title: Anticoagulated peripheral blood_34FSY-0_JTTZR_3

first: Tingting

last: Bao

address: No. 5, Bei Xian Ge, Xicheng District, Beijing

institute: Guang'anmen Hospital, China Academy of Chinese Medical Sciences

description: Gene expression in anticoagulated peripheral blood before treatment in disease group

hyb_protocol: 1.Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2.Equilibrate water bath to 60°C.  3.For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    For 8*60K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul      4.Mix well but gently on a vortex mixer.  5.Incubate at 60°C for exactly 30 minutes to fragment RNA.   6.Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60k  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul 25ul    7.Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8.Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9.Place sample on ice and load onto the array as soon as possible.   10.Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11.Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization   Components 1*244K 2*105K 4*44K 8*15K 8*60K  Volume Prepared 500ul 250ul 110ul 50ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul 40ul    12.Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13.Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14.Hand-tighten the clamp onto the chamber.  15.Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16.Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17.Hybridize at 65°C for 17 hours.

scan_protocol: 1.Assemble the slides into an slide holder.   2.Place assembled slide holders into scanner carousel.  3.Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4.Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Software:  Agilent Feature Extraction    Procedure:  1.Open the Agilent Feature Extraction (FE) software.  2.Add the images (.tif) to be extracted to the FE Project.  3.Set FE Project Properties.  4.Check the Extraction Set Configuration.  5.Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6.Select Project > Start Extracting and export data to txt.

label: Arraystar RNA Flash Labeling Kit

label_protocol: 1.Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2.Add 1.2 μL of T7 Promoter Primer.   3.Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4.Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5.Place the reactions on ice and incubate for 5 minutes.  6.Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7.Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8.Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9.Incubate samples at 40°C in a circulating water bath for 2 hours.  10.Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11.Move samples to ice. Incubate for 5 minutes.  12.Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13.Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14.Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15.Incubate samples in a circulating water bath at 40°C for 2 hours.

extract_protocol: 200 μl blood sample, 750 μl TRIREAGENT BD reagent and 20 μl were added to a centrifuge tube of 1.5 ml glacial acetic acid and mixed. The homogenized sample is incubated at 15-30°C for 5 minutes so that the nucleic acid protein complex is completely dissociated. Each 750 μl of TRIREAGENTBD reagent homogenized sample was added with 0.2 ml of chloroform, mixed well, and incubated at 15 to 30°C for 2 to 3 minutes. The sample was then centrifuged at 12,000 × g for 15 minutes at 4°C. After centrifugation, the mixed liquid will be divided into the lower red phenol-chloroform phase, the middle layer, and the upper colorless water phase. The RNA is all distributed in the water phase. The volume of the water phase is approximately 60% of the TRIREAGENT BD added during the homogenization. The aqueous phase is transferred to a new centrifuge tube, and 500 μl isopropanol is added, and mixed to precipitate the RNA. After mixing, incubate at 15 to 30°C for 10 minutes, and centrifuge at 12,000 × g at 4°C for 10 minutes. At this time, the RNA precipitate that is not visible before centrifugation will form a gelatinous precipitate on the bottom and side walls of the tube. After the RNA is washed, the RNA pellet is re-dissolved. The NanoDrop ND-1000 was used to check the quality of the extracted RNA, and the RNA integrity was assessed by standard denaturing gel electrophoresis.

treatment_protocol: The blood samples of patients in the healthy control group, disease group 0 weeks, and disease group 24 weeks were stored -80℃ for subsequent detection and analysis of LncRNA expression differences.

value: peripheral blood

tag: sample name

tag: gender

value: female

tag: treatment status

value: before treatment

tag: disease state

value: obese type 2 diabetes mellitus and dyslipidemia


title: Anticoagulated peripheral blood_TQY-6_JTTZR_5

status: Public on Jan 14 2022

type: RNA

city: Beijing

country: China

description: Gene expression in anticoagulated peripheral blood after treatment in disease group

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: age

value: after treatment


title: Anticoagulated peripheral blood_TQY-6_JTTZR_6

value: male


title: Anticoagulated peripheral blood_YDG-0_JTTZR_5


title: Anticoagulated peripheral blood_27JXY_Control_6

description: Gene expression in anticoagulated peripheral blood in control group

value: control


title: Anticoagulated peripheral blood_ZXC-0_JTTZR_6


title: V5-C4-2-tetE2F1K185R-GSK_rep1

type: SRA

city: Boston

first: Changmeng

last: Cai

state: MA

address: 100 William T Morrissey Blvd

country: USA

institute: University of Massachusetts Boston

description:
V5_C42_E2F1_K185R_siNTC_GSK.bw
V5_C42_E2F1_K185R_siNTC_GSK_peaks.narrowPeak.gz

library_source: genomic

data_processing:
The sequence quality of raw reads was checked by FastQC (version 0.11.9).
Raw reads were mapped to the hg19 human genome using bwa (version 0.7.9a) with aln and samse sub-commands.
Samtools (version 1.2) was used to convert sam files to bam format.
MACS2 (version 2.1.0) was used to call peak on the bam files.
bedGraph files generated from MACS2 were converted into bigwig files with UCSC tools (version 369).
Genome_build: hg19
Supplementary_files_format_and_content: bw, narrowPeak

molecule: genomic DNA

source_name: C4-2 cell

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using the SMARTer ThruPLEX DNA-Seq Prep Kit (Takara Bio USA).

tag: cell type

value: prostate cancer cell line

tag: medium condition

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

tag: cell line

tag: treatment

value: 50uM GSK2879552 for 24 hours

tag: chip antibody

value: anti-V5 (Thermo Scientific)


title: Anticoagulated peripheral blood_15FSY-6_JTTZR_3


title: RNA_ILC2_BATF_ko_2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

library_source: transcriptomic

data_processing:
Reads were aligned to mouse reference genome mm10 using Star.
Genome_build: mm10

organism: Mus musculus

extract_protocol: Bulk RNA sequencing was performed according to a published Smart-seq2 protocol with minor modification. https://doi.org/10.1038/nprot.2014.006

treatment_protocol: 2000 ILC2s (Lin-CD90.2+ST2+) from the lungs of WT and cKO mice after influenza virus infection at day 9 were directly sorted into lysis buffer containing Protector RNase Inhibitor (Roche). Three replicates from each group were subsequently sequenced. 2 ng of purified RNA were used as input for SMART-Seq2 protocol .

tag: strain

value: Batffl/flPLZF-Cre+

tag: infection

value: influenza A/PR8/34

value: Lung

tag: genotype/variation

value: BATF KO


title: ht_Sham_rep11_batchB

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.4.11
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 1.16/2.1/2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to rat genome using STAR (Dobin et al., 2013)  v2.7.2b with default parameters based on RefSeq annotation version 106 for GCF_000001895.5/Rnor_6.0
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 106 for GCF_000001895.5/Rnor_6.0) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Genome_build: GCF_000001895.5/Rnor_6.0 (primary assembly and mitochondrion)
Supplementary_files_format_and_content: Character (TAB) separated value file containing mRNA abundance measurements

organism: Rattus norvegicus

source_name: Hypothalamus

extract_protocol:
Using a microscope with an attached freezing plate, hypothalami were removed from the brains and frozen on dry ice in Eppendorf tubes immediately. Tissue was homogenized using QIAGEN Tissue Lyser II (85300; QIAGEN) and further purified using Proteinase K (PK) Solution (MC5005; Promega). Prior to extraction, RNA integrity and concentration were tested using NanoDrop™ 2000c spectrophotometer (Thermo Fisher Scientific). In the following step, mRNA was extracted using Promega’s “Maxwell SimplyRNA Tissue Kit” (AS1340).
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was >7.2. DNA libraries suitable for sequencing were prepared from 100 ng of total RNA with oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) according to manufacturer’s instructions. After 15 cycles of PCR amplification, the size distribution of the barcoded DNA libraries was estimated ~285/335 bp (batch A/batch B) by electrophoresis on Agilent DNA 1000 Bioanalyzer microfluidic chips.

value: Hypothalamus

tag: group

value: Sham

value: Wistar rat

tag: batch

value: B


title: RNA_ILC2_BATF_ko_1


title: Anticoagulated peripheral blood_31GSQ-6_JTTZR_4

value: peripheral blood

value: female


title: V5-C4-2-tetE2F1K185R-Dox_rep1

description:
V5_C42_E2F1_K185R_siRB.bw
V5_C42_E2F1_K185R_siRB_peaks.narrowPeak.gz

value: 0.25ug/ml doxycycline for 3 days


title: ht_Sham_rep10_batchB


title: ht_Sham_rep09_batchB


title: V5-C4-2-tetE2F1K185R-Veh_rep2

description:
V5_C42_E2F1_K185R_siNTC.bw
V5_C42_E2F1_K185R_siNTC_peaks.narrowPeak.gz

value: untreated


title: RNA_ILC2_BATF_ko_3

value: Batffl/flPLZF-Cre-


title: RNA_ILC2_WT_3

value: Wild type


title: Anticoagulated peripheral blood_16GSQ-0_JTTZR_2

description: Gene expression in anticoagulated peripheral blood before treatment in disease groupv

value: before treatment

value: obese type 2 diabetes mellitus and dyslipidemia


title: V5-C4-2-tetE2F1K185R-Dox_rep2

value: prostate cancer cell line

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: anti-V5 (Thermo Scientific)


title: V5-C4-2-tetE2F1K185R-Veh_rep1


title: RNA_ILC2_WT_2

value: influenza A/PR8/34

value: Lung


title: V5-C4-2-tetE2F1-Dox-GSK_rep2

description:
V5_C42_E2F1_WT_siRB_GSK.bw
V5_C42_E2F1_WT_siRB_GSK_peaks.narrowPeak.gz

value: 0.25ug/ml doxycycline for 3 days, then treat 50uM GSK2879552 for 24 hours


title: V5-C4-2-tetE2F1-Dox-GSK_rep1


title: ChIP_BATF_ILC2_2

data_processing:
Reads were aligned to mouse reference genome mm10 using Bowtie2.
Reads were then filtered using SAMtools
Peaks were called using SEACR (version1.1) (Meers et al., 2019) with options: 0.01 non stringent.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

treatment_protocol: ILC2s were sorted from the lungs of C57BL/6 mice and cultured for 2 weeks to expand the cells. 100,000 ILC2s were processed and library construction according to CUT&Tag ChIP-Seq approach mentioned (version 2) (Kaya-Okur et al., 2019) (step wise protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).

value: C57BL/6 mice

value: influenza virus

tag: antibody

value: anti-BATF


title: Anticoagulated peripheral blood_3ZXC-6_JTTZR_2

value: peripheral blood

tag: sample name

value: male

value: after treatment


title: ht_Saline_rep08_batchB

value: Hypothalamus

value: Saline

value: Wistar rat

value: B


title: ChIP_BATF_ILC2_1

extract_protocol: (Kaya-Okur et al., 2019) (step wise protocol can be found at https://www.protocols.io/view/bench-top-cut-amp-tag-z6hf9b6).


