title: stz0 mono hi

description:
Cell lysate
stz0_mono_hi_S109


title: wt NaOCl batch 1 rep3

status: Public on May 25 2022

type: SRA

city: Seoul

first: Sungmin

last: Hwang

address: Hwarangno 14-gil 5, Seongbuk-gu

country: South Korea

institute: Korea Institute of Science and Technology

library_source: transcriptomic

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
The sequencing artifacts and contamination of raw sequencing reads were assessed by FastQC v.0.11.9 and further adapter, poor-quality or short reads (< 10 bp) were trimmed by Cutadapt v.1.18.
The number of reads mapped to each transcript was counted by HTSeq v.0.11.0
Assembly: The preprocessed reads were aligned to the reference genome of GCF_000025685.1_ASM2568v1_genomic.gff by Bowtie2 v.2.3.4.3, followed by sorting and indexing by Samtools v.1.9.
Supplementary files format and content: DESeq2 v.1.32.0 was used to normalize the read counts and the resulting count matrix contains the raw gene counts for every gene except rRNAs and every sample.

molecule: total RNA

organism: Haloferax volcanii

source_name: Haloferax volcanii

growth_protocol: Strains H26 wild-type and mutant (ΔoxsR) were streaked on fresh ATCC974 medium plates from -80°C stock and grown for five days. Colonies were transferred to fresh ATCC974 liquid media in 13 ×100 mm culture tube and incubated at 42°C for 17 h (aeration by rotary shaking, 200 rpm) to log-phase (OD600nm of 0.3 to 0.7). Cells were transferred to fresh ATCC974 liquid medium in 13 ×100 mm culture tube and similarly incubated for 15 h until early log phase (OD600 nm of 0.3 to 0.5). The culture was transferred to a 125 mL Erlenmeyer flask in 50 mL of ATCC974 liquid medium and similarly incubated for 10 h to reach an early log phase. An aliquot (10 mL) of cell culture was transferred to 15 mL conical tubes for each strain and centrifuged for 5 min at 5,000 x g at room temperature to remove the complex medium. Cells were washed twice with GMM to remove any remaining ATCC974 medium. The cells were resuspended 50 mL of GMM and divided into two 125 mL Erlenmeyer flasks (25 mL per flask). Cells were exposed to 1.5 mM of HOCl or the mock only water for 1 h at 42°C with aeration at 200 rpm. After treatment, 10 mL cultures were transferred to 15 mL conical tubes and harvested by centrifugation (5 min at 5,000 x g, 22°C). The supernatant was removed, and the cell pellets were flash frozen on an ice bath with 100 % ethanol and NaCl. Cell pellets were stored at -80°C.

extract_protocol:
The RNA was extracted using TRI Reagent® (#T9424, Sigma-Aldrich). To verify RNA integrity, the samples were separated by 0.8 % (w/v) agarose gel electrophoresis (at 90 V for 20 min) in 1X TAE buffer using 2X RNA Loading Dye (#R0641, Thermo Fisher Scientific). The samples were then treated with TURBO DNase-free kit (AM1907, Invitrogen) to remove traces of DNA.
Only RNA samples with DNA below the limit of PCR detection were further processed. From each sample preparation, total RNA ≥ 6 μg in 50 μL with RIN value ≥ 6 was used to prepare a cDNA library and analyzed by high throughput sequencing (Novogene). The abundance of rRNA was reduced using the Ribo-ZeroTM Magnetic kit, and the cDNA was prepared using a 250 to 300 bp insert strand-specific library. The library was sequenced using the Illumina Platform PE150, Q30≥ 80% yielding 2G raw data / sample.

tag: strain

value: wt

tag: treatment

value: NaOCl treated


title: ctl 3 mono hi

status: Public on Aug 18 2021

city: Phoenix

first: Eric

last: Alsop

state: AZ

address: 445 N. Fifth Street

country: USA

institute: TGen

description:
Cell lysate
ctl_3_mono_hi_S88

data_processing:
cutadapt for quality filtering
sRNABench for small RNA
normalization in DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: miRNA_ALL_norm_counts.txt

organism: Mus musculus

source_name: Monocytes Ly-6Chi sorted from WT mice treated with citrate buffer

extract_protocol:
Qiagen miRNeasy Mini Kit
NextFlex v3

tag: cell type

value: Monocytes Ly-6Chi

tag: agent

value: citrate buffer

tag: genotype

value: WT


title: ctl 2 mono hi

description:
Cell lysate
ctl_2_mono_hi_S87


title: A5+6 hi

description:
Cell lysate
A5_6_hi_10_11_2017_S61

source_name: Monocytes Ly-6Chi sorted from Akita mice

value: Akita


title: A1+2 hi

description:
Cell lysate
A1_2_hi_10_11_2017_S60


title: A3+4 hi

description:
Cell lysate
A3_4_hi_10_11_2017_S59


title: A5 hi

description:
Cell lysate
A5_hi_10_04_2017_S58


title: wt NaOCl batch 1 rep1


title: A3 hi

description:
Cell lysate
A3_hi_10_04_2017_S57


title: A1 hi

description:
Cell lysate
A1_hi_10_04_2018_S56


title: WT3+4 hi 10.11.2017

description:
Cell lysate
WT3_4_hi_10_11_2017_10_11_2018_S55

source_name: Monocytes Ly-6Chi sorted from WT mice


title: WT3+4 hi

description:
Cell lysate
WT3_4_hi_10_04_2017_S54


title: WT1+2  hi

description:
Cell lysate
WT1_2_hi_10_11_2018_S53


title: WT4 hi

description:
Cell lysate
WT4_hi_10_04_2017_S52


title: WT5 hi

description:
Cell lysate
WT5_hi_10_11_2018_S51


title: HG-media-6

description:
Cell lysate
HG_media_20_S38

source_name: BMDM cultured in 25mM glucose

value: BMDM cultured in 25mM glucose

value: 25mM glucose


title: HG-media-4

description:
Cell lysate
HG_media_19_S42


title: Brain CD45+ cells, Cd300a-fl/fl, naïve

status: Public on Dec 22 2021

city: Tsukuba

first: Akira

last: Shibuya

state: Ibaraki

address: 1-1-1 Tennodai

department: Immunology

country: Japan

institute: University of Tsukuba

data_processing:
Read alignment and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in sparse matrix format; barcodes.tsv: barcode ids per sample; genes.tsv: gene ids per sample

molecule: polyA RNA

source_name: Brain CD45+ cells

extract_protocol:
To isolate the brain cells, mice were sedated under deep anesthesia and perfused with PBS transcardially. Collected brain tissues were transferred to dounce homogenizer with 3.5ml of RPMI-1640 and grinded using loose and tight plunger. Homogenates were filtered through 70 micrometre cell strainer and then subjected to Percoll (GE Healthcare) gradient centrifugation. Cells were collected from the interlayer between 40% and 70% Percoll layers. Collected cells were filtered through 70 micrometre nylon mesh to obtain single-cell suspensions and PI-CD45+ hematopoietic cells were sorted by flow cytometry.
10X Genomics, Chromium Single Cell 3’ Library and Gel Bead Kit v3.

treatment_protocol: Transient cerebral ischemia (MCAO) was induced using the intraluminal filament technique. A silicon-coated nylon monofilament (Doccol Corporation) was inserted into the right internal carotid artery and left in situ for 60 min. Operation time per animal did not exceed 15 min. During the MCAO procedure, mice were kept on the 40°C heater and after 60 min, the inserted monofilament was withdrawn to allow reperfusion. We only included mice that showed reduction of blood flow of right middle cerebral artery which confirmed by doppler ultrasound.

value: Brain CD45+ cells


title: HG-media-2

description:
Cell lysate
HG_media_18_S28


title: HG-media-1

description:
Cell lysate
HG_media_17_S30


title: WT2 hi

description:
Cell lysate
WT2_hi_10_04_2017_S50


title: LG media-6

description:
Cell lysate
LG_media_16_S36

source_name: BMDM cultured in 5.5mM glucose

value: BMDM cultured in 5.5mM glucose

value: 5.5mM glucose


title: LG media-5

description:
Cell lysate
LG_media_15_S37


title: LG media-1

description:
Cell lysate
LG_media_13_S34


title: LG media-3

description:
Cell lysate
LG_media_14_S29


title: HG exo 12.18.19

description:
Exosomes
HG_exo_28_S40

source_name: Exosomes produced by BMDM cultured in 25mM glucose

value: Exosomes


title: 50od

status: Public on Nov 11 2021

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Pool of PCR products

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
CRISPResso Analysis of genome editing outcomes.
Either wild-type or integrated donor sequences are used as reference.
Genome_build: NM_145383.2 ; NM_214221.1
Supplementary_files_format_and_content: *_CRISPResso_quantification_of_editing_frequency.txt: CRISPResso quantification of editing frequency.
Supplementary_files_format_and_content: HITI_INDEL.fasta: CRISPRESSO Amplicons Reference.
Supplementary_files_format_and_content: HITI_INDEL_guides.txt: CRISPRESSO sgRNA Reference.

molecule: genomic DNA

source_name: retina

extract_protocol:
Genomic DNA was extracted from frozen mouse and pig retina. 150 bp regions flanking the on-target sits of mRho/pRHO gRNAs were amplified by PCR. PCR products were pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

treatment_protocol: gRNA-treated mouse and pig retina.

