the microarray analysis.

value: seedling

tag: age

value: 38 day


title: HT29_ORF_ITLN1_311

source_name: HT-29 ITLN1 transduction, UniqueID 311


title: HT29_ORF_RPS6KA4_188

source_name: HT-29 RPS6KA4 transduction, UniqueID 188


title: HT29_ORF_RTEL1_2084

source_name: HT-29 RTEL1 transduction, UniqueID 2084


title: HT29_ORF_SFMBT1_197

source_name: HT-29 SFMBT1 transduction, UniqueID 197


title: Fei-0_high_CO2, replicate 2

description: Gene expression in Fei-0

source_name: seedling, 38DAY, Fei-0, high CO2 condition, replicate 2


title: Sf-1_ambient_CO2, replicate 2

description: Gene expression in Sf-1

source_name: seedling, 38DAY, Sf-1, ambient CO2 condition, replicate 2


title: Bur-0_high_CO2, replicate 2

description: Gene expression in Bur-0

source_name: seedling, 38DAY, Bur-0, high CO2 condition, replicate 2


title: Bur-0_ambient_CO2, replicate 1

description: Gene expression in Bur-0

source_name: seedling, 38DAY, Bur-0, ambient CO2 condition, replicate 1


title: HT29_ORF_LRRK2_316

source_name: HT-29 LRRK2 transduction, UniqueID 316


title: HT29_ORF_CLN3_343

source_name: HT-29 CLN3 transduction, UniqueID 343


title: HT29_ORF_ITLN1_310

source_name: HT-29 ITLN1 transduction, UniqueID 310


title: HT29_ORF_KIF21B_104

source_name: HT-29 KIF21B transduction, UniqueID 104


title: HT29_ORF_ZMIZ1_422

source_name: HT-29 ZMIZ1 transduction, UniqueID 422


title: HT29_ORF_DENND1B_235

source_name: HT-29 DENND1B transduction, UniqueID 235


title: Bur-0_high_CO2, replicate 1

description: Gene expression in Bur-0

source_name: seedling, 38DAY, Bur-0, high CO2 condition, replicate 1


title: Fei-0_ambient_CO2, replicate 1

description: Gene expression in Fei-0

source_name: seedling, 38DAY, Fei-0, ambient CO2 condition, replicate 1


title: Sf-1_high_CO2, replicate 2

description: Gene expression in Sf-1

source_name: seedling, 38DAY, Sf-1, high CO2 condition, replicate 2


title: Fei-0_ambient_CO2, replicate 2

description: Gene expression in Fei-0

source_name: seedling, 38DAY, Fei-0, ambient CO2 condition, replicate 2


title: HT29_ORF_MMP24_374

source_name: HT-29 MMP24 transduction, UniqueID 374


title: Sf-1_high_CO2, replicate 1

description: Gene expression in Sf-1

source_name: seedling, 38DAY, Sf-1, high CO2 condition, replicate 1


title: Col-0_ambient_CO2, replicate 2

description: Gene expression in Col-1

source_name: seedling, 38DAY, Col-0, ambient CO2 condition, replicate 2


title: HT29_ORF_RPS6KA4_187

source_name: HT-29 RPS6KA4 transduction, UniqueID 187


title: Col-0_high_CO2, replicate 1

description: Gene expression in Col-1

source_name: seedling, 38DAY, Col-0, high CO2 condition, replicate 1


title: Fei-0_high_CO2, replicate 1

description: Gene expression in Fei-0

source_name: seedling, 38DAY, Fei-0, high CO2 condition, replicate 1


title: oocyte [Ooc]

city: Shanghai

first: Xiaoguo

last: Zheng

address: 145 Guangyuan Road

institute: Shanghai Jiaotong University

description: WGBS

data_processing:
The raw data derived from both WGBS and scWGBS were filtered to obtain clean reads. Adaptor-polluted reads, low-quality reads, and reads with over 10% Ns were removed. Clean reads were mapped to the reference genome (mm10, UCSC) by Bismark (ver. 2.2.3), and only uniquely mapped reads were retained. Cytosines were considered to be methylated based on the binomial test followed by adjusting the false discovery rate using the Benjamini-Hochberg method. The methylation level of a single cytosine was calculated as mC/(mC+umC), where mC was the number of methylated reads and umC was the number of the unmethylated reads. Reads from different strand were merged for further analysis.
DMRs were identified using Bioconductor package DSS (v2.14.0) which uses biological replicates and information from CpG sites across the genome to stabilize the estimation of the dispersion parameters59. The core of DSS is a procedure based on Bayesian hierarchical model to estimate and shrink CpG site-specific dispersions, then conduct Wald tests for detecting differential methylation. Only CpGs that were covered at least fivefold were considered for a given comparison.
We first performed statistical tests of differentially methylated loci using DMLtest function (smoothing = TRUE, smoothing.span=500) in DSS; the results were then used to detect differentially methylated cytosines (DMCs) with the parameters: absolute delta beta value (|Δβ|DMC) > 0.1, p.threshold < 0.01 (the threshold for p-value here actually refers to local false discovery rate-FDR).
The DMCs were then merged into blocks if they both showed similar methylation patterns using callDMR function with the parameters: |Δβ|DMR > 0.1, the minimum length for a DMR ≥ 50 bp, the minimum number of CpG sites for DMR ≥ 4 and p.threshold (FDR) < 0.01. Merging nearby CpG sites (refer in particular to not differentially methylated CpG sites) into blocks can cause some regions with methylation difference smaller than theoretical value.
Thus, we further filtered out DMRs with standards: |Δβ|DMR ≥ 0.1 or variated more than 20% (as some of the regions changed from un-methylated/low-methylated to methylated/high-methylated. Although the |Δβ| value was small, their alterations were relatively large when compared to their original status). DMRs-related genes were then annotated using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: txt files about metylated reads and unmethylated reads in each CpG site