title: ht_Sham_rep07_batchB

value: Sham


title: ht_Sham_rep01_batchA

value: A


title: ht_Sham_rep03_batchA


title: ht_Sham_rep08_batchB


title: ht_Sham_rep05_batchA


title: ht_Sham_rep02_batchA


title: ht_Sham_rep04_batchA


title: ht_Sham_rep06_batchB


title: RNA_ILC2_WT_1

value: Batffl/flPLZF-Cre-

value: Wild type


title: Anticoagulated peripheral blood_8ZXF_Control_4

tag: gender

value: control


title: V5-C4-2-tetE2F1-GSK_rep2

description:
V5_C42_E2F1_WT_siNTC_GSK.bw
V5_C42_E2F1_WT_siNTC_GSK_peaks.narrowPeak.gz

value: prostate cancer cell line

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: 50uM GSK2879552 for 24 hours

value: anti-V5 (Thermo Scientific)


title: V5-C4-2-tetE2F1-GSK_rep1


title: ht_Saline_rep06_batchB


title: ChIP_IGG_ILC2_2

value: C57BL/6 mice

value: influenza virus

value: Lung

value: Rabbit normal serum IgG1


title: Anticoagulated peripheral blood_8ZXF_Control_3

value: peripheral blood

value: female

tag: treatment status


title: Anticoagulated peripheral blood_8ZXF_Control_5

value: male

tag: disease state


title: Anticoagulated peripheral blood_2LP-0_JTTZR_1

tag: tissue

value: before treatment

value: obese type 2 diabetes mellitus and dyslipidemia


title: Anticoagulated peripheral blood_TQY-0_JTTZR_4

tag: age


title: ht_Saline_rep07_batchB

value: Hypothalamus

value: Saline

value: Wistar rat

value: B


title: ht_Saline_rep05_batchB


title: Anticoagulated peripheral blood_4CGL_Control_2

value: control


title: Anticoagulated peripheral blood_3JLM_Control_1


title: V5-C4-2-tetE2F1-Dox_rep2

description:
V5_C42_E2F1_WT_siRB.bw
V5_C42_E2F1_WT_siRB_peaks.narrowPeak.gz

tag: cell type

value: prostate cancer cell line

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

value: 0.25ug/ml doxycycline for 3 days


title: Anticoagulated peripheral blood_1LP-6_JTTZR_1

value: after treatment


title: ht_Saline_rep04_batchB


title: ChIP_IGG_ILC2_1

value: C57BL/6 mice

value: influenza virus


title: ht_Saline_rep03_batchA

value: A


title: V5-C4-2-tetE2F1-Veh_rep1

description:
V5_C42_E2F1_WT_siNTC.bw
V5_C42_E2F1_WT_siNTC_peaks.narrowPeak.gz

tag: medium condition

value: untreated

value: anti-V5 (Thermo Scientific)


title: ht_Saline_rep02_batchA


title: ht_Saline_rep01_batchA


title: V5-C4-2-tetE2F1-Veh_rep2

tag: cell line


title: BATF_KO_ILC2_Rep1

data_processing:
Reads were aligned to mouse reference genome mm9 using Bowtie2.
Reads were then filtered using SAMtools (-F1796).
Peaks were called using MACS2 (--no model --shift -100 --ext size 200 -q 0.01) (version 2.1.1).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using the bamCoverage function of deepTools.

extract_protocol: ATAC-seq was performed according to a published protocol (Buenrostro et al., 2015) with minor modification.

treatment_protocol: Batffl/flPLZF-Cre– or Batffl/flPLZF-Cre+ mice were used for ATAC-seq experiments. 50,000-80,000 ILC2 cells were sorted from the lungs of WT and cKO mice after influenza virus infection at day 9.

value: Batffl/flPLZF-Cre+

value: influenza A/PR8/34

value: Lung


title: V5-C4-2-tetE2F1-Dox_rep1

tag: treatment


title: ht_PYY_rep01_batchB

value: Hypothalamus

value: PYY


title: ht_PYY_rep02_batchB

value: Wistar rat


title: ht_PYY_rep03_batchB

value: B


title: ht_PYY_Lira_rep09_batchB


title: BATF_KO_ILC2_Rep2


title: WT_ILC2_Rep2

value: Batffl/flPLZF-Cre-

value: wild type


title: ht_PYY_rep04_batchB


title: WT_ILC2_Rep1


title: RB-C4-2-Ctrl_rep1

description:
C42_Rb_Veh.bw
C42_Rb_Veh_peaks.narrowPeak.gz

value: prostate cancer cell line

value: In RPMI 1640 medium with 5% charcoal-stripped FBS (CSS)

tag: chip antibody

value: anti-RB (cell signaling)


title: ht_PYY_Lira_rep08_batchB

tag: strain


title: RB-C4-2-Ctrl_rep2


title: ht_PYY_Lira_rep04_batchA


title: ht_PYY_Lira_rep10_batchB


title: ht_PYY_Lira_rep06_batchB


title: ht_PYY_Lira_rep05_batchA


title: Transitional GFP+ Late Repli-seq rep1

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

description: Transitional GFP+ Late rep1

data_processing:
Library strategy: Repli-seq
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 reference genome mm9 using BWA.
Coverage over 100 kbp genomic bins were count across the genome, followed by the Loess smoothing of bin counts as described in (C. Marchal et al., Nat Protoc, 2018).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig, smoothen genome coverage over 100Kb.

source_name: Embryonic stem cells

growth_protocol: Mouse E14 ES cell lines were cultured in DMEM with GlutaMAX (Invitrogen) containing 15% FCS, LIF, penicillin/streptomycin, 0.1 mM 2-mercaptoethanol, 3 mM CHIR99021 (a GSK3b inhibitor) and 1 mM PD0325901 (a MEK inhibitor) on the gelatin-coated plate.

extract_protocol:
Genomic DNA was isolated from each fraction using SDS-proteinase K buffer and purified by phenol-chloroform extraction. Genomic DNA was fragmented using the Covaris sonicator to get 700 bp average fragment size. The sheared BrdU-labeled DNA from each fraction was immunoprecipitated using 0.5 μg of mouse anti-BrdU antibody followed by 50 μL of precleared-Dynabeads sheep anti-mouse IgG (Invitrogen, 11201D). The immunoprecipitated pellet was digested overnight with Proteinase K and purified by phenol-chloroform extraction.
The replication timing libraries were prepared based on Accel-NGS methyl seq library kit (Swift Biosciences, MI, USA) according to the manufacturer’s protocol. The BrDU immuno-precipitated DNA was denatured and subjected to Adaptase reaction. This step was followed by an extension reaction with two cleanup steps utilizing Agencourt Ampure XP beads (Beckman Coulter, IN, USA). The elute was subjected to ligation step with a follow-up of Ampure bead mediated purification. Indexing PCR was done with appropriate and unique adaptor primer for an individual sample preparation. PCR program consisted of 98ºC for 30 seconds, then 9 cycles of 98ºC for 10 seconds, 60ºC for 30 seconds and 60ºC for 60 seconds followed by a 4ºC hold cycle. The PCR product was further purified by Ampure beads and eluted out in a 20μl volume using TE buffer provided by the manufacturer. The libraries were checked for size, using Agilent 2200 Tape Station (Agilent, CA, USA) utilizing DNA high sensitivity tape (Agilent, CA, USA). Up to 12 libraries were pooled together after Qubit quantification with Qubit DNA HS assay kit (Thermofisher Scientific, NY, USA) and loaded into Nextseq 500/550 high output cartridge (Illumina, CA, USA) for 75 cycle single end sequencing.

treatment_protocol: A double thymidine block was used for cell synchronization at G1/S border. Cells were blocked for 12 h with 2.5 mM thymidine, released for 9 h by washing out the thymidine, and then blocked again with 2.5 mM thymidine for 14 h to arrest all the cells at the beginning of S-phase. Cell cycle arrest was subsequently released with two washed of warm thymidine-free medium. After release, cells were pulse labeled with the nucleotide analog 5-bromo-2-deoxyuridine (BrdU) for 2 h to mark nascent DNA replicating early-, mid-, late-S-phase, respectively. 6h after releasing from block, the cells were sorted into ESCs and 2CLCs according to the GFP fluorescence using FACS.

value: Embryonic stem cell line

tag: gfp

value: Plus

tag: s-phase fraction

value: Late

tag: ip antibody

value: BrdU (Sigma, B8434)


title: ht_PYY_Lira_rep07_batchB

tag: group

tag: batch


title: ht_PYY_Lira_rep03_batchA

value: A


title: Transitional GFP+ Late Repli-seq rep2

description: Transitional GFP+ Late rep2


title: ht_PYY_Lira_rep02_batchA


title: Transitional GFP+ Mid Repli-seq rep2

description: Transitional GFP+ Mid rep2

value: Mid


title: Transitional GFP+ Mid Repli-seq rep1

description: Transitional GFP+ Mid rep1


title: ht_PYY_Lira_rep01_batchA


title: ht_Lira_rep05_batchB

value: Lira


title: ht_Lira_rep04_batchB


title: ht_Lira_rep01_batchB


title: ht_Lira_rep03_batchB


title: ht_Lira_rep02_batchB


title: ht_Lean_rep06_batchA

value: Lean


title: Transitional GFP+ Early Repli-seq rep2

description: Transitional GFP+ Early rep2

value: Early


title: ht_Lean_rep02_batchA

value: Hypothalamus


title: ht_Lean_rep04_batchA

value: Wistar rat


title: Transitional GFP- Late Repli-seq rep1

description: Transitional GFP- Late rep1

value: Minus


title: ht_Lean_rep01_batchA


title: Transitional GFP- Late Repli-seq rep2

description: Transitional GFP- Late rep2


title: ht_Lean_rep03_batchA


title: Transitional GFP- Mid Repli-seq rep1

description: Transitional GFP- Mid rep1


title: Transitional GFP- Mid Repli-seq rep2

description: Transitional GFP- Mid rep2


title: Transitional GFP- Early Repli-seq rep2

description: Transitional GFP- Early rep2


title: ht_Lean_rep05_batchA


title: ht_Bypass_rep14_batchB

value: Bypass

value: B


title: GFP+(ESC) Late Repli-seq rep2

description: GFP+(ESC) Late rep2

extract_protocol:
Cells were pulse labeled with the nucleotide analog 5-bromo-2-deoxyuridine (BrdU) for 2 h to mark nascent DNA. The cells were sorted into early-, mid- and late S-phase fractions 20,000 cells each on the basis of DNA content using FACS. Genomic DNA was isolated from each fraction using SDS-proteinase K buffer and purified by phenol-chloroform extraction. Genomic DNA was fragmented using the Covaris sonicator to get 700 bp average fragment size. The sheared BrdU-labeled DNA from each fraction was immunoprecipitated using 0.5 μg of mouse anti-BrdU antibody followed by 50 μL of precleared-Dynabeads sheep anti-mouse IgG (Invitrogen, 11201D). The immunoprecipitated pellet was digested overnight with Proteinase K and purified by phenol-chloroform extraction.
The replication timing libraries were prepared based on Accel-NGS methyl seq library kit (Swift Biosciences, MI, USA) according to the manufacturer’s protocol. The BrDU immuno-precipitated DNA was denatured and subjected to Adaptase reaction. This step was followed by an extension reaction with two cleanup steps utilizing Agencourt Ampure XP beads (Beckman Coulter, IN, USA). The elute was subjected to ligation step with a follow-up of Ampure bead mediated purification. Indexing PCR was done with appropriate and unique adaptor primer for an individual sample preparation. PCR program consisted of 98ºC for 30 seconds, then 9 cycles of 98ºC for 10 seconds, 60ºC for 30 seconds and 60ºC for 60 seconds followed by a 4ºC hold cycle. The PCR product was further purified by Ampure beads and eluted out in a 20μl volume using TE buffer provided by the manufacturer. The libraries were checked for size, using Agilent 2200 Tape Station (Agilent, CA, USA) utilizing DNA high sensitivity tape (Agilent, CA, USA). Up to 12 libraries were pooled together after Qubit quantification with Qubit DNA HS assay kit (Thermofisher Scientific, NY, USA) and loaded into Nextseq 500/550 high output cartridge (Illumina, CA, USA) for 75 cycle single end sequencing.