tag: tissue

value: retina

value: wild type


title: LG exo 12.11.19

description:
Exosomes
LG_exo_25_S39

source_name: Exosomes produced by BMDM cultured in 5.5mM glucose


title: LG exo 12.18.19

description:
Exosomes
LG_exo_27_S33


title: LG exo 01.08.20

description:
Exosomes
LG_exo_23_S35


title: HG exo 01.15.20

description:
Exosomes
HG_exo_22_S43


title: HG exo 01.08.20

description:
Exosomes
HG_exo_24_S32


title: HG exo 12.11.19

description:
Exosomes
HG_exo_26_S31


title: HG-media-6 [RNA-Seq]

data_processing:
cutadapt for quality filtering
STAR alignment to genome
FeatureCounts for gene counting from BAM
Genome_build: GRCm38.88
Supplementary_files_format_and_content: genecounts_renamed_normalized.txt

source_name: Cell lysate

extract_protocol:
Qiagen miRNeasy Mini Kit
SMARTer HI

value: Bone marrow-derived macrophage

value: 25 mM Glucose


title: LG exo 01.15.20

description:
Exosomes
LG_exo_21_S41


title: HG-media-4 [RNA-Seq]


title: HG-media-1 [RNA-Seq]


title: HG-media-2 [RNA-Seq]


title: LG media-6 [RNA-Seq]

value: 5.5mM Glucose + 19.5mM Mannitol


title: LG media-5 [RNA-Seq]


title: LG media-1 [RNA-Seq]


title: BMDM stim HGexo 01-15-20 [RNA-Seq]

value: BMDM-HG-exo


title: BMDM stim HGexo 12-18-19 [RNA-Seq]


title: LG media-3 [RNA-Seq]


title: BMDM stim LGexo 01-15-20 [RNA-Seq]

value: BMDM-NG-exo


title: BMDM stim LGexo 12-18-19 [RNA-Seq]


title: BMDM stim LGexo 12-11-19 [RNA-Seq]


title: BMDM stim LGexo 01-08-20 [RNA-Seq]


title: Unstim 01-15-20 [RNA-Seq]

value: PBS


title: Unstim 12-11-19 [RNA-Seq]


title: Unstim 12-18-19 [RNA-Seq]


title: Unstim 01-08-2020 [RNA-Seq]


title: LH_12_2_4_bis

status: Public on Jun 10 2021

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with htseq-count 0.9.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: mouse fibroblasts

growth_protocol:
This study used fibroblasts extracted from a knockin mouse Per2::LUC.
cells were expanded in DMEM, 4.5 g/L glucose content, 10% FBS at 37 °C and with humidified 5% CO2.

extract_protocol:
Total RNA was extracted used RNeasy Plus Micro kit, according to manufacturer protocol
3'DGE mRNA-seq research sequencing service (Next Generation Diagnostics srl)

treatment_protocol: 3 cycles of 24h each alternating every 12h High (H) and Low (L) glucose-insulin content media. The treatment protocols implemented are : HL (12hH-12hL for 3 cycles), LH (12hL-12hH for 3 cycles), and HH (12hH-12hH for 3 cycles)

tag: expansion passages

value: PER2::LUC sv

tag: metabolic treatment

value: LH

tag: time


title: LH_12_2_1_bis


title: LH_20_1_4_bis


title: LH_12_2_2_bis


title: LH_20_1_3_bis


title: HL_16_6_4_bis

value: HL


title: LH_20_1_2_bis


title: HL_12_5_4_bis


title: HL_16_6_1_bis


title: HL_12_5_2_bis


title: Primed hiPSC microfluidics day 7 rep. 3

description: 3'DGE mRNA-seq

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Homo sapiens

source_name: HPD06 induced primed (isogenic, naïve hiPSCs-derived)

extract_protocol:
RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following manufacturer instructions.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

value: Human primed induced pluripotent stem cells

tag: culture system

value: Microfluidics

tag: culture conditions

value: On 2.5percent Matrigel growth factor reduced (MRF, Corning), cultured in Essential 8 medium (E8, Stemcell Technologies)

tag: time point

value: Day 7 after seeding


title: HL_12_5_1_bis


title: HL_08_4_4_bis


title: HL_08_4_3_bis


title: HL_16_6_3_bis


title: HL_08_4_2_bis


title: HL_12_2_4_bis


title: HL_04_3_1_bis


title: HL_04_3_4_bis


title: HL_04_3_2_bis


title: HL_08_4_1_bis


title: HL_12_2_3_bis


title: HL_12_2_2_bis


title: LH_16_6_4_bis


title: HL_12_2_1_bis


title: LH_16_6_3_bis


title: LH_16_6_1_bis


title: Primed hiPSC microfluidics day 4 rep. 3

description: 3'DGE mRNA-seq

value: Day 4 after seeding


title: LH_12_5_3_bis


title: LH_12_5_1_bis


title: LH_12_5_2_bis


title: LH_20_4_4_bis


title: LH_12_5_4_bis


title: LH_20_4_3_bis


title: LH_20_4_2_bis


title: LH_20_4_1_bis


title: LH_16_3_4_bis


title: LH_16_6_2_bis


title: HL_20_1_4_bis


title: LH_16_3_1_bis


title: LH_16_3_2_bis


title: LH_16_3_3_bis


title: HL_20_1_3_bis


title: HH_16_6_4_bis

value: HH


title: HL_20_1_2_bis


title: HH_16_6_3_bis


title: HH_16_6_2_bis


title: HH_16_6_1_bis


title: HH_12_5_3_bis


title: HH_12_5_2_bis


title: HH_08_4_4_bis


title: HH_04_3_4_bis


title: HH_08_4_1_bis


title: HH_04_3_1_bis


title: HH_12_2_1_bis


title: HH_04_3_3_bis


title: HH_12_2_3_bis


title: HH_20_1_3_bis


title: HH_20_1_2_bis


title: HH_20_1_1_bis


title: LH_12_2_4


title: HH_20_1_4_bis


title: LH_12_2_2


title: LH_12_2_1


title: LH_20_1_4


title: LH_20_1_3


title: LH_20_1_2


title: HL_16_6_4


title: HL_16_6_2


title: HL_16_6_3


title: HL_16_6_1


title: HL_08_4_4


title: HL_12_5_4


title: HL_12_5_2


title: HL_12_5_1


title: HL_08_4_3


title: HL_08_4_2


title: HL_08_4_1


title: HL_04_3_2


title: HL_04_3_4


title: HL_04_3_1


title: HL_12_2_4


title: HL_12_2_3


title: HL_12_2_2


title: LH_16_6_3


title: HL_12_2_1


title: LH_16_6_1


title: LH_16_6_2


title: LH_12_5_3


title: LH_12_5_4


title: LH_12_5_2


title: LH_12_5_1


title: LH_20_4_3


title: LH_20_4_4


title: LH_20_4_2


title: LH_16_6_4


title: LH_20_4_1


title: LH_16_3_4


title: LH_16_3_3


title: LH_16_3_1


title: LH_16_3_2


title: HL_20_1_4


title: HL_20_1_3


title: HL_20_1_2


title: HH_16_6_3


title: HH_16_6_2


title: HH_16_6_1


title: HH_12_5_2


title: HH_12_5_3


title: HH_08_4_1


title: HH_08_4_4


title: HH_12_5_1


title: HH_16_6_4


title: HH_04_3_4


title: HH_04_3_1


title: HH_04_3_3


title: HH_12_2_3


title: HH_12_2_4


title: HH_12_2_1


title: HH_20_1_4


title: HH_20_1_3


title: HH_20_1_2


title: HH_20_1_1


title: 14d after tMCAO 2

status: Public on May 19 2021

city: Pittsburgh

first: Xiaoming

last: Hu

state: PA

address: 200 lothrop street

department: Neurology

institute: University of Pittsburgh

description: Sorted CD45 positive cells

data_processing:
Single cell RNA-seq raw data were processed by Cell Ranger version 3.0.1 (10X Genomics) and aligned to the GRCm38 (mm10) mouse reference genome
Seurat V2.3.4 was used for the downstream analysis, including tSNE, heatmap, and violin plots
We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Genome_build: GRCm38.95

source_name: Brain CD45+ immune cell

extract_protocol:
Ischemic hemispheres were perfused with ice-cold saline and freshly harvested at 5 or 14 days after tMCAO. Single cell suspensions were prepared for flow cytometry. Single cells were incubated with anti-CD45-PE-Cy5 antibody for 30 minutes on ice at 4 ℃ in the dark. The CD45high cells were sorted by FACSAriaTM (BD Bioscience).
Single live cells were separated into Gel bead in emulsion (GEM)s formed by oil micro-droplets by the Chromium instrument (10X Genomics) using Single Cell 3' v2 reagents. Each GEM contains a gel bead and a cell. A greater than 1000-fold excess of partitions compared to cells assures that most GEMs were only one cell/GEM. The reaction mixture/emulsion with captured and barcoded mRNAs were removed from the Chromium instrument followed by reverse transcription. The cDNA samples were fragmented and amplified per 10X protocol. The libraries were then purified, quantified, and sequenced on an Illumina HiSeq.

tag: model

value: tMCAO

tag: days after tmcao


title: D42_w118-VG-3

status: Public on Mar 31 2021

data_processing:
qualtity trimming with cutadapt (v.1.14)
Alignment to the fly genome with STAR (v.2.5.3a)
Generating raw counts tables for genes using feature counts (v.1.5.3)
Genome_build: dmel r6.27
Supplementary_files_format_and_content: counts table of raw gene counts

organism: Drosophila melanogaster

growth_protocol: Drosophila genotypes were raised at 25*C.

extract_protocol:
RNA was extracted from the samples using a RNEAsy kit by Qiagen
SMART-seq v4 Ultra Low Input RNA Kit by Clontech
Samples were sequenced by the Bejing Genomics Institute using a HiSeq4000.