source_name: oocyte

extract_protocol:
Due to the limited amount of DNA obtained from embryos and maternal oocytes for construction of bisulfite sequencing libraries, we used the scWGBS method to perform the bisulfite sequencing for one oocyte and 12 embryo samples. Briefly, 2× lysis buffer and 0.5 μl proteinase K were added to gathered cells followed by incubation at 37°C for 1 h. Bisulfite conversion was performed on cell lysates using an EZ DNA Methylation-Gold kit as well as WGBS. After purification, DNA was eluted in 10 mM Tris-Cl and combined with oligo 1. Before incubation at 65°C for 3 min, 50 U of Klenow exo– (Sigma-Aldrich) were added, and the samples were incubated at 4°C for 5 min and at 37°C for 30 min.
Samples were incubated at 95°C for 1 min and transferred immediately to ice before the addition of fresh oligo 1 (10 pmol), Klenow exo– (25 U), and dNTPs (1 nmol) in a 2.5 μl total. The samples were incubated at 4°C for 5 min and at 37°C for 30 min. The random priming and extension were repeated a further three times (five rounds in total). Samples were then incubated with 40 U exonuclease I (New England Biolabs) for 1 h at 37°C before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter, Brea, CA, USA). Samples were eluted in 10 mM Tris-HCl (pH 8.5) and incubated with washed Streptavidin Dynabeads M-280 (Life Technologies, Carlsbad, CA, USA) for 20 min with rotation at room temperature. Beads were twice washed and resuspended in dNTPs, 0.4 μM oligo 2 and 1× Blue Buffer. Samples were incubated at 95°C for 45 s and transferred immediately to ice before addition of 100 U Klenow exo– and incubation at 4°C for 5 min, +1°C/15 s to 37°C, 37°C for 90 min. Libraries were then PCR-amplified as follows: at 95°C for 2 min, 12–13 cycles of (at 94°C for 80 s, at 65°C for 30 s, at 72°C for 30 s), at 72°C for 3 min, and a 4°C hold. Purified libraries were assessed for quality and quantity using Agilent Bioanalyzer and StepOnePlus Real-Time PCR System. Single cell libraries were prepared for 125-bp paired-end sequencing on a HiSeq 2500.

value: oocyte

tag: treatment/group

value: untreated mather

tag: parent information

value: DBA/2J ♀

tag: strain background


title: HT29_ORF_SLC22A5_199

source_name: HT-29 SLC22A5 transduction, UniqueID 199


title: Te-0_high_CO2, replicate 2

description: Gene expression in Te-0

source_name: seedling, 38DAY, Te-0, high CO2 condition, replicate 2


title: Embryo-Stress-F2-E7.5 [S2b]

description: WGBS

value: embryos

value: treated offspring-F2

value: F1 ♂ × DBA/2J ♀


title: HT29_ORF_SFMBT1_196

source_name: HT-29 SFMBT1 transduction, UniqueID 196


title: HT29_ORF_CUL2_40

source_name: HT-29 CUL2 transduction, UniqueID 40


title: HT29_ORF_RNF186_351

source_name: HT-29 RNF186 transduction, UniqueID 351


title: HT29_ORF_LACC1_348

source_name: HT-29 LACC1 transduction, UniqueID 348


title: Sf-1_ambient_CO2, replicate 1

description: Gene expression in Sf-1

source_name: seedling, 38DAY, Sf-1, ambient CO2 condition, replicate 1


title: Col-0_high_CO2, replicate 2

description: Gene expression in Col-1

source_name: seedling, 38DAY, Col-0, high CO2 condition, replicate 2


title: HT29_ORF_RCL1_136

source_name: HT-29 RCL1 transduction, UniqueID 136


title: Yeg-1_high_CO2, replicate 2

description: Gene expression in Yeg-1

source_name: seedling, 38DAY, Yeg-1, high CO2 condition, replicate 2


title: HT29_ORF_POFUT1_160

source_name: HT-29 POFUT1 transduction, UniqueID 160


title: Yeg-1_ambient_CO2, replicate 1

description: Gene expression in Yeg-1

source_name: seedling, 38DAY, Yeg-1, ambient CO2 condition, replicate 1


title: HT29_ORF_GIPC2_73

source_name: HT-29 GIPC2 transduction, UniqueID 73


title: HT29_ORF_KIF21B_103

source_name: HT-29 KIF21B transduction, UniqueID 103


title: Embryo-Stress-F2-ICM [S2a]

description: WGBS


title: Yeg-1_high_CO2, replicate 1

description: Gene expression in Yeg-1

source_name: seedling, 38DAY, Yeg-1, high CO2 condition, replicate 1


title: Te-0_ambient_CO2, replicate 1

description: Gene expression in Te-0

source_name: seedling, 38DAY, Te-0, ambient CO2 condition, replicate 1


title: Embryo-Stress-F2-PGC [S2c]

description: WGBS


title: Te-0_ambient_CO2, replicate 2

description: Gene expression in Te-0

source_name: seedling, 38DAY, Te-0, ambient CO2 condition, replicate 2


title: HT29_ORF_ZMIZ1_423

source_name: HT-29 ZMIZ1 transduction, UniqueID 423


title: Te-0_high_CO2, replicate 1

description: Gene expression in Te-0

source_name: seedling, 38DAY, Te-0, high CO2 condition, replicate 1


title: HT29_ORF_GSDMB_306

source_name: HT-29 GSDMB transduction, UniqueID 306

value: GSDMB


title: Embryo-Control-F2-E7.5 [C2b]

description: WGBS

value: untreated offspring-F2


title: HT29_ORF_SATB1_321

source_name: HT-29 SATB1 transduction, UniqueID 321


title: Embryo-Control-F1-PGC [C1c]

description: WGBS

value: untreated offspring-F1

value: C57BL/6J-Pouf1gfp/gfp × DBA/2J ♀


title: HT29_ORF_LRRC32_118

source_name: HT-29 LRRC32 transduction, UniqueID 118


title: HT29_ORF_RNFT1_291

source_name: HT-29 RNFT1 transduction, UniqueID 291


title: HT29_ORF_AAMP_7

source_name: HT-29 AAMP transduction, UniqueID 7

value: AAMP


title: HT29_ORF_FUT2_72

source_name: HT-29 FUT2 transduction, UniqueID 72


title: Yeg-1_ambient_CO2, replicate 2

description: Gene expression in Yeg-1

source_name: seedling, 38DAY, Yeg-1, ambient CO2 condition, replicate 2


title: Embryo-Stress-F1-PGC [S1c]

description: WGBS

value: treated offspring-F1


title: HT29_ORF_RCL1_138

source_name: HT-29 RCL1 transduction, UniqueID 138


title: Embryo-Stress-F1-ICM [S1a]