title: Transitional GFP- Early Repli-seq rep1

description: Transitional GFP- Early rep1


title: ht_Bypass_rep13_batchB


title: ht_Bypass_rep07_batchA


title: ht_Bypass_rep11_batchA


title: ht_Bypass_rep12_batchB


title: ht_Bypass_rep08_batchA


title: ht_Bypass_rep10_batchA


title: GFP+(ESC) Late Repli-seq rep1

description: GFP+(ESC) Late rep1


title: ht_Bypass_rep09_batchA


title: ht_Bypass_rep06_batchA


title: Transitional GFP+ Early Repli-seq rep1

description: Transitional GFP+ Early rep1


title: ht_Bypass_rep05_batchA


title: ht_Bypass_rep04_batchA


title: GFP+(ESC) Mid Repli-seq rep2

description: GFP+(ESC) Mid rep2


title: ht_Bypass_rep03_batchA


title: ht_Bypass_rep02_batchA


title: GFP+(ESC) Mid Repli-seq rep1

description: GFP+(ESC) Mid rep1


title: GFP+(ESC) Early Repli-seq rep1

description: GFP+(ESC) Early rep1


title: ht_BWM_rep07_batchA

value: BWM


title: ht_Bypass_rep01_batchA


title: ht_BWM_rep04_batchA


title: GFP+(ESC) Early Repli-seq rep2

description: GFP+(ESC) Early rep2


title: ht_BWM_rep03_batchA


title: GFP-(ESC) Late Repli-seq rep2

description: GFP-(ESC) Late rep2


title: ht_BWM_rep05_batchA


title: ht_BWM_rep02_batchA


title: ht_BWM_rep06_batchA


title: GFP-(ESC) Late Repli-seq rep1

description: GFP-(ESC) Late rep1


title: siG3bp1-2

city: Newark

first: Danish

last: Sayed

state: NJ

address: 185 south orange avenue

department: CBMM

institute: Rutgers-NJMS

data_processing:
RNAseq analsyis done by Active Motif (Data Explain file attached in Pdf format). Some steps are briefly described below
Paired-end 42bp sequencing reads mapped to the genome (rn6) using STAR algorithm, alignment stored in BAM format
The number of fragments overlapping predefined genimocfeatures of inters are counted. Only reads that have both ends aligned are counted. Gene anotations used were obtained from Subread package (originally from NCBI RefSeq)
DESeq2 is used to identify statisticaly significant differential genes. Data normaliation: DESeq2 expects un-normalized count matirx of sequencing grafments. The model internally corrects for library size using their median-of-ratios method.
After dfferential test has been applied, the p-value is caluclated for each gene and adjusted to control the number of false positives by multiple testing adjustment procedure.  DESeq2 filters out genes with low counts by independent filtering, using average counts of each gene (baseMean), across all samples and omits genes with average normalized counts below the filtering threshold. This threshold is automatically determined to maximize detection power at a specificed false discovery rate (FDR).
Genome_build: rn6

source_name: Neonatal ventricular myocytes

growth_protocol: Primary ventricular cardiomyocyte cultures from 1day old Sprague Dawley rat pups

extract_protocol:
frozed Cell pellet (active Motif protocol) was sent o Active Motif for RNA extraction
Directional Poly-A RNAseq libraries were prepared and sequenced as P42 (42-bp paired-ends reads) on Illumina NextSeq 500 by Active Motif

treatment_protocol: NRVMs from 3 independent cultures were infected with ad-siG3bp1 or ad-siLUC (control) for 48hrs,(knockdown of endogenous G3bp1 validated independent cultures), cells were collected and cell pellet was snap freezed according to Active Motif protocol

value: Neonatal ventricular myocytes

value: NRVM infected with siG3bp1

value: 1 day old pups

value: Sprague Dawley


title: siLUC-2

description: 02_4444Rutgers_siLuciferase-control-2_RNAseq_rn_i25

value: NRVM infected with siLUC


title: GFP-(ESC) Mid Repli-seq rep1

description: GFP-(ESC) Mid rep1

value: Embryonic stem cell line

value: BrdU (Sigma, B8434)


title: siLUC-3

description: 03_4444Rutgers_siLuciferase-control-3_RNAseq_rn_i27


title: siG3bp1-3


title: siLUC-1

description: 01_4444Rutgers_siLuciferase-control-1_RNAseq_rn_i23


title: GFP-(ESC) Mid Repli-seq rep2

description: GFP-(ESC) Mid rep2

value: Mid


title: ht_BWM_rep01_batchA

value: A


title: GFP-(ESC) Early Repli-seq rep2

description: GFP-(ESC) Early rep2


title: GFP-(ESC) Early Repli-seq rep1

description: GFP-(ESC) Early rep1


title: 650d_female_5

city: Mexico

first: CONSUELO

last: LOMAS

state: MEXICO

address: Vasco de Quiroga 15, Belisario Domínguez Sección XVI,

department: REPRODUCTIVE BIOLOGY

country: Mexico

institute: INCMNSZ

description: PROCESSED DATA FEMALE

data_processing:
Libraries were normalized to 10 nM and were diluted/denatured to 20 pM before loading on the cBot 2X100 Paired end sequencing was performed on the Illumina HiSeq 2500 sequencer.
Output demultiplexed reads were exported to Partek Flow for analysis.
Read FASTQ files were quality trimmed to Phred 30 at each end.
Trimmed reads were aligned to the Rattus norvegicus genomic reference (RGSC 5.0/rn5) with STAR aligner v2.3.1j.
Gene and transcript abundance were quantified against rn5 RefSeq annotation and normalized for transcript abundance for all samples as a dataset using RPKM.
Genome_build: RGSC 5.0/rn5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample .

source_name: Liver

extract_protocol:
F1 liver tissue samples (10ãƒ»0 mg) were homogenized with the BioSpec BeadBeater and RNA was extracted using the QIagen miRNeasy mini kit (Qiagen), according to the manufacturer's instructions, n= 6 for all groups. RNA isolated quantity and quality were determined by using a Nanodrop spectrophotometer (Nanodrop Technologies, DE, USA) and stored at -80°C until use.
cDNA libraries were prepared from 1 ?g total RNA using an Illumina TruSeq RNA LS Sample Preparation kit v2 according to the manufacturer's instructions (Illumina, San Diego, CA, USA). Final individual cDNA libraries were assessed for quality and fragment size using the Agilent DNA 1000. Sequencing libraries were quantified with KAPA Library Quantification kit for Illumina platforms.

value: Wistar

value: Liver

tag: Sex

value: female

value: post natal day 650


title: 650d_female_4

description: PROCESSED DATA FEMALE


title: 650d_female_3

description: PROCESSED DATA FEMALE


title: 650d_female_2

description: PROCESSED DATA FEMALE


title: 650d_female_1

description: PROCESSED DATA FEMALE


title: ATAC_Nav_BM_800

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the hg38 version of the human genome using Bowtie.
For each sample peaks of accessibility were identified and annotated using MACS2.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bw: Reads per million normalized bigWig files.

extract_protocol: Cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

tag: subject id

tag: gender

value: Male

tag: race

value: Caucasian

tag: ethnicity

value: Non-Hispanic

tag: diagnosis

value: Healthy

value: Bone Marrow

tag: cell subset

value: Naive B cells


title: ATAC_Nav_BM_66294_513

tag: age

value: Female

tag: tissue


title: 110d_female_5

description: PROCESSED DATA FEMALE

value: post natal day 110


title: ATAC_Nav_BM_66294_510

value: Hispanic


title: 110d_female_3

description: PROCESSED DATA FEMALE


title: siG3bp1-1

tag: cell type

value: Neonatal ventricular myocytes

tag: treatment

value: NRVM infected with siG3bp1

value: 1 day old pups

value: Sprague Dawley


title: ATAC_Nav_BM_2252


title: 110d_female_1

description: PROCESSED DATA FEMALE

tag: strain

value: Wistar


title: ATAC_Nav_BM_2206


title: 650d_male_4

description: PROCESSED DATA MALE

value: Liver

value: male


title: 110d_female_6

description: PROCESSED DATA FEMALE

value: female


title: 650d_female_6

description: PROCESSED DATA FEMALE

value: post natal day 650


title: 650d_male_1

description: PROCESSED DATA MALE


title: 650d_male_3

description: PROCESSED DATA MALE


title: 650d_male_2

description: PROCESSED DATA MALE


title: ATAC_Nav_BM_208

value: African-American


title: 110d_female_4

description: PROCESSED DATA FEMALE


title: 110d_male_6

description: PROCESSED DATA MALE


title: ATAC_Nav_BM_207_1177_blue

value: Caucasian

value: Non-Hispanic


title: ATAC_Nav_BM_1895

value: Asian

value: Healthy

value: Bone Marrow


title: 110d_male_5

description: PROCESSED DATA MALE

value: post natal day 110


title: 110d_male_4

description: PROCESSED DATA MALE


title: ATAC_Nav_BM_66294_512

value: Female

value: Hispanic

value: Naive B cells


title: ATAC_Nav_BL_57983_163

value: Blood


title: 110d_male_3

description: PROCESSED DATA MALE


title: ATAC_Nav_BL_2206

value: Male


title: 110d_female_2

description: PROCESSED DATA FEMALE

value: Wistar


title: 110d_male_2

description: PROCESSED DATA MALE

value: Liver


title: 650d_male_6

description: PROCESSED DATA MALE

value: male


title: 110d_male_1

description: PROCESSED DATA MALE


title: 650d_male_5

description: PROCESSED DATA MALE


title: ATAC_Nav_BL_1895


title: FACI-3

city: Hong Kong

first: Yun

last: Cheng

state: Hong Kong

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

data_processing:
Sequenced libraries were evaluated with FastQC
Software SOAPnuke was used to filter reads
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts)  software was used for RNA-seq reads alignment to reference genome
We detect DEGs with DEseq2. Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: txt files include read counts for each sample

source_name: Intestinal Epithelium

extract_protocol:
Intestinal epithelium was isolated by EDTA-DTT separation method. The total RNA from the intestinal epithelium of 4-month-old WT and Faci-/- mice (n = 3 per group) was extracted by RNAiso Plus reagent (Takara)
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols

tag: genotype

value: FACI-/-


title: MIA RR

city: Nagoya

first: YOICHI

last: MATSUO

state: Aichi

address: 1 Kawasumi Mizuhocho Mizuhoku

department: Gastroenterological Surgery

country: Japan

institute: Nagoya City University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Ver.3.0 Microarray (Agilent, G4851C) 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) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. The 75th percentile shift normalization was performed using Agilent GeneSpring GX.