treatment_protocol: At the 3rd instar larvae stage, larvae were either subjected to immunoprecipiation (100 larvae, IP and INPUT samples) or Ventral ganglion dissections (15 larvae, VG samples)

tag: genotype/variation

tag: developmental stage/tissue

value: 3rd instar larvae

tag: sample type

value: VG


title: 5d after tMCAO 1

description: Sorted CD45 positive cells

tag: strain


title: 5d after tMCAO 2

description: Sorted CD45 positive cells


title: D42_w118-VG-2


title: D42_TDP43WT-VG-1


title: D42_TDP43WT-VG-3


title: D42_TDP43WT-VG-2


title: 14d after tMCAO 1

description: Sorted CD45 positive cells


title: D42_TDP43WT-IP-4

value: IP


title: D42_w118-VG-1


title: D42_TDP43WT-IP-2


title: D42_TDP43WT-IP-3


title: D42_TDP43WT-INPUT-4

value: INPUT


title: D42_TDP43WT-INPUT-3


title: D42_TDP43WT-INPUT-2


title: D42_RPL10-VG-1

data_processing:
library strategy: Translating ribosome affinity purification (TRAP)-seq
qualtity trimming with cutadapt (v.1.14)
Alignment to the fly genome with STAR (v.2.5.3a)
Generating raw counts tables for genes using feature counts (v.1.5.3)
Genome_build: dmel r6.27
Supplementary_files_format_and_content: counts table of raw gene counts


title: D42_RPL10-VG-2


title: D42_RPL10-VG-3


title: D42_RPL10TDP43WT-VG-3


title: D42_RPL10TDP43WT-VG-2


title: D42_RPL10TDP43WT-VG-1


title: D42_RPL10TDP43WT-IP-4


title: D42_RPL10TDP43WT-IP-1


title: D42_RPL10TDP43WT-IP-3


title: D42_RPL10TDP43WT-INPUT-4


title: D42_RPL10TDP43WT-INPUT-1


title: D42_RPL10TDP43WT-INPUT-3


title: D42_RPL10-IP-2


title: D42_RPL10-IP-1


title: D42_RPL10-INPUT-2


title: D42_RPL10-INPUT-1


title: D42_RPL10G298S.9-VG-3


title: D42_RPL10G298S.9-VG-2


title: D42_RPL10G298S.9-VG-1


title: D42_RPL10G298S.9-IP-2


title: D42_RPL10G298S.9-IP-3


title: D42_RPL10G298S.9-IP-4


title: D42_RPL10G298S.9-INPUT-4


title: D42_RPL10G298S.9-INPUT-3


title: D42_RPL10G298S.9-INPUT-2


title: D42_G298S.9-VG-3


title: D42_G298S.9-VG-2


title: D42_G298S.9-VG-1


title: D42_G298S.9-IP-4


title: D42_G298S.9-IP-2


title: D42_G298S.9-IP-1


title: D42_G298S.9-INPUT-4


title: D42_G298S.9-INPUT-2


title: D42_G298S.9-INPUT-1


title: Nalm6 cells, THZ1_2

status: Public on Feb 20 2021

city: Shanghai

first: duan

middle: cai

last: wen

address: 1678 dongfang road

country: China

institute: Shanghai Children's Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Cutadapt
Sequenced reads were mapped to GRCh37 whole genome using STAR with parameters --outFileNamePrefix starout  --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesCommand gunzip -c
The raw gene counts was calculated using htseq with parameters -f sam -r name -s reverse -t exon -i gene_id -m union
The gene expression level (FPKM) was calculated according to the RSEM
Genome_build: GRCh37
Supplementary_files_format_and_content: gene_expression.txt (tab-delimited text file includes FPKM values for each Sample)
Supplementary_files_format_and_content: Raw_gene_counts_matrix.txt (Matrix table with raw gene counts for every gene and every sample)

extract_protocol:
Total cellular RNA was isolated using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nalm6 cells were seeded at a density of 1× 10e6 cells/ml and treated with 500nm THZ1or DMSO for 24h.

tag: cell line

tag: treatment


title: Nalm6 cells, DMSO_2

value: DMSO


title: Nalm6 cells, DMSO_3


title: Nalm6 cells, DMSO_1


title: Nalm6 cells, THZ1_3


title: Nalm6 cells, THZ1_1


title: SNS-032_3

status: Public on Feb 09 2021

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05
Sequenced reads were mapped to GRCh38 whole genome using HISAT2 v2.0.4 with parameters --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000
The gene expression level (FPKM) was calculated according to the RSEM
Genome_build: GCF_000001405.38_GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: celllines

extract_protocol:
Total cellular RNA was isolated using the TRIzol reagent.
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: REH cells were seeded at a density of 1× 106 cells/ml and treated with 200nm SNS_032 or DMSO for 24h.

value: REH cells

tag: agent

value: SNA-032 treated


title: SNS-032_2


title: SNS-032_1


title: DMSO_3

value: DMSO treated


title: DMSO_2


title: DMSO_1


title: Replicate 5 H53 wildtype with 2mM H2O2

status: Public on Dec 08 2020

city: Baltimore

first: Diego

middle: Rivera

last: Gelsinger

state: MD

address: 910 Light Street, Apartment 2

department: Biology

institute: The Johns Hopkins Univeristy

data_processing:
We used a read count-based differential expression analysis to identify putative targets of SHOxi that were differentially expressed during oxidative stress and in ΔSHOxi. The program featureCounts was used to rapidly count reads that map to the NCBI H. volcanii annotation. featureCounts was run with strand-specific options on, paired-end mode on or off, multi-mapping off. The read counts were then used in the R differential expression software package DESeq2 (ref). Briefly, read counts were converted into a data matrix and normalized by sequencing depth and geometric mean. Differential expression was calculated by finding the difference in read counts between the SHOxi knockout oxidative stress state to the normalized read counts from the wild-type oxidative stress normalized read counts. The differentially expressed mRNAs were filtered based on the statistical parameter of False Discovery Rate (FDR) under 5%. In addition, only mRNAs with converse differential expression levels (FDR < 5%) in our previous wild type no challenge/oxi stress differential expression comparison (Gelsinger & DiRuggiero, 2018b) were labeled as specific putative targets of SHOxi. Alll libraries deposited here were used as well as WT no challenge and WT oxidative stress mRNA-seq libraries previously deposited on GEO: GSE103893. Read counts from previous libraries are noted in GEO_submission_raw_readcounts.txt with (GSE103893).
Genome_build: ASM2568v1 GCF_000025685.1
Supplementary_files_format_and_content: .xlsx, .txt

organism: Haloferax volcanii DS2

source_name: Cellular culture

growth_protocol: H. volcanii auxotrophic strain H53 (Δpyre2, ΔtrpA) and H98 (Δpyre2, ΔthyH) were used for all experiments. Culturing in liquid and solid media was done in rich medium (Hv-YPC) or selection medium (Hv-Cab), at 42°C and with shaking at 220 rpm (Amerix Gyromax 737) (Dyall-Smith, 2009). Uracil, tryptophan, thymidine, and hypoxanthine were added to a final concentration of 50 µg/mL, each.

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep kit with the following modifications: H. volcanii liquid culture is slimy and viscous thus to increase cellular lysis a 23 G needle and syringe were used to break down the cell pellet after addition of RNA lysis buffer to the frozen pellets to insure complete cell lysis. Total RNA was then extracted following the standard kit protocol. Total RNA was DNase I (NEB) treated (37 °C for 2 hours) as previously described (Gelsinger et al. 2018).
Total RNA was then rRNA-depleted using the Ribo-zero Bacteria kit (Illumina). Strand-specific libraries were prepared using the SMART-seq Ultralow RNA input kit (Takara), insert sizes checked with the Bioanalyzer RNA pico kit (Agilent), and either paired-end sequenced (2 x 150 bp) or single-end sequenced (100 bp) on the Illumina HiSeq 2500 platform at the Johns Hopkins University Genetic Resources Core Facility (GRCF).

treatment_protocol: H. volcanii liquid cultures were exposed to H2O2 as previously described (Gelsinger & DiRuggiero, 2018b). In brief, cultures were grown in 160 mL of Hv-YPC or Hv-Cab under optimal conditions to an OD of 0.4 (mid exponential phase). 2 mM H2O2 was directly added to the cultures followed by an hour incubation at 42 °C with shaking at 220 rpm. Cultures were then rapidly cooled down, centrifuged at 5,000 x g for 5 minutes and the pellets resuspended in 18% sea water. The cell suspensions were then transferred to a 1 mL tube and centrifuged at 6,000 x g for 3 minutes, the pellets were flash frozen and stored at -80 °C until ready for RNA extraction.

tag: strain/background

value: auxotrophic strain H53 (<delta>pyre2, <delta>trpA)

tag: genotype/variatiion

value: wild type

value: 2mM H2O2


title: Replicate 4 H53 wildtype with 2mM H2O2


title: Replicate 2 H53 wildtype with 2mM H2O2 [re-analysis]


title: Replicate 3 H53 wildtype with no challenge [re-analysis]


title: Replicate 4 H53 wildtype with no challenge


title: Replicate 3 H53 wildtype with 2mM H2O2 [re-analysis]


title: Replicate 1 H53 wildtype with 2mM H2O2 [re-analysis]


title: Replicate 2 H53 wildtype with no challenge [re-analysis]


title: Replicate 3 H98 SHOxi knockout (ΔSHOxi) with 2mM H2O2

value: H98 (<delta>pyre2, <delta>thyH)

value: SHOxi knockout


title: Replicate 1 H53 wildtype with no challenge [re-analysis]


title: Replicate 2 H98 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Replicate 1 H98 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Replicate 4 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Replicate 3 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Replicate 2 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: Replicate 1 H53 SHOxi knockout (ΔSHOxi) with 2mM H2O2


title: K120R_NT (untreated)

status: Public on Dec 02 2020

city: New York

first: Manoj

last: Kandpal

state: NY

address: 1230 York Ave

department: Hospital Bioinformatics

institute: Rockefeller University

data_processing:
Base-calling was performed onboard the NextSeq 500 using the integrated instrument computer.
FASTQ generation was performed in the Illumina BaseSpace cloud using bcl2fastq with default parameters.
Read alignment was performed using bwa mem with default parameters
samtools rmdup was used to filter duplicate reads
peak calling was performed using macs2 with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bam file contains aligned reads
Supplementary_files_format_and_content: bed: peak summits locations for every peak
Supplementary_files_format_and_content: narrowPeak: peak locations together with peak summit, pvalue and qvalue
Supplementary_files_format_and_content: peaks excel file: tabular file which contains information about called peaks. Additional information includes pileup and fold enrichment

source_name: H1299 cells

growth_protocol: The p53-null human lung cancer cell line H1299 (ATCC) was cultured in Dulbecco’s Modified Eagle Medium (DMEM, Corning) supplemented with 10% Fetal Bovine Serum (FBS, GeminiBio) at 37°C and 5% CO2. They were routinly re-plated every 4 days, and used for experimets after no more than 20 passages.

extract_protocol:
Cell lysates were clarified from sonicated nuclei and hp53-DNA complexes were isolated with p53-specific antibody.
Library preparation was done using Swift’s Biosciences Accel-NGS 2S Plus Library Kits for Illumina platforms. 10 ng of DNA was used for library preparation and kit’s protocol was followed for a 200 base pair insert. An additional two sided bead clean up was done after the PCR step using SPRI beads with the formula .6X, then using the supernatant, 1.2x. The library was pooled to 1 nM and the sequenced on a NextSeq 500 using the standard loading protocol.