description: WGBS


title: Embryo-Control-F2-PGC [C2c]

description: WGBS


title: Embryo-Control-F2-ICM [C2a]

description: WGBS


title: Abeta_1

city: Daejeon

first: C Justin

last: Lee

address: 55, Expo-ro, Doryong-dong, Yuseong-gu

department: Center for Cognition and Sociality

country: South Korea

institute: Institute for Basic Science

description: mRNA library prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)

data_processing:
BCL files obtained from Illumina HiSeq2500 were converted to fastq and demultiplexed based on the index primer sequences. The data was imported to Partek Genomic Suite (Copyright 2009, Partek Inc., St. Louis, MO, USA), where further processing was carried out.
Read quality was checked for each sample using FastQC (Flow version 10.0.21.0328)
High-quality reads were aligned using STAR (2.7.3a)
Aligned reads were quantified to the mouse genome assembly (mm10, Ensemble transcripts release 99) and normalised to the median ratio (for analysis using DeSeq2).
Differential analysis was carried out using DeSeq2, pathway analysis was carried out with reference to the KEGG database.
Genome_build: Alignment was to the mouse genome assembly (mm10, GRCm39).
Supplementary_files_format_and_content: Processed data files include detailed results of the DeSeq2 differential analysis (Deseq2.txt) and results of diferential pathway analysis (PathwayAnalysis.txt)

source_name: Primary mouse astrocyte culture

growth_protocol: Primary astrocyte cultures were grown in Dulbecco’s modified Eagle’s medium (DMEM, Corning) supplemented with 4.5 g/L glucose, L-glutamine, sodium pyruvate, 10% heat-inactivated horse serum, 10% heat-inactivated fetal bovine serum, and 1000 units/ml of penicillin–streptomycin. Cultures were maintained at 37oC in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from the cell culture using Rnasy Mini Kit (Qiagen, #74104).
1μg of total RNA was enriched for Poly-mRNA (Dynabeads mRNA purification kit, Invitrogen) and reverse transcribed to double-stranded cDNA. The cDNA was end-repaired, adenylated and ligated to Illumina indices prior to 14 cycles of PCR amplification (Ultra RNA library prep kit, NEBNext). Sequencing was performed using 20pM hybridization to  a 2x75 paired-end flow cell in HiSeq2500 (Illumina).

treatment_protocol: At DIV7, cells were washed treated with 1μM Aβ (Abcam), in the presence or absence of 50μM DFMO (Sigma-Aldrich) for 5 days.

tag: strain

value: Primary mouse astrocyte culture

value: P0-P1 pups, DIV 12

value: ABeta (1uM, 5 days)


title: Control_2

value: Naive


title: DFMO

value: ABeta (1uM) + DFMO (50uM), 5 days


title: Embryo-Stress-F1-E7.5 [S1b]

description: WGBS


title: Embryo-Control-F1-E7.5 [C1b]

description: WGBS


title: HT29_ORF_LACC1_347

source_name: HT-29 LACC1 transduction, UniqueID 347


title: LPS_WT_1

city: Shang Hai

first: Pan

last: Jia

state: — Please Select —

address: No.320.Yueyang Road,Shanghai

institute: Shanghai Institute of Nutrition and Health Chinese Academy of Science

description:
LPS_WT
LPS_WT_1.fq.gz
LPS_WT_2.fq.gz

data_processing:
Illumina Casava1.7 software used for basecalling.Basecalls performed using CASAVA version 1.4.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.ChIP-seq reads were aligned to the mm10 genome assembly using EasyAlign version 3.2 with the following configurations…
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.Data were filtered using the following specifications…
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …wig files were generated using …; Scores represent …

source_name: Bone Marrow

growth_protocol: BMDMs were cultured in 1640 meidum with 10% FBS and 20ng/mL M-CSF.Raw264.7 cells were cultured in 1640 meidum with 10% FBS

extract_protocol:
For total RNA, medium were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. For DNA,Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols.Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
RNA-Seq,ChIP-Seq,ATAC-seq

treatment_protocol: Cells were treated with vehicle or LPS

value: BMDMs

tag: genotype

value: WT


title: HT29_ORF_SATB1_320

source_name: HT-29 SATB1 transduction, UniqueID 320


title: HT29_ORF_GSDMB_305

source_name: HT-29 GSDMB transduction, UniqueID 305


title: HT29_ORF_SFMBT1_198

source_name: HT-29 SFMBT1 transduction, UniqueID 198


title: HT29_ORF_RXFP4_192

source_name: HT-29 RXFP4 transduction, UniqueID 192


title: HT29_ORF_OTUD3_153

source_name: HT-29 OTUD3 transduction, UniqueID 153


title: HT29_ORF_RXFP4_191

source_name: HT-29 RXFP4 transduction, UniqueID 191


title: HT29_ORF_RNF186_350

source_name: HT-29 RNF186 transduction, UniqueID 350


title: Embryo-Control-F1-ICM [C1a]

description: WGBS


title: HT29_ORF_RNFT1_290

source_name: HT-29 RNFT1 transduction, UniqueID 290


title: Abeta_2


title: Control_1


title: HT29_ORF_CUL2_41

source_name: HT-29 CUL2 transduction, UniqueID 41


title: HT29_ORF_CUL2_42

source_name: HT-29 CUL2 transduction, UniqueID 42


title: HT29_ORF_FUT2_71

source_name: HT-29 FUT2 transduction, UniqueID 71


title: HT29_ORF_CPSF3L_36

source_name: HT-29 CPSF3L transduction, UniqueID 36


title: HT29_ORF_AAMP_9

source_name: HT-29 AAMP transduction, UniqueID 9


title: NT_WT_1

description:
NT_WT
NT_WT_1.fq.gz
NT_WT_2.fq.gz


title: Z8 KO+DE-A-NT_BMRC200002503-1A_1

description:
Z8 KO+DE-A-NT_BMRC200002503-1A_1.clean.fq.gz
Z8 KO+DE-A-NT_BMRC200002503-1A_2.clean.fq.gz

value: Zmynd8 KO+ D/E-A


title: HT29_ORF_CPSF3L_35

source_name: HT-29 CPSF3L transduction, UniqueID 35


title: Z8 KO-LPS_BMRC200002504-1A_1

description:
Z8 KO-LPS_BMRC200002504-1A_1.clean.fq.gz
Z8 KO-LPS_BMRC200002504-1A_2.clean.fq.gz