source_name: radiation-resistant MIA PaCa-2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng Total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The MIA PaCa-2, PANC-1, and SW1990 cell lines and FBs were maintained in DMEM (Sigma Aldrich; Merck KGaA). Both the RPMI-1640 medium and DMEM were supplemented with 10% fetal bovine serum (FBS) (Gibco/Thermo Fisher Scientific). All media were supplemented with 10 mg/ml streptomycin, 10,000 U/ml penicillin, and 25μg amphotericin B (Gibco/Thermo Fisher Scientific). All cell lines were cultured at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy mini Kit (Qiagen) following the manufacturer's instructions. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PaCa cell lines (AsPC-1, BxPC-3, MIA PaCa-2, and SW1990) were seeded in a 100 mm dish and cultured. Upon reaching 50% confluence, the cells were irradiated with 2 Gy radiation and incubated until reaching 90% confluence, after which the cells were passaged. With each passage, the irradiation process was repeated until the total radiation dose reached at least 60 Gy.

tag: cell line

value: MIA PaCa-2

tag: phenotype

value: radiation resistant


title: MIA normal

source_name: MIA PaCa-2

value: normal


title: cd41:GFPlow-runx1-/- bloodless 16dpf

city: Bethesda

first: Kai

last: Yu

state: Maryland

address: 50 South Drive, Bldg 50, Room 5151

institute: NHGRI

data_processing:
Sequences from the Chromium platform were de-multiplexed and aligned using CellRanger ver. 2.0.2 from 10x Genomics using custom zebrafish reference genome (GRCz10) and transcript annotation reference (GRCz10.87) with default parameters.
Genome_build: GRCz10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, features.tsv, matrix.mtx

molecule: polyA RNA

organism: Danio rerio

source_name: sorted cd41:GFPlow

extract_protocol:
Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium.
Single-cell RNA-seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis, cDNA preparation and library construction were prepared following the manufacturer's protocol.

value: EK

tag: genotype/variation

value: runx1-/- (del8, hg96)-tg(cd41:GFP)

value: 16 dpf

value: sorted cd41:GFPlow


title: ATAC_Nav_BL_115

value: Asian

value: Non-Hispanic

value: Healthy


title: FACI-2


title: ATAC_Nav_BL_114

value: Female

value: Caucasian

value: Naive B cells


title: cd41:GFPlow-WT 16dpf

value: WT- tg(cd41:GFP)


title: cd41:GFPlow-runx1-/- 6dpf

value: 6 dpf


title: cd41:GFPlow-runx1-/- 10dpf

value: 10 dpf


title: WT-3

value: wild type


title: FACI-1

value: FACI-/-


title: cd41:GFPlow-WT 10dpf


title: WT-2


title: ATAC_PopD_800_S8

value: Male

value: Bone Marrow

value: Antibody-secreting cells (ASC)


title: WT-1


title: cd41:GFPlow-WT 6dpf

value: EK


title: ATAC_PopD_66294_513

value: Hispanic


title: cd41:GFPlow-runx1-/- 2.5dpf

value: runx1-/- (del8, hg96)-tg(cd41:GFP)

value: 2.5 dpf

value: sorted cd41:GFPlow


title: Epithelium from mouse YM4

city: Philadelphia

first: Kelly

middle: A

last: Whelan

state: PA

address: 3307 N Broad St. PAHB Rm 203

department: Fels Institute

institute: Temple University

description:
Illumina sequenced bulk RNA-Seq data
YM4

data_processing:
bcl2fastq
Genome alignment and gene-level summarization was done using Rsubread (v2.8)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene matrix in txt with transcript counts

source_name: Esophageal Epithelium

extract_protocol:
Total RNA was extracted and purified using RNeasy mini kit (Catalogue No. 74104, Qiagen), following manufacturer's instructions.
NEB RNA ultra II kit was used to prepare the bulk mRNA library.  mRNA was first enriched by magnetic beads with oligod(T). mRNA was fragmentated and cDNA was generated via reverse trancription. Illumina adapters were ligated to the cDNAs to make mRNAseq libraries.

value: Esophageal Epithelium

value: Young

value: M


title: cd41:GFPlow-runx1-/- recovered16dpf

value: 16 dpf


title: Epithelium from mouse YF5

description:
Illumina sequenced bulk RNA-Seq data
YF5

value: F


title: ATAC_PopD_66294_510

value: Caucasian

value: Non-Hispanic


title: C. elegans CB Dox 3

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

description: CB Dox 3

data_processing:
FastQC (default parameters) was used to verify the quality of the mapping. No low-quality reads were present and no trimming was needed.
generate STAR (version 2.73a) genome indexes with following parameters: STAR --runThreadN 16 --runMode genomeGenerate --limitGenomeGenerateRAM 33524399488 --genomeFastaFiles Caenorhabditis_elegans.WBcel235.dna_rm.toplevel.fa --sjdbGTFfile Caenorhabditis_elegans.WBcel235.89.gtf --sjdbOverhang 99
Map reads for each sample using STAR (version 2.73a) aligner with the following parameters: STAR --runThreadN 16 --genomeDir ./Data/stargenome/$STARGENOMENAME --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesIn $R1 --outFileNamePrefix ./Data/mapped/$SAMPLE
Counts for each sample features (outputed by STAR) where read into R
The obtained STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package edgeR (version 3.24.3) using a generalized-linear model. The trimmed mean of M values (TMM) method was chosen to normalize the counts and the Cox-Reid common dispersion method for computing the dispersion parameter (tag wise dispersion was also computed).
A threshold of 1 log2 absolute fold change and p-value larger than 0.05 were considered when identifying the differentially expressed genes.
The clusterProfiler (version 3.10.1) package was then used to perform various Enrichment Analysis on the obtained results.
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans CB4856

growth_protocol: Worms of each strain were cultured on plates seeded with E. coli OP50, then eggs were obtained by alkaline hypochlorite treatment of gravid adults. A synchronized L1 population was obtained by incubating the egg suspension in M9 butter overnight at room temperature. Approximately 2000 L1 worms were transferred onto plates with or without 15 μg/mL Dox seeded with E. coli HT115. L4 worms were harvested after 50 h by three times of washing with M9 buffer. Tubes containing worm pellets were immediately submerged in liquid nitrogen for snap freezing and stored at -80ºC until use.  Three biological replicates were collected for each condition.

extract_protocol:
On the day of the extraction, 1 mL of TriPure Isolation Reagent was added to each tube. The samples were then frozen and thawed quickly eight times with liquid nitrogen and 37ºC water bath to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel.
BGISeq-500 library construction Protocol

treatment_protocol: DOX: 15 μg/mL doxycycline

value: Worms coming from synchronized adults, L1's hatched o/n and seeded on Treatment plates (large plates with 600uL of 10xHT115; Approx. 1000 worms per plate) DOX:15ug/mL doxycycline

tag: experimental group

value: Treatment

tag: concentration (ng/μl)

tag: volume (μl)

tag: total quantity (μg)

tag: rin

tag: harvest date

tag: experiment start


title: Stroma from mouse Y3S

description:
Illumina sequenced bulk RNA-Seq data
Y3S

source_name: Esophageal Stroma

value: Esophageal Stroma

tag: Sex


title: ATAC_PopD_207_1177

tag: subject id

tag: age

tag: gender

value: Female

tag: race

tag: ethnicity

value: Bone Marrow

tag: cell subset


title: Epithelium from mouse Y3E

description:
Illumina sequenced bulk RNA-Seq data
Y3E

tag: tissue

tag: strain


title: C. elegans CB Dox 2

description: CB Dox 2

tag: treatment


title: Stroma from mouse Y1S

description:
Illumina sequenced bulk RNA-Seq data
Y1S


title: ATAC_Nav_BL_113

tag: diagnosis

value: Healthy

value: Blood

value: Naive B cells


title: ATAC_PopD_1464_S4

value: African-American

value: Antibody-secreting cells (ASC)


title: C. elegans CB Dox 1

description: CB Dox 1

tag: experimental group

tag: concentration (ng/μl)


title: Epithelium from mouse OM8

description:
Illumina sequenced bulk RNA-Seq data
OM8

value: Esophageal Epithelium

value: Aged


title: ATAC_PopB_800_S7

value: Male


title: Epithelium from mouse Y1E

description:
Illumina sequenced bulk RNA-Seq data
Y1E

value: Young


title: ATAC_PopB_66294_513


title: Epithelium from mouse OF5

description:
Illumina sequenced bulk RNA-Seq data
OF5


title: C. elegans CB Control 1

description: CB Control 1

value: Worms coming from synchronized adults, L1's hatched o/n and seeded on Treatment plates (large plates with 600uL of 10xHT115; Approx. 1000 worms per plate)

value: Control

tag: volume (μl)

tag: total quantity (μg)


title: ATAC_PopB_66294_510

value: Caucasian

value: Not Indicated


title: ATAC_PopB_66294_512


title: C. elegans CB Control 2

description: CB Control 2

tag: rin

tag: harvest date


title: C. elegans N2 Dox 2

description: N2 Dox 2

source_name: Caenorhabditis elegans N2

value: Worms coming from synchronized adults, L1's hatched o/n and seeded on Treatment plates (large plates with 600uL of 10xHT115; Approx. 1000 worms per plate) DOX:15ug/mL doxycycline

value: Treatment

tag: experiment start


title: Epithelium from mouse O3E

description:
Illumina sequenced bulk RNA-Seq data
O3E

tag: Sex


title: C. elegans N2 Dox 3

description: N2 Dox 3


title: ATAC_PopB_208_2308

tag: subject id

tag: age

value: Female

value: Hispanic


title: Stroma from mouse O3S

description:
Illumina sequenced bulk RNA-Seq data
O3S

value: Esophageal Stroma


title: cd41:GFPlow-WT 2.5dpf

value: EK

tag: genotype/variation

value: WT- tg(cd41:GFP)

value: 2.5 dpf

value: sorted cd41:GFPlow


title: Stroma from mouse O2S

description:
Illumina sequenced bulk RNA-Seq data
O2S


title: ATAC_PopB_207_1177

tag: gender

tag: race

value: African-American

tag: ethnicity

value: Non-Hispanic

value: Bone Marrow

value: Antibody-secreting cells (ASC)


title: ATAC_PopD_66294_512

tag: tissue

tag: cell subset


title: C. elegans N2 Dox 1

description: N2 Dox 1

tag: strain

tag: treatment


title: C. elegans N2 Control 3

description: N2 Control 3

value: Worms coming from synchronized adults, L1's hatched o/n and seeded on Treatment plates (large plates with 600uL of 10xHT115; Approx. 1000 worms per plate)

tag: experimental group

tag: concentration (ng/μl)


title: ATAC_PopB_1_2206

value: Male


title: C. elegans CB Control 3

description: CB Control 3

value: Control

tag: volume (μl)

tag: total quantity (μg)