treatment_protocol: Tet(+) samples were treated with 1 ug/ul of Tetracycle for 24 h before the harvest. Additionally, all samples were cross-linked with the 3% formaldehyde and the reaction was quinched with 7.5% glycine.

tag: stable cell line

value: Tet Repressor expression

value: No treatment

tag: antibody

value: anti-p53 (FL393-x, Santa Cruz)


title: BRD4: OCI-AML3 cells Combination Rep2 ChIP-seq

status: Public on Nov 04 2020

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Bowtie2 version 2.1.0 with parameters --phred33 -p 16 -x hg19 --solexa-quals -p 8
Peaks of genomic occupancy were determined using SICER version 1.1 with the parameters hg19 1 200 150 0.75 200 .01
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including peak genomic locations and intensities

source_name: OCI-AML3 cells

growth_protocol: OCI-AML3 cells were obtained from DSMZ and were cultured at 37°C in a humidifed incubator with 5% CO2.

extract_protocol:
Crosslinking was quenched wih 2.5M Glycine, then chromatin lysates were produced using lysis buffer plus protease inhibitors. Samples were then sonicated on ice for 12 cycles of 30 seconds on, 1 minute off, and debris pelleted.  Input controls were removed from each sample.
Sonicated lysates were precleared with magnetic beads, then incubated overnight with antibody-bound beads. ChIP samples were then eluted in 50mM Tris-HCl, pH 8; 10mM EDTA; 1% SDS, and crosslinks were reversed by heating at 65°C for 6-18 hours. TE was added to each ChIP or Input sample. Solutions were incubated with RNaseA for 37 °C for 30 minutes, then with proteinase K at 55 °C for 1-2 hours. DNA samples were then purified using a  Qiagen MinElute PCR purification kit.
Libraries were constructed using the NEBNext Ultra DNA Lib Prep kit with NEBNext Multiplex Oligos.

treatment_protocol: Cells were treated with drugs at the stated concentrations for 6 hrs before proteins were crosslinked to DNA with paraformaldehyde.

tag: tissue

value: OCI-AML3 cells

tag: drug treatment


title: WT_Tet (treated)

value: Tet treatment


title: WT_NT (untreated)


title: BRD4: OCI-AML3 cells Nutlin-3a Rep2 ChIP-seq

value: Nutlin-3a (2.5uM)


title: BRD4: OCI-AML3 cells Combination Rep1 ChIP-seq


title: K120R_Tet (treated)


title: BRD4: OCI-AML3 cells Nutlin-3a Rep1 ChIP-seq


title: BRD4: OCI-AML3 cells CPI-203 Rep1 ChIP-seq


title: BRD4: OCI-AML3 cells DMSO Rep2 ChIP-seq


title: BRD4: OCI-AML3 cells CPI-203 Rep2 ChIP-seq


title: BRD4: OCI-AML3 cells DMSO Rep1 ChIP-seq


title: p53: OCI-AML3 cells Combination Rep4 ChIP-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Bowtie2 version 2.1.0 with parameters --phred33 -p 16 -x hg19 --solexa-quals -p 8
Peaks of genomic occupancy were determined using MACS version 1.4.2 with the parameters --format BAM --gsize hs --pvalue 1e-5 --bdg --single-profile –call-subpeaks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including peak genomic locations and intensities


title: p53: OCI-AML3 cells Combination Rep3 ChIP-seq


title: p53: OCI-AML3 cells Combination Rep2 ChIP-seq


title: p53: OCI-AML3 cells Combination Rep1 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep4 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep3 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep2 ChIP-seq


title: p53: OCI-AML3 cells CPI-203 Rep3 ChIP-seq


title: p53: OCI-AML3 cells Nutlin-3a Rep1 ChIP-seq


title: p53: OCI-AML3 cells CPI-203 Rep4 ChIP-seq


title: p53: OCI-AML3 cells DMSO Rep4 ChIP-seq


title: p53: OCI-AML3 cells CPI-203 Rep2 ChIP-seq


title: p53: OCI-AML3 cells DMSO Rep3 ChIP-seq


title: p53: OCI-AML3 cells CPI-203 Rep1 ChIP-seq


title: p53: OCI-AML3 cells DMSO Rep2 ChIP-seq


title: p53: OCI-AML3 cells DMSO Rep1 ChIP-seq


title: OCI-AML3 cells shp53 Combination Rep3 RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

growth_protocol:
OCI-AML3 cells were obtained from DSMZ and were cultured at 37°C in a humidifed incubator with 5% CO2.
Virus expressing either empty vector or sh-p53 was produced from HEK293T packaging lines, then used to infect OCI-AML3 cells for 3-6 hrs, before cells were grown overnight. A second round of infection was then performed.

extract_protocol:
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
RNA libraries were prepared using an Illumina TruSeq Stranded Lib Prep kit

treatment_protocol: Cells with and without p53 were treated with drugs at the stated concentrations for 24 hrs prior to RNA extraction.

tag: gene knockdown

value: shRNA knockdown of p53


title: OCI-AML3 cells shp53 Combination Rep2 RNA-seq


title: OCI-AML3 cells shp53 Combination Rep1 RNA-seq


title: OCI-AML3 cells shp53 Nutlin-3a Rep1 RNA-seq


title: OCI-AML3 cells shp53 CPI-203 Rep2 RNA-seq


title: OCI-AML3 cells shp53 CPI-203 Rep3 RNA-seq


title: OCI-AML3 cells shp53 Nutlin-3a Rep3 RNA-seq


title: OCI-AML3 cells shp53 Nutlin-3a Rep2 RNA-seq


title: OCI-AML3 cells shp53 DMSO Rep3 RNA-seq


title: OCI-AML3 cells EV Combination Rep3 RNA-seq

value: Empty vector control


title: OCI-AML3 cells shp53 DMSO Rep2 RNA-seq

value: DMSO


title: OCI-AML3 cells shp53 DMSO Rep1 RNA-seq


title: OCI-AML3 cells EV Combination Rep2 RNA-seq


title: OCI-AML3 cells shp53 CPI-203 Rep1 RNA-seq


title: OCI-AML3 cells EV Combination Rep1 RNA-seq


title: OCI-AML3 cells EV Nutlin-3a Rep3 RNA-seq


title: OCI-AML3 cells EV Nutlin-3a Rep2 RNA-seq


title: OCI-AML3 cells EV Nutlin-3a Rep1 RNA-seq


title: OCI-AML3 cells EV CPI-203 Rep3 RNA-seq


title: OCI-AML3 cells EV DMSO Rep2 RNA-seq


title: OCI-AML3 cells Combination Rep2 RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2 version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

treatment_protocol: Cells were treated with drugs at the stated concentrations for 24 hrs prior to RNA extraction.


title: OCI-AML3 cells EV CPI-203 Rep1 RNA-seq


title: OCI-AML3 cells EV CPI-203 Rep2 RNA-seq


title: OCI-AML3 cells Combination Rep3 RNA-seq


title: OCI-AML3 cells EV DMSO Rep3 RNA-seq


title: OCI-AML3 cells Nutlin-3a Rep1 RNA-seq


title: OCI-AML3 cells Nutlin-3a Rep2 RNA-seq


title: OCI-AML3 cells Nutlin-3a Rep3 RNA-seq


title: OCI-AML3 cells EV DMSO Rep1 RNA-seq


title: OCI-AML3 cells Combination Rep1 RNA-seq


title: OCI-AML3 cells CPI-203 Rep3 RNA-seq


title: OCI-AML3 cells CPI-203 Rep2 RNA-seq


title: OCI-AML3 cells DMSO Rep3 RNA-seq


title: OCI-AML3 cells DMSO Rep2 RNA-seq


title: Ped_Tissue_patient7corpusCF_repl1

status: Public on Oct 01 2020

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with htseq-count 0.9.1 by using cellRanger pre-build genes annotations (Ensembl Assembly 93)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Pediatric tissue from stomach mucosa, corpus, cystic fibrosis

growth_protocol: Cell were passaged every 6-8 days. To passage the organoids, Matrigel droplets were disrupted by pipetting in the well and transferred to tubes on ice. Cells were washed with 10 mL of cold basal ADMEM+++ and centrifuged at 200 g at 4°C. (First method) For single cell dissociation, supernatant was discarded, and the pellet resuspended in 1 mL of TrypLE (Thermo Fisher) and incubated for 5 min. After incubation organoids were disaggregated by pipetting, and 10 mL of ice-cold ADMEM+++ was added to dilute and inhibit TrypLE. (Second method) For standard organoid passage during expansion, the organoid pellet was resuspended in 1.5 mL of ice-cold ADMEM+++ and organoids were manually disrupted by narrowed (flamed) glass pipette pre-coated in BSA 1% in PBS, to avoid adhesion to the glass. Cells were washed, pelleted and supernatant discarded. Almost-dry pellets of disaggregated organoids (or single cells) were thoroughly resuspended in cold liquid Matrigel, aliquoted in 30 µL droplets in pre-warmed multi-well plates and incubated at 37C for 20 min to form a gel. Rho-kinase inhibitor (Tocris) was added to single cell dissociated organoids. Medium was added and changed every 3 days.