value: Zmynd8 KO


title: HT29_ORF_AAMP_8

source_name: HT-29 AAMP transduction, UniqueID 8


title: Z8 KO+Z8-LPS_BMRC200002505-1A_1

description:
Z8 KO+Z8-LPS_BMRC200002505-1A_1.clean.fq.gz
Z8 KO+Z8-LPS_BMRC200002505-1A_2.clean.fq.gz

value: Zmynd8 KO+ Zmynd8


title: HT29_ORF_RNF186_349

source_name: HT-29 RNF186 transduction, UniqueID 349


title: HT29_ORF_OTUD3_152

source_name: HT-29 OTUD3 transduction, UniqueID 152


title: HT29_ORF_RCL1_137

source_name: HT-29 RCL1 transduction, UniqueID 137


title: Z8 KO+Z8-NT_BMRC200002502-1A_1

description:
Z8 KO+Z8-NT_BMRC200002502-1A_1.clean.fq.gz
Z8 KO+Z8-NT_BMRC200002502-1A_2.clean.fq.gz

source_name: Bone Marrow


title: Col-0_ambient_CO2, replicate 1

description: Gene expression in Col-1

source_name: seedling, 38DAY, Col-0, ambient CO2 condition, replicate 1

value: seedling

value: 38 day


title: Z8 KO-NT_BMRC200002501-1A_1

description:
Z8 KO-NT_BMRC200002501-1A_1.clean.fq.gz
Z8 KO-NT_BMRC200002501-1A_2.clean.fq.gz


title: HT29_ORF_SATB1_319

source_name: HT-29 SATB1 transduction, UniqueID 319


title: HT29_ORF_RXFP4_190

source_name: HT-29 RXFP4 transduction, UniqueID 190


title: p65 KO+K122R_FMRC202450924-1a_1

description:
p65 KO+K122R_FMRC202450924-1a_1.clean.fq.gz
p65 KO+K122R_FMRC202450924-1a_2.clean.fq.gz


title: HT29_ORF_GSDMB_304

source_name: HT-29 GSDMB transduction, UniqueID 304

value: GSDMB


title: HT29_ORF_RNFT1_289

source_name: HT-29 RNFT1 transduction, UniqueID 289


title: Input-Z8 KO-NT_BMRC200002494-1A_1

description:
Input-Z8 KO-NT_BMRC200002494-1A_1.clean.fq.gz
Input-Z8 KO-NT_BMRC200002494-1A_2.clean.fq.gz


title: p65 KO_FMRC202450922-1a_1

description:
p65 KO_FMRC202450922-1a_1.clean.fq.gz
p65 KO_FMRC202450922-1a_2.clean.fq.gz

value: p65 KO


title: Input-Z8 KO+Z8-LPS_BMRC200002498-1A_1

description:
Input-Z8 KO+Z8-LPS_BMRC200002498-1A_1.clean.fq.gz
Input-Z8 KO+Z8-LPS_BMRC200002498-1A_2.clean.fq.gz


title: HT29_ORF_CDC37_285

source_name: HT-29 CDC37 transduction, UniqueID 285


title: Z8 KO-Lsd1_BMRC200005356-1A_1

description:
Z8 KO-Lsd1_BMRC200005356-1A_1.clean.fq.gz
Z8 KO-LSD1_BMRC200005356-1A_2.clean.fq.gz

value: Zmynd8 cKO


title: HT29_ORF_FUT2_70

source_name: HT-29 FUT2 transduction, UniqueID 70


title: Input-Z8 KO+Z8-NT_BMRC200002495-1A_1

description:
Input-Z8 KO+Z8-NT_BMRC200002495-1A_1.clean.fq.gz
Input-Z8 KO+Z8-NT_BMRC200002495-1A_2.clean.fq.gz


title: Input-Z8 KO+DE-A-NT_BMRC200002496-1A_1

description:
Input-Z8 KO+DE-A-NT_BMRC200002496-1A_1.clean.fq.gz
Input-Z8 KO+DE-A-NT_BMRC200002496-1A_2.clean.fq.gz


title: WT-Lsd1_BMRC200005353-1A_1

description:
WT-Lsd1_BMRC200005353-1A_1.clean.fq.gz
WT-Lsd1_BMRC200005353-1A_2.clean.fq.gz


title: Input-Z8 KO+DE-A-LPS_BMRC200002499-1A_1

description:
Input-Z8 KO+DE-A-LPS_BMRC200002499-1A_1.clean.fq.gz
Input-Z8 KO+DE-A-LPS_BMRC200002499-1A_2.clean.fq.gz


title: Input-Z8 KO-LPS_BMRC200002497-1A_1

description:
Input-Z8 KO-LPS_BMRC200002497-1A_1.clean.fq.gz
Input-Z8 KO-LPS_BMRC200002497-1A_2.clean.fq.gz


description:
Input p65 KO+K122R LPS_FMRC202450921-1a_1.clean.fq.gz
Input p65 KO+K122R LPS_FMRC202450921-1a_2.clean.fq.gz


title: p65 KO+WT_FMRC202450923-1a_1

description:
p65 KO+WT_FMRC202450923-1a_1.clean.fq.gz
p65 KO+WT_FMRC202450923-1a_2.clean.fq.gz

value: p65 KO+ WT


title: HT29_ORF_FOSL1_61

source_name: HT-29 FOSL1 transduction, UniqueID 61


title: HT29_ORF_ACTL6B_270

source_name: HT-29 ACTL6B transduction, UniqueID 270


title: HT29_ORF_USP12_246

source_name: HT-29 USP12 transduction, UniqueID 246


title: HT29_ORF_OTUD3_151

source_name: HT-29 OTUD3 transduction, UniqueID 151


title: Z8 KO-H3K4me1_FMRC202440234-1a_1

description:
Z8 KO-H3K4me1_FMRC202440234-1a_1.clean.fq.gz
Z8 KO-H3K4me1_FMRC202440234-1a_2.clean.fq.gz


title: Input p65 KO +WT LPS_FMRC202450920-1a_1

description:
Input p65 KO +WT LPS_FMRC202450920-1a_1.clean.fq.gz
Input p65 KO +WT LPS_FMRC202450920-1a_2.clean.fq.gz