title: C. elegans N2 Control 2

description: N2 Control 2

tag: rin

tag: harvest date


title: Stroma from mouse O1S

description:
Illumina sequenced bulk RNA-Seq data
O1S

value: Aged

tag: Sex


title: C. elegans N2 Control 1

description: N2 Control 1

tag: experiment start


title: ATAC_PopB_1895_S14

tag: subject id

tag: age

value: Caucasian


title: Epithelium from mouse O1E

description:
Illumina sequenced bulk RNA-Seq data
O1E

value: Esophageal Epithelium


title: ATAC_PopA_800_S6

tag: gender


title: ATAC_PopA_66294_512

value: Female

tag: race

value: Asian

value: Blood


title: Old Female CD4+ Effector Memory #3

city: Irvine

first: Haik

last: Mkhikian

state: California

address: D440 Medical Sciences I

institute: UC Irvine

data_processing:
Read quality was assessed using FastQC v0.11.2
Raw reads were trimmed and filtered by a length of 20bases using Trimmomatic v0.35
Trimmed reads were mapped using splice aware aligner Tophat2 v2.1.0
Aligned Bam files were processed to Samtools v1.3
Gene Expression was quantified using Subread v2.0.1 FeatureCounts v1.5.0-p3 for raw counts
Genome_build: mm10
Supplementary_files_format_and_content: all_merged.txt: tab delimited file, raw counts of all samples

source_name: lymph nodes and spleen

extract_protocol:
Lymphocytes were prepared from pooled lymph nodes (axillary, brachial, cervical, inguinal) and splenocytes then purified for CD4+ T cells through negative selection by EasySep CD4+ T cell Isolation Kit (STEMCELL Technologies, Cat#19852). Cell suspensions are then stained and FACS-sorted for either naïve (CD3+CD4+CD25-CD62L+CD44-) or memory (CD3+CD4+CD25-CD62L-CD44+) populations by BD FACSAria Fusion Sorter. RNA was isolated using RNeasy Plus Micro Kit (Qiagen, Cat#74034). Subsequently, 125ng of total RNA was used for the construction of sequencing libraries using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, Cat#E7645).
RNA libraries were prepared for sequencing according to New England Biolab's instructions accompanying the aforementioned kit with the additional use of AMPure XP beads (Beckman Coulter, Cat# A63880), NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, Cat# E7490), and NEBNext Multiplex Oligos for Illumina (NEB, Index Primers Set 1 Cat#E7335 and Index Primers Set 2 Cat# E7500).

value: lymph nodes and spleen

value: 85 weeks

value: female

tag: cell type

value: CD4+ Effector Memory


title: CTRL-Rep2 [AorteH]

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR) pipeline.
In this pipeline, reads underwent a quality check using FastQC .
Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm38.cdna.all.fa file.
Then, Estimated transcript abundances from Salmon were imported into R using the tximeta package  and analyzed for differential gene expression with edgeR
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: csv file including the RNASEQ counts for each sample

extract_protocol:
One third of aorta was immediately frozen in liquid nitrogen in dry Eppendorf. Because of low yield RNA extracted in preliminary experiments, to ensure sufficient amount and quality of RNA for sequencing, tissue of two animal was pooled in 1 ml of Tri-Reagent (TR118, MRC) for subsequent homogenization with the use of a Precellys Evolution homogenizer (Bertin Instrument, France). Total RNA was extract with the PureLink™ RNA Micro Scale Kit (Invitrogen) according manufacturer’s instructions, including DNAse step
Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16). Libraries were equimolarly pooled and sequenced on a single lane on an Illumina NovaSeq 6000 platform. All libraries were paired-end (2x100 bp reads) sequenced and a minimum of 35 million paired-end reads were generated per sample.

tag: treatment/time point

value: untreated

tag: tissue

value: Aorta


title: ATAC_PopB_2_2206

tag: ethnicity

value: Non-Hispanic

value: Bone Marrow

tag: cell subset


title: CTRL-Rep1 [AorteG]

tag: strain


title: ATAC_PopA_66294_510

value: Hispanic

value: Antibody-secreting cells (ASC)


title: ATAC_PopA_208_2308


title: Angio 2w+3W-Rep2 [AorteF]

source_name: Angio 2w+3W_aorta

value: treated and sacrificed 3w after the end of treatement


title: Old Female CD4+ Effector Memory #1


title: Angio 2w+3W-Rep1 [AorteE]


title: Angio 2w+2W -Rep2 [AorteD]

source_name: Angio 2w+2W _aorta

value: treated and sacrificed 2w after the end of treatement


title: Young Female CD4+ Effector Memory #2

value: 10 weeks


title: ATAC_PopA_207_1177


title: ATAC_PopA_1895_S13

value: Male

value: Caucasian


title: ATAC_PopA_1464_S2

value: Female

value: Asian


title: Old Male CD4+ Effector Memory #3

value: lymph nodes and spleen

value: 86 weeks

value: male


title: Angio 2w-rep2 [AorteB]

source_name: Angio 2w_aorta

value: treated and sacrificed at the end of treatement


title: Young Female CD4+ Effector Memory #1

value: female

value: CD4+ Effector Memory


title: ATAC_Pop3_red_115_2267

value: Non-Hispanic

value: Blood


title: Old Male CD4+ Effector Memory #2

value: 83 weeks


title: Angio 2w-rep1 [AorteA]

value: Aorta


title: Old Male CD4+ Effector Memory #1


title: Epithelium from mouse O2E

description:
Illumina sequenced bulk RNA-Seq data
O2E

value: Esophageal Epithelium

value: Aged


title: ATAC_Pop3_57983_162

value: Antibody-secreting cells (ASC)


title: ATAC_Pop3_57983_163


title: Old Female CD4+ Effector Memory #2

value: 85 weeks


title: ATAC_Pop3_2206_S16

value: Male

value: Caucasian


title: ATAC_Pop3_1895_S11


title: ATAC_5827_d7

source_name: In vitro differentiated plasma cells

tag: culture day

value: Female

value: Asian


title: Young Female CD4+ Effector Memory #3

value: lymph nodes and spleen

value: 11 weeks


title: ATAC_5827_d1


title: Angio 2w+2W -Rep1 [AorteC]

value: treated and sacrificed 2w after the end of treatement


title: Old Female CD4+ Naïve #3

value: female

value: CD4+ Naive


title: ATAC_5827_d14

value: Non-Hispanic


title: ATAC_Pop2_57983_163

value: Blood


title: Old Female CD4+ Naïve #2


title: ATAC_5827_d0


title: Old Female CD4+ Naïve #1


title: gastric csncer,NOl6 normal,rep2

city: nanjing

first: lei

last: he

address: hanzhongmen

institute: The Second Affiliated Hospital of Nanjing Medical University

hyb_protocol: 130 µ L hybridization solution was added to the chip and hybridized at 45℃ at 60rpm for 16 hours (no more than 18 hours). After hybridization, the chip was removed and automatically washed and stained  in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing:
The chip probe number and FC information of the probe in the data were input into IPA software (Fold Change, i.e., expression level of treatment group but not control group    Ratio).
P-value and Z-score are most commonly used in IPA analysis

label: biotin

source_name: Gastric cancer cells in logarithmic growth phase

label_protocol: After total RNA samples were analyzed by Agilent 2100, GeneChip 3 'IVT Express Kit was used to prepare aRNA    (Amplified RNA). That is, cDNA is synthesized by one strand, and then double strand DNA template is synthesized by two strands    ARNA (amplified RNA) with biotin markers were obtained by in vitro inversion.

growth_protocol: The AGS cells were cultured in DMEM medium containing fetal bovine serum at 37℃ in an atmosphere of 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The conventionally cultured AGS cells were collected into the EP tube, centrifuged at 2000rpm for 5 min, and 1mltrizol solution was added to the precipitate for treatment

tag: genotype

value: wildtype

value: AGS gastric cancer cells


title: ATAC_58271_d7


title: gastric csncer,NOl6 knockdown,rep3

value: NOl6 knockdown


title: Young Male CD4+ Effector Memory #3

value: 8 weeks

value: male

value: CD4+ Effector Memory


title: runx1-/- kidney6 [runx1]

data_processing:
RNA-seq reads were aligned to the zebrafish genome reference (GRCz11) and transcript reference (GRCz11.99) using hisat2 (2.2.1.0)
We used htseq-count (v0.11.4) to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset.  DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix.
Genome_build: GRCz11
Supplementary_files_format_and_content: raw counts

source_name: adult kidney

extract_protocol:
Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from ~2.5 months old fish ( pool of 3 kidneys/replicate) and immediately collected in Trizol (#15596018, Invitrogen). Samples were then put in a heatblock at 52C for 10 min and then overnight in -80C, RNA was extracted following the manufacturer protocol using Direct-zolTM RNA MiniPrep Kit (Zymo Research  #R2051).
Sequencing libraries were prepaired using paired-end library preparation (TruSeq RNA Library Prep Kit v2)

value: EK

value: kidney

tag: biopsy time

value: 2.5 month


title: runx1-/- kidney5 [runx1]


title: Young Female CD4+ Naïve #3


title: Young Male CD4+ Effector Memory #2

value: 7 weeks


title: Young Female CD4+ Naïve #2

value: lymph nodes and spleen

value: 10 weeks


title: ATAC_58271_d1

value: Male

value: Caucasian

value: Antibody-secreting cells (ASC)


title: gastric csncer,NOl6 normal,rep3


title: gastric csncer,NOl6 knockdown,rep1


title: Young Male CD4+ Effector Memory #1


title: ATAC_Pop2_115_2267

value: Female

value: Asian

value: Non-Hispanic


title: WT kidney3 [runx1]

value: WT


title: ATAC_Pop2_57983_162

value: Blood


title: ATAC_58271_d14


title: gastric csncer,NOl6 normal,rep1

value: wildtype

value: AGS gastric cancer cells


title: ATAC_Pop3_114_2266


title: Young Female CD4+ Naïve #1

value: female

value: CD4+ Naive


title: ATAC_Pop2_114_2266


title: ATAC_Pop3_113_2265


title: WT kidney2 [runx1]

value: EK

value: kidney


title: Old Male CD4+ Naïve #3

value: 86 weeks

value: male


title: ATAC_58271_d0


title: ATAC_Pop2_113_2265


title: WT kidney1 [runx1]

value: 2.5 month


title: ATAC_101_d7


title: gastric csncer,NOl6 knockdown,rep2

value: NOl6 knockdown


title: Old Male CD4+ Naïve #2

value: lymph nodes and spleen

value: 83 weeks


title: runx1-/- kidney3

data_processing:
RNA-seq reads were aligned to the zebrafish genome reference (GRCz10) and transcript reference (GRCz10.87) using STAR (v2.5.26).
We used RSEM to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix.
Genome_build: GRCz10
Supplementary_files_format_and_content: *.count.txt: Gene expression count matrix.

extract_protocol:
RNA-seq on kidney: Wild type and runx1del25/del25 kidneys were dissected from ~2.5 months old fish (n= 3 for each genotype, pool of 3 kidneys/replicate) and immediately collected in Trizol (#15596018, Invitrogen). Samples were then put in a heatblock at 52oC for 10 min and then overnight in -80oC. RNA was extracted following the manufacturer protocol using Direct-zolTM RNA MiniPrep Kit (Zymo Research #R2051).
Sequencing libraries were prepared using paired-end library preparation (TruSeq RNA Library Prep Kit v2).

tag: genotype/variation

value: 2.5 months


title: Old Male CD4+ Naïve #1


title: ATAC_101_d1

value: Female

value: Asian

value: Antibody-secreting cells (ASC)


title: runx1-/- kidney2


title: ATAC_Pop2_1895_S10

value: Male

value: Caucasian

value: Hispanic

value: Blood


title: ATAC_101_d14

value: Non-Hispanic


title: fbn6_2-RNAseq

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include read count values for each sample

organism: Arabidopsis thaliana

source_name: 3-week-old plants

growth_protocol: A. thaliana plants were grown on potting soil (Stender, Schermbeck, Germany) under controlled greenhouse conditions (daylight supplemented with illumination from HQI Powerstar 400W/D, providing a total fluence of ~120 µmol photons m-2 s-1 on leaf surfaces; 16 h light/8 h dark cycle). Wuxal Super fertilizer (8 % N, 8 % P2O5, and 6 % K2O; MANNA) was used according to the manufacturer’s instructions.