extract_protocol:
For RNA isolation from stomach tissues, i) pediatric stomach biopsies consisted of only mucosal layer from surgical samples; ii) Late fetal stomachs were cut open and mucosal layer was isolated; iii) early fetal stomachs were processed with no layer isolation, given the small size of the samples. Mucus was removed from all the samples with a glass coverslip to prevent RNA loss during the isolation protocol, and tissues washed in ice-cold PBS. Then the tissues were finely cut with a scalpel on a Petri-dish on ice and transferred to 1.5 mL tubes. RNA was isolated from cultured organoids in Matrigel with 30 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Cells were then washed in ice cold PBS to remove matrix leftovers that could interfere with RNA isolation. Organoids were centrifuged at 200 g at 4°C and supernatant discarded. Dry pellets of tissues and organoids were lysed with RLT buffer (Qiagen). RNA was isolated with RNeasy Mini Kit (Qiagen) following manufacturer’s instructions. Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific).
Libraries were prepared from  total RNA using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina, following manufacturer protocol

treatment_protocol: All organoid lines are expanded in the same WENR culture medium, with no different treatment protocol among them

tag: passage

value: not applicable

tag: culture method


title: OCI-AML3 cells DMSO Rep1 RNA-seq


title: OCI-AML3 cells CPI-203 Rep1 RNA-seq


title: Ped_Tissue_patient5corpus_repl1

source_name: Pediatric tissue from stomach mucosa, corpus


title: Ped_Tissue_patient5antrum_repl1

source_name: Pediatric tissue from stomach mucosa, antrum


title: Ped_Tissue_patient6corpus_repl1


title: Ped_Tissue_patient3antrum_repl1


title: Ped_Tissue_patient3corpus_repl1


title: Fet_Tissue_W15_repl2

source_name: Fetal tissue from stomach mucosa and submucosa (PCW 15)


title: Ped_Tissue_patient4corpus_repl1

source_name: Pediatric tissue from stomach mucosa, sorpus


title: Ped_Tissue_patient3corpusGC_repl3

source_name: Pediatric tissue from stomach mucosa, corpus, gastric closure


title: Fet_Tissue_W15_repl1


title: Fet_Tissue_W11_repl1

source_name: Fetal tissue from stomach mucosa and submucosa (PCW 11)


title: Fet_Tissue_W20_repl2

source_name: Fetal tissue from stomach mucosa (PCW 20)


title: Fet_Tissue_W20_repl1


title: Fet_Tissue_W18_repl2

source_name: Fetal tissue from stomach mucosa (PCW 18)


title: Fet_Tissue_W18_repl1


title: Fet_Tissue_W10_repl1

source_name: Fetal tissue from stomach mucosa and submucosa (PCW 10)


title: Fet_Org_W11_repl4

source_name: Cultured organoid from fetal stomach tissue (PCW 11)

value: P 6

value: Split at single cells with TrypLE; plated in 30 uL droplets of Matrigel Growth Factor Reduced; expanded for 8 days in gastric culture medium WENR (wnt, egf, noggin, r-spondin); isolated from Matrigel using 20 min of ice cold Cell Release Solution ECM digestion; RNA extracted in RLT buffer.


title: Fet_Tissue_W17_repl1

source_name: Fetal tissue from stomach mucosa (PCW 17)


title: Fet_Org_W11_repl3


title: Fet_Org_W11_repl2


title: Fet_Org_W11_repl1


title: Fet_Org_W8_repl4

source_name: Cultured organoid from fetal stomach tissue (PCW 8)


title: Fet_Tissue_W17_repl2


title: Fet_Org_W8_repl3


title: Fet_Org_W8_repl2


title: Fet_Org_W8_repl1


title: Fet_Org_W20_repl4

source_name: Cultured organoid from fetal stomach tissue (PCW 20)


title: Fet_Org_W18_repl4

source_name: Cultured organoid from fetal stomach tissue (PCW 18)

value: P 9


title: Fet_Org_W20_repl1


title: Fet_Org_W20_repl2


title: Fet_Org_W20_repl3


title: Fet_Org_W18_repl2


title: Fet_Org_W18_repl1


title: Ped_Org_patient2_repl4

source_name: Cultured organoid from pediatric stomach tissue


title: Ped_Org_patient2_repl2


title: Ped_Org_patient2_repl3


title: Fet_Org_W18_repl3


title: Ped_Org_patient2_repl1


title: Ped_Org_patient1_repl3


title: Ped_Org_patient1_repl4


title: Ped_Org_patient1_repl2


title: Ped_Org_patient1_repl1


title: 20w_minus_2

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Alignment was performed with STAR 2.6.0a on hg38 reference assembly obtained from cellRanger website (Ensembl 93)
The expression levels of genes were determined with RSEM 1.3.0 by using gencode pre-build genes annotations (hg38 primary assembly)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include expected counts for each sample as output from RSEM

growth_protocol: Fully grown gastric organoids at day 7 after single cell disaggregation were removed from surrounding extracellular matrix using a modified published protocol. Matrigel was dissolved with 60 min treatment of the droplets with Cell Recovery Solution (Corning) at 4°C. Organoids were retrieved from the plates using 1% BSA-coated cut-end tips and transferred to 1% BSA-coated 15 mL tubes. Cells were extensively washed with ice-cold PBS and centrifuged at 200 g for 5 min at 4°C. Supernatant was discarded, the pellet was resuspended in complete medium and transferred to non-tissue culture treated low-adhesive multiwell plates (pre-coated in 1% BSA). Organoids were cultured in suspension for 3 days to allow reversion of polarity, before use in infection experiments.

extract_protocol:
Pelletted organoids were extracted in RLT buffer
cDNA was synthesized using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, following manufacturer suggested protocol. cDNA generated with SMART-Seq v4 Kit were used for preparation of library with NEXTERA XT DNA Library Preparation kit, following the suggested protocol.

treatment_protocol: Reversed-polarity organoids were infected at a MOI of 1 by incubation with 250 µl of an expansion medium viral suspension for 2 hours. After infection, organoids were washed twice in DMEM to remove unbound virus. RP-GOs were dispersed in a 400 µl expansion medium at 37 °C with 5% CO2. For all organoid cultures 50 µl of supernatant were harvested at 0, 24, 48, and 72 hours post infection. An equal volume of expansion medium replaced the sampled supernatant at each collection time. An extra sample at 96 hours post infection was collected for the RP-GOs. Samples were stored at -80°C before titration through the FFA.

value: negative paired control


title: 11w_minus_3


title: 20w_minus_1


title: 20w_minus_3


title: 11y_minus_3

source_name: Cultured organoid from pediatric stomach tissue (age 11 year)


title: 11y_minus_2


title: 11y_minus_1


title: 20w_plus_2

value: SARS-CoV-2 infected at MOI 1


title: 20w_plus_1


title: 11w_plus_2


title: 11w_plus_3


title: 11y_plus_2


title: 11y_plus_3


title: 11y_plus_1


title: extracellular exosome, WT_12_29_2017_104

status: Public on Aug 06 2020

description: small RNA

data_processing:
NEXTFLEX smallRNA kit adapter trimming with cutadapt
smallRNA alignment and counts table generation with sRNABench (v. 0514)
collapsing miRNA counts into single counts table
Genome_build: mm10
Supplementary_files_format_and_content: miRNA raw counts table

source_name: bone marrow

extract_protocol:
Cell culture supernatant was harvested and centrifuged to remove debris. OptiPrep density gradient was used to purify exosomes
libraries were prepared using the PerkinElmer NextFlex smallRNA seq kit

tag: cell type

value: extracellular exosome

value: control (wild type)

value: Excised bone


title: extracellular exosome, WT_04_05_2018_168

description: small RNA


title: cell lysate, WT_3_21_18_12

description: small RNA

value: cell lysate


title: extracellular exosome, WT_03_16_2018_106

description: small RNA


title: cell lysate, WT_3_14_18_9

description: small RNA


title: extracellular exosome, WT_01_25_2018_105

description: small RNA


title: extracellular exosome, IL4_12_29_2017_101

description: small RNA

value: stimulated macrophages


title: cell lysate, WT_1_23_18_78

description: small RNA


title: extracellular exosome, IL4_04_05_2018_167

description: small RNA


title: cell lysate, IL4_3_21_18_5

description: small RNA


title: extracellular exosome, IL4_03_16_2018_103

description: small RNA


title: cell lysate, IL4_3_14_18_2

description: small RNA


title: extracellular exosome, IL4_01_25_2018_102

description: small RNA


title: cell lysate, IL4_1_23_18_74

description: small RNA


title: MDA_48h_5FU-3

status: Public on Aug 05 2020

first: Jian

last: Cui

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-5FU-3

data_processing:
NextSeq500 75bp PE v2 High Output run, with 27 multiplexed samples per run
The fastq files were generated and trimmed through Basespace with application “FASTQ Generation v1.0.0”.
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg38, UCSC for Hep G2, and hg19, UCSC  for MDA-MB-231
Supplementary_files_format_and_content: .csv files delimited matrix showing raw counts of refGenes

growth_protocol: Both Hep G2 and MDA-MB-231 cell lines were purchased from ATCC (MA, USA). Cells were cultured in DMEM medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) at 37 °C with 5% CO2

extract_protocol:
The treated cells were harvested, and the cell pellets were snap frozen with liquid nitrogen and stored at−80°C.Total RNA was isolated with PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. After quantified using a NanoDrop Spectrophotometer ND-1000 (Thermo Fisher Scientific), the quality of the total RNA was verified on a Bioanalyzer by Cancer Genome Facility (SA, Australia) ensuring all samples had RINs >7.0. For both cell lines, the sequencing was performed in Ramaciotti Centrefor Genomics (NSW, Australia). The sample preparation for each cell line was TruSeq Stranded mRNA-seq with dual indexed, on the NextSeq500 v2 platform. The parameter was 75bp paired-end High Output.
Total RNA was isolated with PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol (Rev: 21 May 2012).  Sample preparation were employing TruSeq Stranded mRNA Library Prep Kit (Illumina) with 1μg input total RNA.

treatment_protocol: Drug treatments were designed as follows: pure complete medium,  vehicle control (VC; 0.25% Tween 80 with 10 mM in PBS), 2 mg/ml CKI, or 5FU (150 μg/ml for Hep G2 and 20 μg/ml for MDA-MB-231). Cells were treated with medium only, vehicle control, CKI, and 5Fu are labelled as “untreated”, “CKI”, and “5FU”.