title: HT29_ORF_SMAD7_213

source_name: HT-29 SMAD7 transduction, UniqueID 213


title: HT29_ORF_CPSF3L_34

source_name: HT-29 CPSF3L transduction, UniqueID 34


title: Input p65 KO LPS_FMRC202450919-1a_1

description:
Input p65 KO LPS_FMRC202450919-1a_1.clean.fq.gz
Input p65 KO LPS_FMRC202450919-1a_2.clean.fq.gz


title: Input-Z8 KO(H3K4me1)_FMRC202440230-1b_1

description:
Input-Z8 KO(H3K4me1)_FMRC202440230-1b_1.clean.fq.gz
Input-Z8 KO(H3K4me1)_FMRC202440230-1b_2.clean.fq.gz


title: 0% 1,6-hex_BMRC200002500-1A_1

description:
0% 1,6-hex_BMRC200002500-1A_1.clean.fq.gz
0% 1,6-hex_BMRC200002500-1A_2.clean.fq.gz


title: Input-Z8 KO-Lsd1_BMRC200005354-1A_1

description:
Input-Z8 KO-Lsd1_BMRC200005354-1A_1.clean.fq.gz
Input-Z8 KO-Lsd1_BMRC200005354-1A_2.clean.fq.gz


title: HT29_ORF_AUH_259

source_name: HT-29 AUH transduction, UniqueID 259

value: AUH


title: Input WT(H3K4me1)_FMRC202440229-1a_1

description:
Input WT(H3K4me1)_FMRC202440229-1a_1.clean.fq.gz
Input WT(H3K4me1)_FMRC202440229-1a_2.clean.fq.gz


title: HT29_ORF_PARK7_156

source_name: HT-29 PARK7 transduction, UniqueID 156


title: HT29_ORF_FOSL2_66

source_name: HT-29 FOSL2 transduction, UniqueID 66


title: HT29_ORF_PUSL1_174

source_name: HT-29 PUSL1 transduction, UniqueID 174


title: WT-H3K4me1_FMRC202440233-1a_1

description:
WT-H3K4me1_FMRC202440233-1a_1.clean.fq.gz
WT-H3K4me1_FMRC202440233-1a_2.clean.fq.gz

source_name: Bone Marrow


title: HT29_ORF_ORMDL3_150

source_name: HT-29 ORMDL3 transduction, UniqueID 150


title: HT29_ORF_NXPE1_143

source_name: HT-29 NXPE1 transduction, UniqueID 143


title: HT29_ORF_KIF3B_106

source_name: HT-29 KIF3B transduction, UniqueID 106


title: Z8 KO+DE-A-LPS_BMRC200002506-1A_1

description:
Z8 KO+DE-A-LPS_BMRC200002506-1A_1.clean.fq.gz
Z8 KO+DE-A-LPS_BMRC200002506-1A_2.clean.fq.gz


title: HT29_ORF_FOSL2_65

source_name: HT-29 FOSL2 transduction, UniqueID 65


title: HT29_ORF_SPRED2_219

source_name: HT-29 SPRED2 transduction, UniqueID 219


title: HT29_ORF_HNF4A_88

source_name: HT-29 HNF4A transduction, UniqueID 88


title: Input-WT-Lsd1_BMRC200005355-1A_1

description:
Input-WT-Lsd1_BMRC200005355-1A_1.clean.fq.gz
Input-WT-Lsd1_BMRC200005355-1A_2.clean.fq.gz


title: M0_ZMYND8

description:
M0
M0_ZMYND8.clean.fq


title: Input-6% 1-6-Hex_BMRC200002492-1A_1

description:
Input-6% 1-6-Hex_BMRC200002492-1A_1.clean.fq.gz
Input-6% 1-6-Hex_BMRC200002492-1A_2.clean.fq.gz


title: HT29_ORF_SMAD3_210

source_name: HT-29 SMAD3 transduction, UniqueID 210


title: HT29_ORF_RIT1_178

source_name: HT-29 RIT1 transduction, UniqueID 178


title: HT29_ORF_FOS_58

source_name: HT-29 FOS transduction, UniqueID 58

value: FOS


title: p65 KO lps

description:
Rawsgp651ps--RawWTlps.all.gene
p65 KO lps.read1_Clean.fastq.gz
p65 KO lps.read2_Clean.fastq.gz


title: Input-0% 1,6-hex_BMRC200002491-1A_1

description:
Input-0% 1,6-hex_BMRC200002491-1A_1.clean.fq.gz
Input-0% 1,6-hex_BMRC200002491-1A_2.clean.fq.gz


title: 6% 1-6-Hex_BMRC200002493-1A_1

description:
6% 1-6-Hex_BMRC200002493-1A_1.clean.fq.gz
6% 1-6-Hex_BMRC200002493-1A_2.clean.fq.gz


title: Z8 KO + D/E-A

description:
SgZ8Z8--SgZ8_D-E-A.all.gene
Z8 KO + D/E-A.read1_Clean.fastq.gz
Z8 KO + D/E-A.read2_Clean.fastq.gz

value: Zmynd8 KO + D/E-A


title: Z8 KO + Z8

description:
SgZ8Z8--SgZ8_D-E-A.all.gene
Z8 KO + Z8.read1_Clean.fastq.gz
Z8 KO + Z8.read2_Clean.fastq.gz


title: HT29_ORF_LACC1_346

source_name: HT-29 LACC1 transduction, UniqueID 346


title: HT29_ORF_NXPE1_144

source_name: HT-29 NXPE1 transduction, UniqueID 144


title: KOM2_S63_L002_R1_001

description:
WTM2_vs_KOM2.degseq.annot
KOM2_S63_L002_R1_001.fastq.gz
KOM2_S63_L002_R2_001.fastq.gz


title: KOM0_S92_L002_R1_001

description:
WTM0_vs_KOM0.degseq.annot
KOM0_S92_L002_R1_001.fastq.gz
KOM0_S92_L002_R2_001.fastq.gz


title: p65 KO +WT lps

description:
RawWTlps--Rawk1221ps.all.gene
p65 KO +WT lps.read1_Clean.fastq.gz
p65 KO +WT lps.read2_Clean.fastq.gz