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq

treatment_protocol: long-day conditions

tag: ecotype

value: fbn6-1 (GK_159E10) mutant


title: fbn6_1-RNAseq


title: runx1-/- kidney1

value: EK

value: kidney


title: Young Male CD4+ Naïve #2

value: 7 weeks

tag: Sex

value: male

value: CD4+ Naive


title: ATAC_101_d0


title: WT kidney3

value: WT


title: NL4.3 integration in ZNF417 ZNF587 dKO 293T rep-2

city: Guangzhou

first: Bo

last: Yang

state: Guangdong

address: Guangzhou, 510150, Guangdong Province, China.

institute: The Third Affiliated Hospital of Guangzhou Medical University

data_processing:
Library strategy: nested PCR
The processes, except for merging of overlapping paired-end read sequences and read mapping, were achieved with in-house PERL scripts (available at https://github.com/odehir/VINSSRM).
The primer sequences for the LTR and linker are found in each 5Â´-end of the original paired-end read sequences (read1 and read2). Each set of overlapping paired-end read sequences was merged into one read (read3).
Then, the merged read sequences and paired-end read sequences were subjected to trimming of linker sequences and subsequent split-read mapping onto the human genome (hg38) and HIV-1 reference sequences (NL4.3).
The integration sites and breakpoints were assigned by nucleobase positions onto the human genome. The breakpoints were used to evaluate whether the integration sites are identified from clonally expanded cells. The LTR ends were assigned by nucleobase positions onto HIV-1 reference genomes. The nucleobase positions of the LTR ends are used to evaluate whether the viral end is intact or aberrant.
Genome_build: hg38
Supplementary_files_format_and_content: processed integration sites in txt format

source_name: ZNF417 ZNF587 DKO 293T

growth_protocol: HEK293T cells were cultured in DMEM High Glucose (Gibco) containing 10% FBS, 2 mM L-glutamine.

extract_protocol:
Genomic DNA was purified from cell lysis with by phenol chloroform. DNA was sheared into 300 bp-500 bp random fragments using Covaris Adaptive Focused Acoustics (Covaris, Woburn, MA).
The sheared DNA fragments were end-repaired and a single dA was added to the 3' ends using KAPA DNA Hyper Prep kit . A partially double stranded linker (5'GTAATACGACTCACTATAGGGCTCCGCTTAAGGGACT3', 5''PO4-GTCCCTTAAGCGGAG-3'-C6) with a one nucleotide 3' T overhang was ligated to the genomic DNA fragments. The 3' dA overhang on the genomic DNA fragments and the 3' T overhang on the linker DNA prevented genomic-genomic DNA and linker-linker ligation, increased the efficiency of the desired ligation, and reduced the artifacts associated with cross-ligation commonly seen with restriction enzyme based linker-mediated PCR (LM-PCR). The integration junctions were selectively amplified using one primer that matched the HIV LTR sequence and the other primer that matched the single stranded portion of the linker. Nested PCR was performed with an inner primer pair; one primer matched the sequence of the LTR and the other primer matched the linker (outer: HIV-3LTR, 5' TGTGACTCTGGTAACTAGAGATCCCTC3'; Inner: HIV-3LTRnest, 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNCCCTTTTAGTCAGTGTGGAAAATC3'; outer: HIV-5LTR,TCAGGGAAGTAGCCTTGTGTGTGGT; inner: HIV-5LTRnest, 5'AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNGTCTTTTTTGGGACCAAATTAGCCC; outer: Linker-P1, 5'GTAATACGACTCACTATAGGGC3'; inner: PE2_Linkernest, 5'CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTNNNNNNAGGGCTCCGCTTAAGGGAC3'; NNNNNN stands for barcodes).

value: ZNF417 ZNF587 dKO


title: WT kidney2

value: 2.5 months


title: Young Male CD4+ Naïve #1

value: lymph nodes and spleen


title: Col_4-RNAseq

value: wild type


title: Col_3-RNAseq


title: NL4.3 integration in control 293T rep-2

source_name: control 293T cells

value: scrambled sgRNA KO


title: CL_proma_rep2

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Leishmania mexicana MHOM/GT/2001/U1103 genome sequences, transcriptome sequences and general feature format (gff) file were downloaded from TriTrypDB release 54 (Nucleic Acids Res 38:D457-462, 2010).
Counts of reads per gene were obtained using STAR aligner (Bioinformatics 29:15-21, 2013).
Relative abundance of transcripts in units of transcripts per million (TPM) was obtained using Salmon (Nat Methods 14:417-419, 2017) with default settings.
Genome_build: Leishmania mexicana MHOM/GT/2001/U1103.
Supplementary_files_format_and_content: tab-delimited text files include raw counts of reads per gene for each sample
Supplementary_files_format_and_content: tab-delimited text files include TPM (transcripts per million) values for each sample

organism: Leishmania mexicana

source_name: promastigote

extract_protocol:
Total non-crosslinked (NC) RNA and protein-cross-linked (CL) RNA from promastigote and axenic amastigote life cycle stages of L. mexicana parasites in biological duplicates were purified using standard Trizol extraction and orthogonal organic phase separation, respectively. The CL samples were treated with 20 U of proteinase K in a protein digestion buffer at 50 oC for 2 h and the released RNA was purified by a subsequent Trizol extraction. All RNA samples were treated with Turbo DNase.
Sequencing libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) following standard Illumina protocols.

value: promastigote

tag: cross-linking

value: cross-linked

tag: uv energy


title: WT kidney1

tag: age


title: Col_2-RNAseq


title: Runx1 KO 3

data_processing:
Low quality reads were discarded if their N-bases ratio above 10% or low-quality bases (<=5) ratio above 50%, adapter sequences contained reads were also discarded.
Data of each sample were then aligned to the mm10 reference genome with hisat2.
HTseq-count (0.9.1) (Anders et al., 2015) were used to calculate the read count of each gene, based on the gene model from Ensembl database (GRCm38.95).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.count.txt: Gene expression count matrix.

source_name: c-Kit+ bone marrow cells

extract_protocol:
Total RNA was extracted with AllPrep DNA/RNA/Protein Mini Kit (QIAGEN).
Poly-A selected stranded mRNA libraries were constructed using the Illumina TruSeq Stranded mRNA Sample Prep Kits and sequenced with a HiSeq2500 sequencer.

value: Runx1 KO

value: c-Kit+ bone marrow cells


title: CL_proma_rep1


title: H49

city: Moscow

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M.tuberculosis genome using bowtie2 v2.3.4.3 with parameters -p 4 --local --dovetail
Fragments counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The files "Counts_HXX.txt" represent these counts (File "Counts_all.csv" contains values for all samples).
Genome_build: AL123456.3
Supplementary_files_format_and_content: Counts - the numbers of overlapping reads for every annotated gene in each sample

organism: Mycobacterium tuberculosis

source_name: lung tissue

extract_protocol:
Total RNA was isolated by phenol- chloroform extraction and cell disruption by with Bead Beater (BioSpec Products, USA) as described (Rustad et al., 2009) and treated with Turbo DNase (Life Technologies, USA) to remove traces of genomic DNA.
RNA samples were depleted of both human and bacterial rRNA using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat), NEBNext® rRNA Depletion Kit (Bacteria) and polyA-transcripts using NEBNext® Poly(A) mRNA Magnetic Isolation Module. Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, USA) according to the manufacturers’ protocol

tag: tissue source

value: human lung


title: NC_proma_rep2

value: non-cross-linked

value: 0 mJ/cm2


title: Runx1 KO 2


title: fbn6_3-RNAseq

value: fbn6-1 (GK_159E10) mutant


title: Pulmonary endothelial cells - ECCTRL_3 [ChIP-seq]

city: Milwaukee

first: Adeleye

middle: J.

last: Afolayan

state: Wisconsin

address: 8701 Watertown Plank Rd., PD278, CRI TBRC, Rm C3278

institute: Medical College of Wisconsin

data_processing:
Quality control was completed using FastQC version 0.11.7, and trimmed using Trimmomatic version 0.38.
ChIP-seq reads were aligned to the UCSC hg37 genome assembly using Bowtie version 1.1.2 with the following configurations…
Picard version 0.118 was used to remove duplicates.
ChIPseeker version 1.16.1 was utilized to annotate and visualize ChIP peaks.
Genome_build: UCSC hg37
Supplementary_files_format_and_content: tab-delimited file which contains information on all called peaks.

source_name: HPAEC cells

growth_protocol: Pulmonary-derived arterial endothelial cells (ATCC) were generated by plating on TC-treated plastic (typically 2–3 × 106 cells into a 100mm dish) with Vasculife EC Media (Lifeline Cell Technology, Frederick, MD, USA).

extract_protocol:
Cells were cross-linked in formalin and collected with a rubber policeman for ChIP extraction, per the EpiQuik Chromatin Immunoprecipitation Kit (Epigenetek, Farmingdale, NY)
Libraries were prepared according to Epigentek's instruction accompanying the EpiNext High-Sensitivity DNA Library Preparation Kit for Illumina.

treatment_protocol: Cells were transfected at ~50% confluency for 24 hours with Fugene 6 transfection reagent (Fugent, Middleton, WI, USA), followed by 24 hours rest. They were then treated with 100 uM H2O2 for one hour prior to harvest.