tag: tumor type

value: breast cancer

tag: time


title: MDA_48h_2mg_CKI-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-CKI-3

value: 2mg CKI


title: MDA_48h_2mg_CKI-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-CKI-2


title: MDA_48h_2mg_CKI-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-CKI-1


title: MDA_48h_VC-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-VC-3

value: VC


title: MDA_48h_VC-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-VC-2


title: MDA_48h_VC-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-VC-1


title: MDA_48h_untreated-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-UT-3

value: untreated


title: MDA_48h_untreated-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-UT-2


title: MDA_48h_untreated-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-UT-1


title: MDA_24h_5FU-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-5FU-3


title: MDA_24h_5FU-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-5FU-2


title: MDA_24h_5FU-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-5FU-1


title: MDA_24h_2mg_CKI-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-CKI-2


title: MDA_24h_2mg_CKI-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-CKI-3


title: MDA_24h_VC-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-VC-2


title: MDA_24h_VC-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-VC-3


title: MDA_24h_2mg_CKI-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-CKI-1


title: MDA_24h_VC-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-VC-1


title: MDA_24h_untreated-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-UT-3


title: MDA_24h_untreated-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-UT-2


title: 11w_minus_2


title: 11w_minus_1


title: MDA_24h_untreated-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-UT-1


title: MDA_0h_untreated-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
0h-UT-2


title: MDA_0h_untreated-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
0h-UT-3


title: MDA_0h_untreated-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
0h-UT-1


title: HEP_48h_5FU-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-5FU-3

value: Hep G2

value: liver cancer


title: HEP_48h_5FU-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-5FU-1


title: HEP_48h_5FU-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-5FU-2


title: HEP_48h_2mg_CKI-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-CKI-3


title: 11w_plus_1


title: HEP_48h_2mg_CKI-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-CKI-2


title: HEP_48h_2mg_CKI-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-CKI-1


title: HEP_48h_VC-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-VC-2


title: HEP_48h_VC-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-VC-3


title: HEP_48h_untreated-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-UT-3


title: HEP_48h_untreated-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-UT-2


title: HEP_48h_VC-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-VC-1


title: HEP_48h_untreated-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-UT-1


title: HEP_24h_5FU-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-5FU-3


title: HEP_24h_5FU-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-5FU-2


title: HEP_24h_5FU-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-5FU-1


title: HEP_24h_2mg_CKI-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-CKI-3


title: HEP_24h_2mg_CKI-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-CKI-2


title: HEP_24h_2mg_CKI-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-CKI-1


title: HEP_24h_VC-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-VC-3


title: MDA_48h_5FU-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-5FU-2


title: MDA_48h_5FU-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-5FU-1


title: HEP_24h_VC-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-VC-2


title: HEP_24h_untreated-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-UT-2


title: HEP_24h_VC-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-VC-1


title: HEP_24h_untreated-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-UT-3


title: HEP_24h_untreated-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-UT-1


title: HEP_0h_untreated-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
0h-UT-3


title: HEP_0h_untreated-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
0h-UT-2


title: EXP1030RNA12

status: Public on Jul 27 2020

city: Tampa

first: Marco

last: Davila

state: FL

address: 12902 Usf Magnolia Dr

department: BMT-CI

institute: Moffitt Cancer Center and Research Institute

data_processing:
Illumina NextSeq 500 pair-end reads from RNA-Seq libraries were first adaptor trimmed
STAR v2.5.3a was used for alignment to the reference genome.
HTSeq v0.6.1 was used for reads counting to estimate expression level of genes
Library size normalization was performed using DESeq2
Genome_build: GRCh37
Supplementary_files_format_and_content: comma-delimited text file including read counts of each gene (in rows) for each sample (in columns)

source_name: Lymphoma tumor biopsy

extract_protocol:
Total RNA was extracted using the Allprep Qiagen Kit according to the manufacturer’s instructions
Total RNA-seq libraries were generated from 100 ng of RNA using the Nugen Ovation Human FFPE RNA-Seq kit according to the manufacturer’s instructions

value: Low

tag: response

value: Insufficient Followup


title: EXP1030RNA11

value: High

value: NDR


title: EXP1030RNA10


title: EXP1030RNA9


title: EXP1030RNA6


title: EXP1030RNA8


title: EXP1030RNA5


title: EXP1030RNA4


title: EXP1030RNA3


title: EXP1030RNA2


title: HEP_0h_untreated-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
0h-UT-1


title: EXP964RNA13

value: DR


title: EXP964RNA7


title: EXP900RNA2


title: EXP964RNA6


title: EXP964RNA8


title: EXP964RNA5


title: EXP964RNA2


title: EXP925RNA9


title: EXP925RNA12


title: EXP925RNA8


title: WL7 (D3R1)

status: Public on Jun 01 2022

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 07

data_processing:
We trimmed and filterd the reads using cutadapt and Trimgalore_v0.4.0with default parameters.
Quality was further checked using fastqc.
We used STAR (version 2.5.2b) to map the filtered reads to genome build GRCh38. We used default parameters and --quantMode GeneCounts
Counts files obtained from STAR were used to provide raw counts to DESSeq2. Differential genes and normalizec counts were obtained using DESeq2.
The cutoff for the differential gene list was set as q-val less than 0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: Files containing raw and normalized count using DESeq2

source_name: day 3 of directed differentiation to nephron progenitor cells

growth_protocol: H9 cells underwent directed differentiation to nephron progenitor cells over 10 days according to the protocol published by Morizane and Bonventre, 2017.

extract_protocol:
RNAeasy MiniKit (Qiagen) and DNA-free™ DNA Removal Kit (Life Technologies, AM1906)
RNA-Seq libraries were generated using Illumina stranded mRNA kits (Illumina). Library QC (quality and quantity) was performed using an Agilent 2100 Bioanalyzer (Agilent).
Sequencing was performed on an Illumina HiSeq4000 (single end 50bp) (Illumina).

treatment_protocol: Cells were collecte at each of the specified time points and RNA was extracted.

value: H9 human embryonic stem cells


title: WL11 (D4R2)

description:
Processed data files: Allsamples_B1_DESeq2_raw_counts.txt, Allsamples_B1_DESeq2_normalized_counts.txt
Processed file column headers: S_ 11

source_name: day 4 of directed differentiation to nephron progenitor cells


title: EXP925RNA5


title: EXP900RNA7


title: EXP925RNA4


title: EXP900RNA6


title: FTO-GFP RNA-seq rep 3

status: Public on Jul 01 2020

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
HTSeq and EdgeR is used for generating raw count and differntial gene lists for RNAseq data
Cutom bash and R scripts were used for generating figures and performing statisitcal analyses
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: ascites

growth_protocol: GFP or FTO overexpressed ovcarian cancer cells were culutured with high glucose DMEM medium contain 10% FBS and 1% penicillin/streptomycin, and MENNA.

extract_protocol:
RNA was harvested using Trizol reagent. gDNA was removed using QIAGEN Rneasy mini kit. And then mRNA was isolated with Ambion Dynabeads mRNA purification kit.
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.

value: ovarian cancer cell

tag: tumor stage

value: high grade serous

value: 4 to 6


title: FTO-GFP RNA-seq rep 2


title: FTO-GFP RNA-seq rep 1


title: GFP RNA-seq rep 3


title: GFP RNA-seq rep 2


title: GFP RNA-seq rep 1


title: FTO-GFP m6A-seq m6A pull-down rep 3

description: diff_peak.bed, diff_peak.xls

data_processing:
Fastq files were pre-processed using TrimGalore (0.4.4) and cutadapt (1.14)
Trimmed reads were aligned to the ENSEMBL human genome version GRCh38 using STAR (2.5.2)
Exomepeak (in R) is used for estimating RNA methylation sites and differntial peaks between two conditions.
IGVtool and MEME-chip is used for geneating tracks and predicting enriched motifs
Genome_build: GRCh38
Supplementary_files_format_and_content: xls, bed

extract_protocol:
Magna MeRIP m6A kit (Millipore, Billerica, MA) was used to examine m6A modifications . Methylated RNAs were immunoprecipitated with beads, eluted by competition with free m6A, and recovered with the RNeasy kit
RNA libraries were prepared for sequencing using NEBNext Ultra II RNA Library Prep kit for Illumina.
MERIP


title: FTO-GFP m6A-seq m6A pull-down rep 2

description: diff_peak.bed, diff_peak.xls


title: FTO-GFP m6A-seq m6A pull-down rep 1

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq m6A pull-down rep 3

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq m6A pull-down rep 2

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq m6A pull-down rep 1

description: diff_peak.bed, diff_peak.xls


title: FTO-GFO m6A-seq input rep 3

description: diff_peak.bed, diff_peak.xls


title: FTO-GFO m6A-seq input rep 2

description: diff_peak.bed, diff_peak.xls


title: FTO-GFO m6A-seq input rep 1

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq input rep 3

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq input rep 2

description: diff_peak.bed, diff_peak.xls


title: GFP m6A-seq input rep 1

description: diff_peak.bed, diff_peak.xls


title: Hepatocytes, ParaTSA 24hr Rep3

status: Public on Jun 30 2020

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demulitplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Reads were then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

source_name: Hepatocytes

extract_protocol:
[Tissue harvesting] Mice were sacrificed by CO2 inhalation, then liver tissue was harvested and stored at -80 degrees celcius before use.
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
mRNA libraries were prepared using the TruSeq Stranded LT kit according to the manufacturer’s protocol (Illumina)

treatment_protocol: [Mouse treatment protocol]  Nine-week-old C57BL/6 mice were given either 0.5 mg/kg Trichostatin A (TSA) or 10% DMSO (vehicle) via intraperitoneal injection, one day prior to paracetamol administration, for 4 days. Paracetamol was delivered at 350mg/kg where appropriate by single IP injection after a 10 hr fast.

tag: strain

tag: time point

value: TSA/Paracetamol

value: Hepatocytes


title: Hepatocytes, ParaTSA 24hr Rep4


title: Hepatocytes, ParaTSA 24hr Rep1


title: Hepatocytes, ParaTSA 24hr Rep2


title: Hepatocytes, ParaDMSO 24hr Rep4

value: DMSO/Paracetamol


title: Hepatocytes, ParaDMSO 24hr Rep3


title: Hepatocytes, ParaTSA 14hr Rep4


title: Hepatocytes, ParaDMSO 24hr Rep1


title: Hepatocytes, ParaDMSO 24hr Rep2


title: Hepatocytes, ParaTSA 14hr Rep2


title: Hepatocytes, ParaTSA 14hr Rep1


title: Hepatocytes, ParaDMSO 14hr Rep4


title: Hepatocytes, ParaDMSO 14hr Rep3


title: Hepatocytes, ParaTSA 14hr Rep3


title: Hepatocytes, ParaDMSO 14hr Rep2


title: oxsR NaOCl batch 2 rep1

status: Public on May 25 2022

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
The sequencing artifacts and contamination of raw sequencing reads were assessed by FastQC v.0.11.9 and further adapter, poor-quality or short reads (< 10 bp) were trimmed by Cutadapt v.1.18.
The number of reads mapped to each transcript was counted by HTSeq v.0.11.0
Assembly: The preprocessed reads were aligned to the reference genome of GCF_000025685.1_ASM2568v1_genomic.gff by Bowtie2 v.2.3.4.3, followed by sorting and indexing by Samtools v.1.9.
Supplementary files format and content: DESeq2 v.1.32.0 was used to normalize the read counts and the resulting count matrix contains the raw gene counts for every gene except rRNAs and every sample.