title: HT29_ORF_SMAD3_209

source_name: HT-29 SMAD3 transduction, UniqueID 209


title: HT29_ORF_SPRED2_218

source_name: HT-29 SPRED2 transduction, UniqueID 218


title: M1_ZMYND8

description:
M1
M1_ZMYND8.clean.fq


title: Input

description:
input
Input.fastq.gz


title: HT29_ORF_USP12_245

source_name: HT-29 USP12 transduction, UniqueID 245


title: WTM1_S93_L002_R1_001

description:
WTM1_vs_KOM1.degseq.annot
WTM1_S93_L002_R1_001.fastq.gz
WTM1_S93_L002_R2_001.fastq.gz


title: HT29_ORF_PUSL1_173

source_name: HT-29 PUSL1 transduction, UniqueID 173


title: Z8 KO

description:
SgZ8--SgZ8Z8.all.gene
Z8 KO.read1_Clean.fastq.gz
Z8 KO.read2_Clean.fastq.gz


title: KO rep4

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

data_processing:
The software STAR (55) (version 2.4.0e) was used to generate genome indices for mouse reference genome (GRCm38/mm10, December 2011), with two particular specifications including gene annotations, i.e., GENCODE (56) (vM23, September 2019), and exon-exon junctions, i.e., 35 nucleotides used in constructing the splice junctions database.
Next, the high quality paired-end RNA-seq reads were aligned to mouse reference genome, and the consequence of alignment served as the input  for featureCounts (57) to quantify raw read counts for 55,385 annotated genes, including 21,856 protein-coding genes.
Moreover, the normalized unit of reads per kilobase per million mapped reads (RPKM) was generated for every gene annotated in GENCODE, in order to fit the primary request of principle component analysis (PCA). The R function prcomp was used to perform PCA by using the genes having RPKM ≥ 1 in at least two samples, and the returned two vectors were used as coordinates to make a scatter plot in a 2-dimensional plane.
We used R package DESeq2 (58) (version 1.14.1) to identify differentially expressed (DEX) genes between WT and KO. The raw read count per gene served as the input for DESeq2. The GC content correction from CQN package was incorporated to DESeq2 (59). Since four samples were collected in either condition, they were treated as biological replicates to improve the reliability of DEX genes identification. Statistical tests for differential expression were based on a model using the negative binomial distribution. The reported statistical significances were corrected for multiple testing using the Benjamini-Hochberg procedure with a false discovery rate less than 0.01. In addition, to be called DEX genes we required the fold change > 1.5. The up- and down- regulated genes in KO condition were separately queried to Gene Ontology Consortium for gene ontology enrichment assessment, including biological process (BP), molecular function (MF), and cellular component (CC).
Moreover, we utilized the software GSEA (60) to survey the statistically significant concordant differences between KO and WT by using the normalized gene RPKM values, and consequently compared the KO up-regulated gene sets to “C7: immunologic signatures” to explore any overrepresented functional term.
Genome_build: GRCm38/mm10, December 2011
Supplementary_files_format_and_content: Count table for each sample

source_name: CD8+ TILs

extract_protocol:
CD8+ TILs were isolated from MC38 tumor-bearing Cd4-Cre+Lsd1f/f and Lsd1f/f mice on day 18 as described above. CD8+ TILs from two individual tumor-carrying Lsd1f/f mice were combined as a biological replicate, and CD8+ TILs from each individual tumor-carrying Cd4-Cre+Lsd1f/f mouse was used as a biological replicate. CD8+ TILs were stained with antibodies against CD45.2 (clone 104), TCR (clone H57-587), CD8 (clone YTS156.7.7), CD44 (clone IM7) and PD-1 (clone 29F.1A12), and 7-AAD Viability Staining Solution was used to exclude dead cells. The CD45.2+TCR+CD8+CD44+PD-1+ cells were then sorted on a BD Aria. Approximately 10,000~20,000 sorted cells for each biological replicate were directly lysed in 1 ml TRIzol Reagent (Life Technologies, cat#15596018). After incubation for 5 mins, 0.2 ml chloroform was added and mixed by inverting the tubes several times. Samples were incubated for 2~3 mins and later centrifuged for 15 minutes at 12,000g at 4 °C. The upper aqueous phase containing the RNA was collected and mixed with equal volume of 70% ethanol, which was then loaded into a spin column from a RNeasy Micro Kit (Qiagen, cat#74004) and subjected to RNA isolation according to the instruction manual. The on-column DNase digestion was conducted to eliminate DNA contamination.
Purified total RNA was quantified by Qubit (Invitrogen) and used to generate rRNA-depleted RNA with a NEBNext® rRNA Depletion Kit (New England Biolabs, cat#E6310S) according to the manufacturer’s instructions. The rRNA-depleted RNA was purified with a RNA Clean & Concentrator-5 kit (Zymo Research, cat#R1016) and then used to generate a directional RNA library with a NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, cat#E7760L) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs, cat#E7335L) according to the manufacturer’s instructions. Library concentrations and quality were assessed on a Bioanalyzer and by qPCR. The library was sequenced at Nextseq 500 (Illumina) to generate reads from paired-ends (43 bp + 42 bp).

value: C57BL/6 mice

value: Implanted MC38 tumor


title: p65 KO + K122lps

description:
RawWTlps--Rawk1221ps.all.gene
p65 KO + K122lps.read1_Clean.fastq.gz
p65 KO + K122lps.read2_Clean.fastq.gz

source_name: Bone Marrow


title: HT29_ORF_USP12_244

source_name: HT-29 USP12 transduction, UniqueID 244


title: HT29_ORF_ORMDL3_149

source_name: HT-29 ORMDL3 transduction, UniqueID 149


title: KO rep3


title: KO rep2


title: HT29_ORF_CDC37_284

source_name: HT-29 CDC37 transduction, UniqueID 284


title: WT rep4


title: WTMO_S91_L002_R1_001

description:
WTM0_vs_KOM0.degseq.annot
WTMO_S91_L002_R1_001.fastq.gz
WTMO_S91_L002_R2_001.fastq.gz


title: HT29_ORF_SMAD7_211

source_name: HT-29 SMAD7 transduction, UniqueID 211


title: HT29_ORF_ACTL6B_268

source_name: HT-29 ACTL6B transduction, UniqueID 268


title: HT29_ORF_ACTL6B_269

source_name: HT-29 ACTL6B transduction, UniqueID 269


title: WTM2_S62_L002_R1_001

description:
WTM2_vs_KOM2.degseq.annot
WTM2_S62_L002_R1_001.fastq.gz
WTM2_S62_L002_R2_001.fastq.gz