tag: chip antibody

value: Input

value: Pulmonary-derived endothelial cells

tag: treatment

value: H2O2 for 1 hour

tag: transfection

value: Nuclear-localizing OLA1 T325D


title: Pulmonary endothelial cells - ECOLA_NLS_1 [ChIP-seq]

tag: cell type


title: Runx1 KO 1


title: Pulmonary endothelial cells - ECCTRL_2 [ChIP-seq]


title: WT control 3

value: WT


title: CL_ama_rep2

source_name: axenic amastigote

tag: tissue

value: axenic amastigote


title: Young Male CD4+ Naïve #3

value: lymph nodes and spleen

value: 8 weeks

value: male

value: CD4+ Naive


title: H46


title: H44


title: WT control 2


title: NC_proma_rep1

value: promastigote


title: JB10: Untransfected (replicate 2)

city: Stanford

first: Augustine

last: Chemparathy

state: CA

address: 290 Jane Stanford Way

department: Bioengineering

institute: Stanford University

description: Untransfected

data_processing:
STAR 2.5.4b was used to generate a genome index with hg19 and GFP. Command: STAR --runMode genomeGenerate --runThreadN 10 --genomeDir {dirname_here} --genomeFastaFiles {fname_here} --sjdbGTFfile {fname_here} --sjdbOverhang 100
STAR 2.5.4b was used to align paired reads to the genome index. Command: STAR --genomeDir {dirname_here} --readFilesIn {fname_here} {fname_here} --runThreadN 10 --outSAMtype BAM SortedByCoordinate --outFileNamePrefix {user_option}  --readFilesCommand gunzip -c
Htseq-count was used to calculate read counts. Command: htseq-count -i gene_id {bam_fname_here} {gtf_fname_here} -r pos -s no -f bam > {output_fname_here}
Fragments per kilobase transcript per million mapped reads (FPKM) were quantified by the following method: for each sample, for each gene HTseq-count values were divided by gene length in kilobases (quantified by GTFtools; Command: python2.7 GTFtools_0.6.9/gtftools.py -l {output_fname} {gtf_fname}) and divided the total sample count in millions.
Genome_build: hg19 with the following GFP sequence:  >GFP  ATGCCCGCCATGAAGATCGAGTGCCGCATCACCGGCACCCTGAACGGCGTGGAGTTCGAGCTGGTGGGCGGCGGAGAGGGCACCCCCGAGCAGGGCCGCATGACCAACAAGATGAAGAGCACCAAAGGCGCCCTGACCTTCAGCCCCTACCTGCTGAGCCACGTGATGGGCTACGGCTTCTACCACTTCGGCACCTACCCCAGCGGCTACGAGAACCCCTTCCTGCACGCCATCAACAACGGCGGCTACACCAACACCCGCATCGAGAAGTACGAGGACGGCGGCGTGCTGCACGTGAGCTTCAGCTACCGCTACGAGGCCGGCCGCGTGATCGGCGACTTCAAGGTGGTGGGCACCGGCTTCCCCGAGGACAGCGTGATCTTCACCGACAAGATCATCCGCAGCAACGCCACCGTGGAGCACCTGCACCCCATGGGCGATAACGTGCTGGTGGGCAGCTTCGCCCGCACCTTCAGCCTGCGCGACGGCGGCTACTACAGCTTCGTGGTGGACAGCCACATGCACTTCAAGAGCGCCATCCACCCCAGCATCCTGCAGAACGGGGGCCCCATGTTCGCCTTCCGCCGCGTGGAGGAGCTGCACAGCAACACCGAGCTGGGCATCGTGGAGTACCAGCACGCCTTCAAGACCCCCATCGCCTTCGCCAGATCTCGAGATATCAGCCATGGCTTCCCGCCGGCGGTGGCGGCGCAGGATGATGGCACGCTGCCCATGTCTTGTGCCCAGGAGAGCGGGATGGACCGTCACCCTGCAGCCTGTGCTTCTGCTAGGATCAATGTG
Supplementary_files_format_and_content: TXT FPKM files are tab-delimited with gene in the first column and FPKM in the second
Supplementary_files_format_and_content: TXT non-FPKM files are tab-delimited with gene in the first column and read count in the second

source_name: HEK293T cells

growth_protocol: HEK reporter cell line stably expressing TRE3G-GFP were seeded in a 6 well plate at density of 2*10^5/ml

extract_protocol:
Total RNA was isolated by using RNeasy Plus Mini Kit (QIAGEN).
Library preparation and next-generation sequencing were performed by Novogene (Chula Vista, CA)

treatment_protocol: Cells were co-transfected next day with TET crRNA or LacZ non-target crRNA with dCas12aWT or vgdCas12a, in duplicates. One day after transfection, transfected cells were placed in antibiotic selection (hygromycin 500µg/ml and puromycin 2µg/ml) for 2 days before harvest.

tag: cell line

value: Untransfected


title: CL_ama_rep1

tag: strain

value: cross-linked


title: WT control 1

value: c-Kit+ bone marrow cells


title: JB9: Untransfected (replicate 1)

description: Untransfected


title: NC_ama_rep2

value: non-cross-linked


title: JB8: VgdCas12-miniVPR + crTet (replicate 2)

description: Mutant dCas12-miniVPR + crTet

value: Transfected with Mutant dCas12-miniVPR + crTet


title: NC_ama_rep1

value: 0 mJ/cm2


title: H29

value: human lung


title: JB7: VgdCas12-miniVPR + crTet (replicate 1)

description: Mutant dCas12-miniVPR + crTet


title: Pulmonary endothelial cells - ECCTRL_1 [ChIP-seq]

value: Pulmonary-derived endothelial cells


title: H15


title: JB6: VgdCas12-miniVPR + crLacZ (non-targeting control) (replicate 2)

value: Transfected with Mutant dCas12-miniVPR + crLacZ (non-targeting control)


title: ST_Y_D2_1

city: Berkeley

first: Sanjay

last: Kumar

address: 274A Stanley Hall, University of California - Berkeley

institute: UC Berkeley

data_processing:
The reads were initially trimmed using BBDuk to remove Illumina adapters and to filter low quality reads.
The samples were then aligned to ratRibosomal genes using bbmap to remove ribosomal contaminated RNA. Any samples less than 21 bases were removed using BBduk.
Read quality analysis was performed using FastQC to assure there was a Phred score > 28.
The reads were aligned to the rattus norvegicus genome (rn6) using hisat2 v2.1.0.
the aligned reads were converted to counts using htseq.
Supplementary_files_format_and_content: csv file, gene counts

source_name: Neuarl Stem Cells

growth_protocol: Adult rat hippocampal neural stem cells were differentiated in 3D hyaluronic acid-based hydrogels.

extract_protocol:
Phenol-free total RNA was extracted from the cell pellets using RNeasy Plus Micro Kit with gDNA eliminator columns (Quiagen) following the manufacturer’s protocol.
RNA-seq library preparation was carried out by the DNA Technologies and Expression Analysis Core at the University of California, Davis Genome Center.
batch-tag-RNA-seq (3’-tag-seq gene expression profiling)

treatment_protocol: mixed differentiation medium (DMEM-F12 with N2 supplemented with 1 μM of retinoic acid and 1% FBS)

value: adult hippocampal neural progenitor cells

tag: stiffness

value: stiff (1.2 kPa)

tag: rgd functionalization

tag: time point

value: 48 hr


title: ST_Y_D2_2


title: H48


title: JB5: VgdCas12-miniVPR + crLacZ (non-targeting control)  (replicate 1)

description: Mutant dCas12-miniVPR + crLacZ (non-targeting control)


title: H12


title: ST_Y_D0_2

value: 12 hr


title: ST_Y_D0_1


title: H9


title: H47


title: JB4: Wildtype dCas12-miniVPR + crLacZ (non-targeting control) (replicate 2)

value: Transfected with Wildtype dCas12-miniVPR + crLacZ (non-targeting control)


title: NPWT-1 [RNA]

city: Xi'an

first: Yunshu

state: Shaanxi

address: Changle West Road

institute: Air Force Medical University

description: mRNA_ncRNA.counts.txt/circRNA_counts.txt

data_processing:
RNA-Seq
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
Unmapped reads were collected to identify the circRNA utilizing ACFS
count counting
miRNA-Seq
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 33bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to mature miRNAs with annotation from miRBase(v.21).
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: dermal wound tissues

growth_protocol: A third-degree scald of 2 cm diameter was generated on the shaved back of each mouse using water vapor by continuous scalding for 4 s; the wound occupied approximately 6–8% of the body surface area. Subsequently, 50 μl of fluorescently labeled P. aeruginosa (1.0 × 106 colony-forming units/ml) was inoculated onto the eschar. When the bacteria solution was completely absorbed, the mice were allowed to recover.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.Part of RNA was utilized to construct rRNA depletion(NEBNext Ultra Directional RNA Library Prep Kit),The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The wounds were covered with polyurethane foam and blocked with a biologic semi-permeable membrane. In the NPWT group, the wounds were subjected to NPWT with continuous negative pressure suction of –120 mmHg. In the control group, the wounds were cleaned with a sterile saline solution, and the dressing was changed once every 24 h. Tissue samples were collected on days 3.

value: dermal wound tissues

tag: protocol

value: negative pressure wound therapy

value: Eight- to twelve-week-old


title: NPWT-2 [RNA]


title: JB2: Wildtype dCas12-miniVPR + crTet (replicate 2)

description: Wildtype dCas12-miniVPR + crTet

value: Transfected with Wildtype dCas12-miniVPR + crTet


title: ST_N_D2_1


title: Control-2 [RNA]

value: control


title: H30


title: Control-1 [RNA]


title: JB3: Wildtype dCas12-miniVPR + crLacZ (non-targeting control)  (replicate 1)


title: ST_N_D2_2


title: ST_N_D0_2


title: JB1: Wildtype dCas12-miniVPR + crTet (replicate 1)

description: Wildtype dCas12-miniVPR + crTet


title: ST_N_D0_1


title: Hek cell line - SYNJ2BP AAA mutant rep 3 [AAA.mito.R3]

city: Neuherberg

first: Yiming

address: Ingolstädter Landstraße 1

institute: Helmholtz Munich

data_processing:
RNA reads were aligned to the human reference genome (Ensembl genome version 101) using STAR 2.7.6a
The quality was checked with fastqc and qualimap
The low quality base pairs were trimmed with Trimomatic
The gene read count values were quantified with featureCounts
Genome_build: human reference genome (Ensembl genome version 101)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SYNJ2BP AAA mutant binding RNA

extract_protocol:
Immunoprecipitation anti-myc (clone 4A6)
rRNA depletion (siTOOLs Biotech, riboPOOls 57) followed by RNAseq library prep (NEB, e7760)

treatment_protocol: Transfection with Ca-phosphate

value: AAA mutant

value: HEK


title: Hek cell line - SYNJ2BP AAA mutant rep 2 [AAA.mito.R2]


title: Hek cell line - SYNJ2BP AAA mutant rep 1 [AAA.mito.R1]


title: Stag2_KO#2_CT26

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

data_processing:
Sequenced reads were aligned to Ensemble database with STAR.
Gene expression values were normalized to obtain RPKM values using RSEM.
Overlap differentially expressed genes in WT /KO HCT-116 and CT26  cells.
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample .

extract_protocol:
Cells were lysed in Trizol reagent and total RNA was extracted.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colorectal cancer cell line

tag: genotype


title: SO_Y_D2_2

value: soft (100 Pa)


title: Stag2_KO#1_CT26


title: Hek cell line - Control rep 3 [WT.Control.R3]

source_name: SYNJ2BP binding RNA

value: untreated


title: PC9_DMSO

first: Jiayuan

last: Zhong

address: 381 Wushan Road, Guangzhou 510640, China

department: School of Mathematics

institute: South China University of technology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: DMSO

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: G and P were maintained in RPMI-1640 (Gibco, USA) supplemented with 10% fetal bovine serum (Gibco, USA), 1% penicillin and streptomycin (Thermo Fisher Scientific) in humidified with 5% CO2 at 37℃.