source_name: Haloferax volcanii

extract_protocol:
The RNA was extracted using TRI Reagent® (#T9424, Sigma-Aldrich). To verify RNA integrity, the samples were separated by 0.8 % (w/v) agarose gel electrophoresis (at 90 V for 20 min) in 1X TAE buffer using 2X RNA Loading Dye (#R0641, Thermo Fisher Scientific). The samples were then treated with TURBO DNase-free kit (AM1907, Invitrogen) to remove traces of DNA.
Only RNA samples with DNA below the limit of PCR detection were further processed. From each sample preparation, total RNA ≥ 6 μg in 50 μL with RIN value ≥ 6 was used to prepare a cDNA library and analyzed by high throughput sequencing (Novogene). The abundance of rRNA was reduced using the Ribo-ZeroTM Magnetic kit, and the cDNA was prepared using a 250 to 300 bp insert strand-specific library. The library was sequenced using the Illumina Platform PE150, Q30≥ 80% yielding 2G raw data / sample.

value: oxsR deletion

tag: treatment

value: NaOCl treated


title: Hfx vol: NEBHvo_120 - rep2

status: Public on Apr 14 2022

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 125 Science Dr.

institute: Duke University

description:
Total RNA depleted using NEBNext Core Depletion set with 120 minutes of RNase digestion
HVO_pyrE_NEBHVO120_2
ΔpyrE

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Hbt sal genome (GCF_000006805.1), Hfx vol (GCF_000025685.1_ASM2568v1), Hca his (GCF_000223905.1_ASM22390v1), or Hfx med (GCF_000306765.2_ASM30676v2) genomes (as appropriate) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset). Note that these BAM files are sorted by name, not by read.
Counts mapping to rRNA genes as a percentage of counts mapping to all genes were obtained and reported.
Supplementary files format and content: *.count: Tab-delimited text files include raw counts.

source_name: Archaeal cells

growth_protocol: Cells (3-4 biological replicates) were precultured to stationary phase, and then diluted back to a starting OD. These cultures were then grown to mid-log phase in appropriate rich media.

extract_protocol:
~3-5mL of cells in mid-log phase were flash-frozen in Liq N2 and stored at -80C. Total RNA was extracted from cell pellets using the Agilent Absolutely RNA Miniprep kit. RNA was measured using Nanodrop and quality-checked using Bioanalyzer.
1-10ng of total RNA was used as input for rRNA removal by the various kits tested here. The kit protocol included creation of a dsDNA library from the depleted RNA as template. This library was quality-checked using DNA High Sensitivity chip on the Bioanalyzer.

tag: genotype

value: <delta>pyrE


title: wt untreated batch 1 rep4

value: wt

value: untreated


title: oxsR untreated batch 1 rep2


title: oxsR NaOCl batch 1 rep1


title: Hepatocytes, TSA 0hr Rep1

value: TSA


title: Hepatocytes, TSA 0hr Rep4


title: Hepatocytes, TSA 0hr Rep3


title: Hepatocytes, ParaDMSO 14hr Rep1


title: Hepatocytes, DMSO 0hr Rep4

value: DMSO


title: Hepatocytes, TSA 0hr Rep2


title: Hepatocytes, DMSO 0hr Rep2


title: IMR90 cells, IR TSA Rep3

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demultiplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each Sample

source_name: IMR90 cells

growth_protocol: Human primary IMR90 fibroblasts were grown in DMEM +20% FBS, 100 u/mL penicillin, 100 ug/ml streptomycin and 2mM glutamine, at 37 degrees celcius in a humidified atmosphere with 5% CO2.

extract_protocol:
Poly-A mRNA was extracted using a Qiagen RNeasy Mini kit with on-column Dnase1 digestion, according to the manufacturer’s protocol.
mRNA libraries were prepared using an Illumina TruSeq Stranded LT kit according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with control or 100 nM Trichostatin A (TSA) for 10 days, and the medium was refreshed daily. To induce senescence, cells were irradiated 8 hrs after commencement of treatment, where indicated.

tag: cell line

tag: cell state

value: Senescent


title: Hepatocytes, DMSO 0hr Rep1


title: Hepatocytes, DMSO 0hr Rep3


title: IMR90 cells, IR No TSA Rep3


title: IMR90 cells, IR No TSA Rep1


title: IMR90 cells, IR TSA Rep1


title: IMR90 cells, IR No TSA Rep2


title: IMR90 cells, Prolif No TSA Rep3

value: Proliferating


title: IMR90 cells, Prolif TSA Rep1


title: IMR90 cells, IR TSA Rep2


title: IMR90 cells, Prolif TSA Rep3


title: IMR90 cells, Prolif No TSA Rep2


title: IMR90 cells, Prolif No TSA Rep1


title: IMR90 cells, Prolif TSA Rep2


title: IMR90 cells, Prolif Parkin Rep3

data_processing:
Illumina RTA v2 software used for basecalling.
Sequenced reads were demultiplexed using the bcl2fastq tool, trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using Tophat2  version 2.0.9 with parameters --b2-sensitive --no-coverage-search -z pigz --solexa-quals -p 8
Fragments Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using Cufflinks version 2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

treatment_protocol:
[infection protocol]  Retroviral vectors LZRS or LZRS-YFP_Parkin were used to transfect Phoenix packaging cells, and virus was harvested after 24 hrs. Filtered viral supernatent was then mixed 1:1 with culture medium, supplemented with 8 ug/ml polybrene, and cultured with IMR90 cells for 20 hrs. Infected cells were selected with 250 uM zeocin.
Infected cells were treated for 48 hrs with 12.5uM CCCP where appropriate.

tag: gene transduction

value: Parkin

value: proliferating


title: IMR90 cells, Prolif EV Rep3

value: Empty vector control


title: IMR90 cells, Prolif Parkin Rep1


title: IMR90 cells, Prolif Parkin Rep2


title: IMR90 cells, Prolif EV Rep1


title: IMR90 cells, IR Parkin CCCP Rep1

value: CCCP

value: senescent


title: IMR90 cells, IR Parkin CCCP Rep2


title: IMR90 cells, IR Parkin CCCP Rep3


title: IMR90 cells, IR CCCP Rep1


title: CT_brain_CD45pos

status: Public on May 18 2020

city: Daejeon

first: Bong Ihn

last: Koh

address: 291 Daehakro

institute: Korea Advanced Institute of Science and Technology

description:
single cell RNA
CD45-+ brain single cell RNA library

data_processing:
Cell Ranger (v3.1.0) was used to process single cell 3' RNA-seq ouput. Breifly, first the cell ranger mkfastq was used to demultiplex illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v3.1.0) and cell-gene raw expression matrices were made. Potential doublets were removed by Scrublet.  Low quality cells (less than 1000 detected genes) were removed. Also, cells with high mitochondrial gene associated UMI count (>7% of total UMI counts) were removed.
After quality control, expression matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Identification of differentially expressed genes and dimensionality reductions were performed by Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Cell-gene expression matrix of log normalized UMI counts for WT and LATS1/2 KO datasets

source_name: CD45-+ brain single cells

extract_protocol:
FACS sorted CD45+ or CD45- cells were processed on the 10X chromium system following the manufacturer's protocols.
Using Chromium Single cell 3' v3 Reagent Kit (10X genomics), cDNA libraries were constructed

tag: sample type

value: FACS sorted

tag: age

value: Adult


title: IMR90 cells, IR Parkin Rep1

tag: drug treatment


title: N2_PA14_3

status: Public on Oct 15 2019

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
htseq-count from HTSeq v0.10.0 was used to quantify genes and transcripts.
DESeq2 v1.22.1 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: wild-type N2, 24-hrs exposure to P. aeruginosa

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain OP50.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli OP50 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with P. aeruginosa PA14 for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.  Total RNA was extracted.

value: wild-type N2

value: 1-day old young adult

tag: infection

value: 24-hrs exposure to P. aeruginosa

tag: tissue

value: whole animal


title: IMR90 cells, IR EV Rep1


title: 20w_plus_3

tag: passage

tag: agent

value: SARS-CoV-2 infected at MOI 1


title: N2_OP50_3

source_name: wild-type N2, uninfected

value: uninfected


title: N2_OP50_2


title: lung tumor_vehicle for continuous_biological rep4

status: Public on Sep 11 2019

type: RNA

city: Spring House

first: Hyejin

last: Choi

address: 1400 McKean Rd

institute: Johnson & Johnson

description:
LungTum_Vehicle_Conti_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

hyb_protocol: Following fragmentation, 5.5 ug of ss-cDNA were hybridized for 16 hr at 45C on Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data was analyzed using the Summarization SST-RMA algorithm in the Transcriptome Analysis Console (TAC) software version 4.0.

label: biotin

source_name: mouse KC375

label_protocol: Biotinylated ss-cDNA were prepared according to the standard WT Pico protocol from 50 ng total RNA (Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays User Guide, 2017, Thermo Fisher Scientific).

growth_protocol: The lung tissue was harvested at the designed time point (when the treatment was complete) and fixed with formaldehyde, then embedded into paraffin and sectioned.

extract_protocol: RNA was extracted from 6-10 paraffin embedded tissue sections using QUICK RNA FFPE kit (ZYMO Research).

treatment_protocol: KRASG12C GEMM mice were treated with selumetinib continuously (daily for 3 weeks) or pulsatilely (1 cycle: 1 week ON + 1 week OFF, total 3 cycles) with their matched control (vehicles).

value: KRASG12C GEMM

value: Lung tumor

value: Vehicle for continuous selumetinib group

tag: genotype/variation

value: Tumor cells harbor an activating mutation of the human version of KRAS (KRASG12C/+) at the collagen I locus.