title: HT29_ORF_PARK7_155

source_name: HT-29 PARK7 transduction, UniqueID 155


title: HT29_ORF_CDC37_283

source_name: HT-29 CDC37 transduction, UniqueID 283


title: HT29_ORF_SMURF1_214

source_name: HT-29 SMURF1 transduction, UniqueID 214


title: KOM1_S94_L002_R1_001

description:
WTM1_vs_KOM1.degseq.annot
KOM1_S94_L002_R1_001.fastq.gz
KOM1_S94_L002_R2_001.fastq.gz


title: HT29_ORF_SSR2_262

source_name: HT-29 SSR2 transduction, UniqueID 262


title: HT29_ORF_SMAD3_208

source_name: HT-29 SMAD3 transduction, UniqueID 208


title: HUVECs treated with HG+IS 30IS-2_L3_A027

city: Taipei

first: yu chin

last: Huang

address: No.1 Jen Ai road section 1

country: Taiwan

institute: NTU

description: HUVECs treated with HG+IS

data_processing:
Differences in the expression of the lncRNAs were calculated based on the trimmed mean of M-values method (Robinson and Oshlack, 2010).
LncRNAs with similar expression patterns were analyzed using the hierarchical complete linkage clustering method in R software (R package, version 3.4.3;www.r‑project.org/)
Significant differences in lncRNA expression levels were determined based on a p value cut‑off of 0.05 and a minimum fold change (FC)of 1.5 using DEseq software package version 1.20.0 (Love et al. , 2014)
The differentially expressed lncRNAs were replaced by log2 values (data values),and the Euclidean distance was calculated
The results were further analyzed using R packages
Genome_build: NONCODEv5 human hg38 lncRNA
Supplementary_files_format_and_content: gene_data.xlsx ,content:read-count,normalized,and cpmpare data of HG vs HG+IS

source_name: HUVECS

growth_protocol: Cells were cultured in EGMTM-2 Endothelial Cell Growth Medium-2 BulletKitTM which contained EBMTM-2 Basal Medium and EGMTM-2 SingleQuotsTM Supplements, then incubated at 37 °C in a humidified atmosphere with 5% CO2. HUVECs at passages 5–8 were used for the in vitro studies.

extract_protocol:
Total RNA was extracted from cultured cells using NucleoZOL reagent according to the manufacturer’s protocol. One μg of total RNA was reverse-transcribed by a High-Capacity cDNA Reverse Transcription Kit
RNA concentration and quality were determined using a Qubit Fluorometer (Thermo Fisher Scientific, USA) and an Agilent 2100 Bioanalyzer which calculates an (RIN).The ribosomal RNAs (rRNA) were eradicated from total RNA using a Ribo-zero rRNA removal kit (Cat. no. 20278677, Illumina, USA). After purification, the RNAs were fragmented into small pieces by using divalent cations with elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments went through an end repair process with addition of a single “A” base and ligation of the adapters.The products were then purified and enriched with PCR to create the final cDNA library.Paired-end reads from each cDNA library were obtained using a NextSeq500 system (Illumina Inc., USA).

treatment_protocol: Cells from the fifth passage were incubated in 30 mM D-glucose (high glucose, HG) or 30 mM D-glucose treated with 0.1 mM IS (HG+IS) for 96 h

tag: cell

value: primary human cells were purchased from Lonza Walkersville, Inc


title: HUVECs treated with HG+IS 30-IS_HLF2GAFXY

description: HUVECs treated with HG+IS


title: HT29_ORF_HNF4A_90

source_name: HT-29 HNF4A transduction, UniqueID 90


title: HUVECs treated with HG 30-1_L3_A012

description: HUVECs treated with HG


title: HT29_ORF_SMAD7_212

source_name: HT-29 SMAD7 transduction, UniqueID 212


title: WT rep2


title: HT29_ORF_SPRED2_217

source_name: HT-29 SPRED2 transduction, UniqueID 217


title: HT29_ORF_TM9SF4_220

source_name: HT-29 TM9SF4 transduction, UniqueID 220


title: WT rep1

source_name: CD8+ TILs


title: SymE_untagged_60min_Rep1 [ChIP-seq]

city: Cambirdge

first: Mary

middle: Katherine

last: Thompson

address: 31 Ames St Room 68-570

department: Biology

institute: Massachusetts Institute of Technology

data_processing:
Reads were mapped to the E. coli MG1655 chromosome using bowtie2 on default settings
.bam files were sorted using SAMtools
sorted .bam files were converted to bedGraphs
bedGraphs were converted to WIGs
WIG files were visualized and further analyzed in Mochiview
Peaks were called from sorted .bams using MACS on default settings
Genome_build: NCBI reference sequence: NC_000913.2
Supplementary_files_format_and_content: WIG files, contain pileup data across the E. coli genome for each sample

organism: Escherichia coli

source_name: Bacterial liquid culture

growth_protocol: E. coli MG1655 cells harboring either pBAD24::symE or pBAD24::symE-SPA were grown overnight in LB containing carbenicillin at 37 °C and then back diluted into fresh LB carbenicillin to OD600 0.02. Cultures were then grown at 37 °C to OD600 0.25 at which point they were induced with 0.2% arabinose. After 30- and 60- minutes of induction, 20 mL samples of each culture were taken.