extract_protocol: Total RNA was isolated from cells by Trizol reagent according to the manufacturer’s protocol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: G was established by continually exposing to stepwise escalation of concentration of gefitinib (Selleckchem, USA) from 0.1 μM to 15 μM over 8 months

tag: phenotype

value: gefitinib-sensitive


title: SO_Y_D2_1


title: PC-9_Gefitinib

source_name: Gefitinib

value: gefitinib resistant


title: HT1080_WT_p4 reanalysis

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

description:
HT1080_WT_p4
Also included in GEO series GSE125941 with sample accession GSM3585514

data_processing:
Alignment was performed using STAR version 2.6 using the ENSEMBL GRCh38 assembly reference genome
Gene expression was quantified using HTseq python framework version 0.9.1
Genome_build: ENSEMBL GRCh38
Supplementary_files_format_and_content: Excel file containing matrix of unnormalized reads mapped to each transcript as a result from HTseq analysis

source_name: Fibrosarcoma cell line

growth_protocol: RPMI 1640 culture media was supplemented with 5% fetal bovine serum, 100 U/ml penicillin and 100 mg/ml streptomycin. Stable expression of FUS-DDIT3-EGFP construct was maintained by addition of 500 µg/ml Geneticin.

extract_protocol:
RNA was extracted using Qiagen RNeasy micro kit, including DNase treatment
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

treatment_protocol: JAK1/2 inhibition was performed in HT1080 FUS-DDIT3-EGFP cells with 2.5 µM ruxolitinib for 24 hours.

tag: transfected gene

value: Untreated


title: Hek cell line - Control rep 2 [WT.Control.R2]

last: Cheng


title: Nipbl_KO#2_CT26


title: HT1080_WT_p3 reanalysis

description:
HT1080_WT_p3
Also included in GEO series GSE125941 with sample accession GSM3585513


title: SO_Y_D0_2

value: adult hippocampal neural progenitor cells


title: Hek cell line - Control rep 1 [WT.Control.R1]


title: Nipbl_KO#1_CT26


title: SO_Y_D0_1


title: HT1080_FUS-DDIT3-EGFP_ruxo_p4

value: Ruxolitinib


title: WT_CT26


title: HT1080_FUS-DDIT3-EGFP_ruxo_p3


title: MLH1 KO CT26_anti-PD-1

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequenced data were analyzed with an MAGeCK algorithm.
The counts were normalized by the total reads for each sample.
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include the normalized counts of sgRNAs.

growth_protocol: 2×10^7 cells/mouse were subcutaneously injected into the flanks of BALB/C mice.

extract_protocol:
Genome DNA in per group was extracted using Wizard ® Genomic DNA Purification Kit (Promega).
Genome DNA in per group was amplified using two-step PCR.

treatment_protocol: i.p. 200 μg/mouse PD-1 monoclonal antibody or vehicle for 5 times.


title: SO_N_D2_2

value: 48 hr


title: HT1080_WT_p1 reanalysis

description:
HT1080_WT_p1
Also included in GEO series GSE125941 with sample accession GSM3585511


title: HT1080_WT_p2 reanalysis

description:
HT1080_WT_p2
Also included in GEO series GSE125941 with sample accession GSM3585512


title: SO_N_D2_1


title: HT1080_FUS-DDIT3-EGFP_ruxo_p2


title: MLH1 KO CT26_Vehicle

value: vehicle


title: SO_N_D0_2

value: 12 hr


title: HT1080_FUS-DDIT3-EGFP_ruxo_p1


title: CT26_anti-PD-1


title: HT1080_FUS-DDIT3-EGFP_p4 reanalysis

description:
HT1080_FUS-DDIT3-EGFP_p4
Also included in GEO series GSE125941 with sample accession GSM3585521


title: HT1080_FUS-DDIT3-EGFP_p1 reanalysis

description:
HT1080_FUS-DDIT3-EGFP_p1
Also included in GEO series GSE125941 with sample accession GSM3585519


title: SO_N_D0_1


title: CT26_Vehicle


title: sparse panicle1 mutant inflorescence_14DAS_rep2

status: Public on Jan 13 2022

city: St. Louis

first: Elizabeth

middle: A.

last: Kellogg

state: MO

address: 975 North Warson Rd.

institute: Donald Danforth Plant Science Center

data_processing:
Adaptors and low-quality reads were trimmed using Trimmomatic (Bolger et al., 2014) and reads were quality-checked using fastqc after trimming.
The S. viridis reference genome (v1) was indexed using bowtie 2 (Langmead and Salzberg, 2012) from Sviridis_311_v1.0.fa.gz file at PhytozomeV11 (phytozome.jgi.doe.gov). Reads were mapped to the reference genome using tophat2 and differentially expressed genes were identified using cuffdiff (Trapnell et al., 2012).
Expression levels quantified in Fragments Per Kilobase of transcript per Million (FPKM) were extracted for 35,214 S. viridis primary transcripts (Tables S5, S6). Gene annotation and grass homolog identification followed Zhu et al. ((2018)).
Genome_build: Genome_build: Sviridis_311_v1
Supplementary_files_format_and_content: Processed data files are MS Excel spreadsheets.  Table S5. RNA-seq library sequencing and mapping statistics.  Table S6.  Expression of all S. viridis genes from each replicate (R1-R4) of the developmental stages (10, 12, 14 DAS) in A10.1 and spp1. Table S7. Expression of differentially expressed genes between A10.1 and spp1 at each developmental stage (10, 12, 14 DAS).

organism: Setaria viridis

growth_protocol: Mutants in the sparse panicle1 locus (spp1) were used in this study. Seeds were planted in MetroMix 360 soil (Sun Gro Horticulture company) and grown in a controlled growth chamber with the following conditions: temperature of 31°C/23°C (day/night), light intensity of 200 µmol/sq.meter/sec for 12 hours (6am-6pm) and 50% relative humidity, at the Donald Danforth Plant Science Center’s Integrated Plant Growth Facility. Plants were fertilized with Jack’s 15-16-17 (Hummert International) twice a week.

extract_protocol:
Inflorescences were hand-dissected into fresh 100% acetone on dry ice from wildtype (A10.1) and mutant (sparse panicle1) S. viridis seedlings at 10, 12, and 14DAS. Depending on the representative size at a given stage, 10-30 individual inflorescence primordia were pooled per biological replicate; three to four biological replicates were collected for each stage. All sampling was performed within a two-hour window in the morning to control for circadian effects. Acetone was removed and samples were flash-frozen in liquid nitrogen and ground into a fine powder using 3mm tungsten-carbide beads (Qiagen) in a Tissue Lyser-II. Total RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) with in-column DNase I treatment following manufacturer's protocols.
RNA-seq libraries were generated from 1µg total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) and size-selected for 200 bp inserts. Libraries were quantified on a bioanalyzer (Agilent 2100) using a DNA 1000 chip to confirm the insert size and quantified again on a Qubit 3.0 Fluorometer (Life Technologies) to ensure different libraries were equally loaded
Libraries were sequenced using standard Illumina protocols (Illumina, Inc.) for either paired-end (PE) sequencing at 100bp on the Illumina HiSeq 2500 platform at the University of Illinois at Urbana-Champaign W.M. Keck Center.

tag: genotype/variation

value: sparse panicle1 mutant

tag: developmental stage


title: sparse panicle1 mutant inflorescence_14DAS_rep3


title: sparse panicle1 mutant inflorescence_14DAS_rep1


title: sparse panicle1 mutant inflorescence_12DAS_rep1


title: sparse panicle1 mutant inflorescence_12DAS_rep4


title: sparse panicle1 mutant inflorescence_12DAS_rep2


title: sparse panicle1 mutant inflorescence_14DAS_rep4


title: sparse panicle1 mutant inflorescence_10DAS_rep4


title: sparse panicle1 mutant inflorescence_10DAS_rep2


title: sparse panicle1 mutant inflorescence_10DAS_rep1


title: sparse panicle1 mutant inflorescence_10DAS_rep3


title: A10.1 (wild type) inflorescence_14DAS_rep3

value: A10.1 (wild type)


title: A10.1 (wild type) inflorescence_14DAS_rep4


title: A10.1 (wild type) inflorescence_14DAS_rep2


title: A10.1 (wild type) inflorescence_14DAS_rep1


title: A10.1 (wild type) inflorescence_12DAS_rep2


title: LN_Saline_73

city: Los Angeles

first: Roberto

last: Spreafico

address: UCLA

department: Institute for Quantitative and Computational Biosciences

institute: University of Califonia Los Angeles

data_processing:
Reads were quality-controlled using FastQC.
Illumina adapters were removed using cutadapt.
Trimmed reads were mapped to the mouse transcriptome (GRCm38) based on Ensembl annotations using Kallisto
Transcript counts were imported and aggregated to gene counts using tximport
Gene counts were analyzed using the R package DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: rlog function from DESeq2 package

source_name: Lymph Node

extract_protocol:
RNA was isolated from TRI Reagent samples using phenol-chloroform extraction or column-based extraction systems (Direct-zol RNA Microprep and Miniprep, Zymo Research) according to the manufacturer’s protocol. RNA concentration and purity (260/280 and 260/230 ratios) were measured by NanoDrop (Thermo Fisher Scientific).
RNA samples were quantified using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) and RNA integrity was checked with RNA Screen Tape on Agilent 2200 TapeStation (Agilent Technologies). RNA sequencing library preparation was prepared using TruSeq Stranded mRNA library Prep kit following manufacturer’s protocol (Illumina, Cat# RS-122-2101). Briefly, mRNAs were first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 8 minutes at 94°C. First strand and second strand cDNA were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were adenylated at 3’ends, and indexed adapter was ligated to cDNA fragments. Limited cycle PCR was used for library enrichment. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using DNA Analysis Screen Tape on the Agilent 2200 TapeStation (Agilent Technologies), and quantified by using Qubit 2.0 Fluorometer (Thermo Fisher Scientific) as well as by quantitative PCR (Applied Biosystems). The sequencing libraries were multiplexed and clustered on 1 lane of flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions. The samples were sequenced using a 2x150 Pair-End (PE) High Output configuration.

value: Lymph Node

value: Saline

value: 24 hr

tag: batch


title: LN_Mannan_71

value: Mannan


title: LN_Saline_74


title: LN_Mannan_72


title: A10.1 (wild type) inflorescence_12DAS_rep1


title: A10.1 (wild type) inflorescence_10DAS_rep4


title: LN_Glucan_70

value: Beta-glucan


title: A10.1 (wild type) inflorescence_10DAS_rep3


title: A10.1 (wild type) inflorescence_12DAS_rep4


title: HT1080_FUS-DDIT3-EGFP_p3 reanalysis

description:
HT1080_FUS-DDIT3-EGFP_p3
Also included in GEO series GSE125941 with sample accession GSM3585520


title: LN_Glucan_69


title: A10.1 (wild type) inflorescence_10DAS_rep2


title: LN_Saline_67

value: 6 hr


title: LN_Saline_68


title: LN_Mannan_65


title: LN_Glucan_64


title: LN_Mannan_66


title: LN_Glucan_63


title: LN_Glucan_41