extract_protocol:
For step by step protocol see publication. Briefly: Samples were taken and crosslinked with formaldehyde. Cells were then lysed and sonicated, incubated with anti-FLAG antibodies and then immune complexes were pulled out with Protein A dynabeads. Beads were washed and then eluted. Crosslinking was reversed and DNA was extracted using a phenol-chloroform extraction.
DNA samples to be sequenced were end-repaired, 3' adenylated and sequencing adaptors were ligated on. Libraries were then PCR amplified and submitted for sequencing

tag: plasmid

value: pBAD24 symE

tag: induction

value: 60 minutes


title: HUVECs treated with HG+IS 30IS-1_L3_A021

description: HUVECs treated with HG+IS


title: WT rep3

tag: tissue


title: HT29_ORF_FOSL2_64

source_name: HT-29 FOSL2 transduction, UniqueID 64


title: HT29_ORF_CEBPB_22

source_name: HT-29 CEBPB transduction, UniqueID 22

value: CEBPB


title: HT29_ORF_ORMDL3_148

source_name: HT-29 ORMDL3 transduction, UniqueID 148


title: HUVECs treated with HG 30-2_L3_A026

description: HUVECs treated with HG


title: HUVECs treated with HG 30-X_HLF2GAFXY

description: HUVECs treated with HG


title: HT29_ORF_PARK7_154

source_name: HT-29 PARK7 transduction, UniqueID 154


title: HT29_ORF_RIPK2_175

source_name: HT-29 RIPK2 transduction, UniqueID 175


title: HT29_ORF_NXPE1_142

source_name: HT-29 NXPE1 transduction, UniqueID 142


title: SymE_untagged_30min_Rep3 [ChIP-seq]

value: 30 minutes


title: SymE_untagged_30min_Rep1 [ChIP-seq]


title: HT29_ORF_NUPR1_139

source_name: HT-29 NUPR1 transduction, UniqueID 139


title: SymE_SPAtagged_60min_Rep1 [ChIP-seq]

value: pBAD24 symESPA


title: HT29_ORF_ARFRP1_15

source_name: HT-29 ARFRP1 transduction, UniqueID 15


title: SymE_SPAtagged_30min_Rep1 [ChIP-seq]


title: HT29_ORF_CPEB4_33

source_name: HT-29 CPEB4 transduction, UniqueID 33


title: HT29_ORF_DUSP16_51

source_name: HT-29 DUSP16 transduction, UniqueID 51


title: HT29_ORF_CTH_39

source_name: HT-29 CTH transduction, UniqueID 39

value: CTH


title: HT29_ORF_ARHGEF2_18

source_name: HT-29 ARHGEF2 transduction, UniqueID 18


title: HT29_ORF_FOS_60

source_name: HT-29 FOS transduction, UniqueID 60


title: SymE_SPAtagged_30min_Rep3 [ChIP-seq]


title: SymE_untagged_30min_Rep2 [ChIP-seq]


title: SymE_SPAtagged_30min_Rep2 [ChIP-seq]


title: RNA_THP1_Tram_IL4_2

city: Charlestown

first: Alexander

middle: G

last: Marneros

address: 13th Street

department: Department of Dermatology, Cutaneous Biology Research Center

institute: Massachusetts General Hospital, Harvard Medical School

data_processing:
We followed the nf-core/rnaseq workflow version 1.3 (https://github.com/nf-core/rnaseq) for all rna-seq data, with default parameters. The detail includes as following:
low-quality reads were eliminated using FastQC and trim_galory software, remaining only high quality reads.
The remaining clean reads were aligned against the iGenome Ensembl human referenece genome GRCh37 using by STAR. STAR is a read aligner designed for RNA sequencing.
Next, we generated counts relative to genes by featureCounts and StringTie with default parameters.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: THP-1 cells were obtained from ATCC (ATCC Cat# TIB-202, RRID:CVCL_0006) and cultured in RPMI1640+10% FBS+1% Anti-Anti (Life technologies, 15240).

extract_protocol:
0.5X10^6 cells were harvested for mRNA using mRNeasy Mini Kit (Qiagen, No. 217004).
We used 0.4 μg total RNA for RNA-seq library preparation by TruSeq Ribo Profile Mammalian Kit (Illumina, RPHMR12126).

treatment_protocol: Primed THP-1 cells with PMA 100 nM were pre-treated with panobinostat (0.0034 μM), Treametinib (0.011 μM ), or DMSO (control) for one hour and then treated with either BSA (control), IL-4 (20 ng/ml, M2 polarization) or IFNγ (20 ng/ml) and LPS (10 ng/ml, M1 polarization) for 24 hours.

tag: cell line

value: TRAM

tag: polarization


title: HT29_ORF_CEBPB_24

source_name: HT-29 CEBPB transduction, UniqueID 24


title: HT29_ORF_FOSL1_63

source_name: HT-29 FOSL1 transduction, UniqueID 63


title: RNA_THP1_Tram_IL4_1

tag: treatment


title: RNA_THP1_Tram_CTRL_1

value: Control


title: HT29_ORF_Empty_6

source_name: HT-29 Empty transduction, UniqueID 6

tag: orf

value: Empty


title: RNA_THP1_Tram_IFNLPS_2

value: IFNLPS


title: RNA_THP1_Pano_IL4_1

value: PANO


title: HT29_ORF_KIF3B_108

source_name: HT-29 KIF3B transduction, UniqueID 108

tag: uniqueid


title: RNA_THP1_Tram_IFNLPS_1


title: RNA_THP1_Tram_CTRL_2


title: RNA_THP1_Pano_IL4_2


title: RNA_THP1_Pano_CTRL_2


title: RNA_THP1_Pano_IFNLPS_1


title: RNA_THP1_DMSO_IL4_1

value: DMSO


title: RNA_THP1_Pano_IFNLPS_2


title: HT29_ORF_NUPR1_141

source_name: HT-29 NUPR1 transduction, UniqueID 141

tag: arraybatch


title: RNA_THP1_Pano_CTRL_1


title: HT29_ORF_RORC_186

source_name: HT-29 RORC transduction, UniqueID 186

value: RORC

tag: transductiondate


title: HT29_ORF_GNB2_81

source_name: HT-29 GNB2 transduction, UniqueID 81


title: HT29_ORF_GNA12_78

source_name: HT-29 GNA12 transduction, UniqueID 78


title: HT29_ORF_TMEM17_228

source_name: HT-29 TMEM17 transduction, UniqueID 228


title: HT29_ORF_IFIH1_96

source_name: HT-29 IFIH1 transduction, UniqueID 96


title: HT29_ORF_NR5A2_132

source_name: HT-29 NR5A2 transduction, UniqueID 132


title: HT29_ORF_RIT1_180

source_name: HT-29 RIT1 transduction, UniqueID 180


title: RNA_THP1_DMSO_IL4_2


title: HT29_ORF_RIPK2_177

source_name: HT-29 RIPK2 transduction, UniqueID 177


title: HT29_ORF_SSR2_264

source_name: HT-29 SSR2 transduction, UniqueID 264


title: RNA_THP1_DMSO_IFNLPS_2