title: lung tumor_vehicle for continuous_biological rep3

description:
LungTum_Vehicle_Conti_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

source_name: mouse KC374


title: lung tumor_vehicle for continuous_biological rep1

description:
LungTum_Vehicle_Conti_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

source_name: mouse KC237


title: lung tumor_continuous_biological rep3

description:
LungTum_Continuous_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC174

value: Selumetinib, continuous


title: lung tumor_continuous_biological rep4

description:
LungTum_Continuous_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC344


title: lung tumor_vehicle for pulsatile_biological rep4

description:
LungTum_Vehicle_Pul_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC197

value: Vehicle for pulsatile selumetinib group


title: lung tumor_vehicle for pulsatile_biological rep1

description:
LungTum_Vehicle_Pul_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC258


title: lung tumor_pulsatile_biological rep3

description:
LungTum_Pulsatile_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC241

value: Selumetinib, pulsatile


title: lung tumor_pulsatile_biological rep2

description:
LungTum_Pulsatile_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC257


title: lung tumor_pulsatile_biological rep1

description:
LungTum_Pulsatile_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC217


title: SWD008: Cachectic from C26m2 metastasis model

status: Public on Jul 01 2018

data_processing:
We use RTA (Illumina) for base calling. Sanger/Illumina 1.9
We map the reads to a reference genome (Mouse: NCBIm37) using Tophat (version 2.1.0) with very-fast (-D 5 -R 1 -N 0 -L 22 -i S,0,2.50) option
Reads across junctions were checked and indicated in the supplied GFF (--no-novel-juncs).
Bam files obtained from TopHat were used to generate the differential gene using the module Cuffdiff (cufflinks-2.2.1) with default settings
The cutoff for the differential gene list was set as q-val less than 0.05
Genome_build: NCBIm37
Supplementary_files_format_and_content: Excel files containing differential list of genes, obtained using cuffdiff

source_name: skeletal muscle

growth_protocol: Mice were housed in the animal facility at Columbia University Medical Center (CUMC) under conventional conditions with constant temperature and humidity and fed a standard diet. Treatment of mice was in accordance with the institutional guidelines of CUMC’s Institute of Comparative Medicine.

extract_protocol:
Total RNA was extracted using Trizol® reagent following manufacturer’s instructions (Thermo Fisher). RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest following the manufacturer’s instructions (QIAGEN). RNA was quantified spectrophotometrically (Nanodrop, Thermo Scientific) and assessed for quality by capillary gel electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies, Inc.).
poly-A pull-down to enrich mRNAs from total RNA samples and Illumina TruSeq RNA prep kit to prepare library.

treatment_protocol: For RNA sequencing, Luciferase labeled C26m2 and 4T1 tumors were resected 2-3 weeks post tumor cell injection. After confirmation of metastasis by bioluminescence imaging and with appearance of cachectic symptoms, mice were euthanized 5 weeks post tumor cell injection. Tibialis anterior muscles from tumor-bearing and age-matched healthy control mice were isolated, snap frozen for subsequent RNA isolation.

value: tibialis anterior muscle

value: 12-14 weeks


title: IMR90 cells, Prolif EV Rep2

value: Empty vector control

value: DMSO

value: proliferating


title: IMR90 cells, IR CCCP Rep3

value: CCCP

value: senescent


title: IMR90 cells, IR Parkin Rep2

value: Parkin


title: IMR90 cells, IR CCCP Rep2


title: IMR90 cells, IR Parkin Rep3


title: SWD007: Cachectic from C26m2 metastasis model


title: IMR90 cells, IR EV Rep3


title: IMR90 cells, IR EV Rep2


title: SWD006: CD2F1 healthy control


title: N2_PA14_5

value: wild-type N2

value: 1-day old young adult

value: 24-hrs exposure to P. aeruginosa

value: whole animal


title: INJ_brain_CD45pos

value: FACS sorted

value: Adult


title: N2_PA14_1


title: N2_PA14_2


title: N2_PA14_4


title: N2_OP50_5

value: uninfected


title: N2_OP50_4


title: SWD004: Cachectic from 4T1 metastasis model

value: Balb/c


title: SWD005: CD2F1 healthy control


title: SWD003: Cachectic from 4T1 metastasis model


title: SWD001: Balb/c healthy control


title: SWD002: Balb/c healthy control


title: Rib_Chondrocyte_H3K27ac_ChIPSeq

status: Public on Jul 01 2015

city: Los Angeles

first: Xinjun

last: He

address: 1425 San Pablo St

department: BROAD CIRM Center

institute: University of Southern California

data_processing:
ChIP libraries were sequenced on Illumina Genome Analyzer II for samples (Rib_Chondrocyte_Sox9_ChIPseq, Rib_Chondrocyte_H3K4me2_ChIPSeq, Rib_Chondrocyte_H3K4me3_ChIPSeq, Rib_Chondrocyte_H3K27me3_ChIPSeq, Rib_Chondrocyte_H3K36me3_ChIPSeq, Rib_Chondrocyte_H3K27ac_ChIPSeq, Rib_Chondrocyte_RNA_Pol_II_ChIPseq, Rib_Chondrocyte_Input_Control_ChIpseq, Rib_Chondrocyte_IgG_Control_ChIpseq), or Hiseq 2000  for samples ( Rib_Chondrocyte_Input_Control_for_p300_ChIPseq, Rib_Chondrocyte_p300_ChIPSeq)
the first 25nt of sequence reads were aligned with Eland software (Illumina), allowing not more than 2 mismatches per reads to mouse genome version mm9/Build 37
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008; Jiang et al., 2010) with a P-value cutoff of 10e-5, by comparing with the input control without antibody immunoprecipitation or an IgG control. Peaks were incorporated into further analysis displaying an FDR<0.01.
Genome_build: mouse mm9
Supplementary_files_format_and_content: bed

source_name: p1 mouse rib chondrocytes

growth_protocol: Neonatal ICR wild-type mice embryonic day 17.5 nasal septum or postnatal day 1 rib

extract_protocol:
Embryonic day 17.5 (E17.5) nasal septum or postnatal day 1 (p1) rib chondrocytes isolated from wild-type ICR mice were immediately cross-linked with 1% formaldehyde for 10 minutes at room temperature, then 0.125 M Glycine was added to quench formaldehyde.  20,000,000 cells were used for a ChIP reaction. Chromatin was sonicated by 10 sessions of 30 pulses (1 sec on and 1 sec off) at 50% amplitude using the Branson sonifier 250D (Branson Ultrasonics Corporation, Danbury, CT) in order to obtain 100 – 600 bp of DNA fragments. One hundred microlitters of Dynabeads M-280 Sheep anti-Mouse IgG or anti-Rabbit IgG was combined with 9 μg of antibodies for targets of interest.
ChIPseq libraries were constructed from input control samples (input DNA and IgG controls) as well as ChIP DNA using ChIP-seq DNA Sample Prep Kit (IP-102-1001; Illumina Inc., San Diego, CA), according to manufacturer’s instruction. Adaptor-modified DNA fragments were enriched by 18 cycles of PCR.

treatment_protocol: Wild type, not treated

tag: strain background

value: ICR

tag: isolation stage

tag: cell type

value: Enzyme digested rib chondrocytes

tag: chip antibody

tag: chip antibody vandor

value: Abcam

tag: chip antibody cat. #


title: Rib_Chondrocyte_H3K4me3_ChIPSeq

value: Millipore


title: Rib_Chondrocyte_Sox9_ChIPseq


title: Rib_Chondrocyte_H3K4me2_ChIPSeq


title: Rib_Chondrocyte_Input_Control_ChIpseq


title: lung tumor_vehicle for continuous_biological rep2

description:
LungTum_Vehicle_Conti_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the continuous selumetinib treatment group.

source_name: mouse KC306

tag: strain

value: KRASG12C GEMM

value: Lung tumor

tag: treatment

value: Vehicle for continuous selumetinib group

value: Tumor cells harbor an activating mutation of the human version of KRAS (KRASG12C/+) at the collagen I locus.


title: N2_OP50_1


title: H3K4me3 _ChIP-seq

status: Public on Jun 23 2015

city: Cleveland

first: Chia-Feng

state: OH

address: 9500 Euclid Avenue,

department: Cardiovascular & Metabolic Sciences

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn5 whole genome using Strand NGS software version 1.6 with default parpemters.
Duplicated reads were filted. Peaks for SOX6, SOX9 and histone modifications were identified using MACS software (version 1.4.5) with default settings
Genome_build: rn5

organism: Rattus norvegicus

source_name: RCS cells

extract_protocol:
RCS cell lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP-seq DNA libraries wereprepared for sequencing using standard Illumina protocols

value: Rat chondrosarcoma cell

tag: chip-seq antibody

value: H3K4me3 (ab8580, Abcam)


title: H3K4me1_ChIP-seq

value: H3K4me1 (ab8895, Abcam)


title: H3K27ac_ChIP-seq

value: H3K27ac (ab4729, Abcam)


title: Input_me1me3K9me3


title: Input_H3K27ac


title: lung tumor_continuous_biological rep2

description:
LungTum_Continuous_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC159

value: Selumetinib, continuous


title: SOX9_ChIP-seq

value: SOX9 (AB5535, Millipore)


title: Input_SOX9


title: Untreated.2

status: Public on Jul 01 2014

description: RNA-Seq of untreated AML3 cells

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to hg18 whole genome using tophat 1.4.1 with parameters –solexa-quals, -p 12, --segment-length 18, -M, -G Homo_sapiens.NCBI36.54.gtf
Aligned reads normalised by library size (number of fragments) and subsequent reads piledup and converted to bigWig format
Genome_build: hg18
Supplementary_files_format_and_content: bigWig files represent pileups of the reads at each base.  bigWig files were normalised by library size and represent the number of reads at a given genomic location per million mapped reads and generated using UCSC wigToBigWig.

growth_protocol: OCI-AML3 cells were cultured in suspension in RPMI media supplemented with FBS 20%, Penicllin 5% and L-Glutamine 5%, incubated at 37°C in humidified conditions and 5% CO2. To passage, cells were counted by haemocytometer and either centrifuged to a pellet and resuspended in fresh media or resuspended in 50% fresh media at a concentration of 0.5 x 106/ml every 2-3 days.

extract_protocol:
RNA was extracted using RNA easy mini kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AzaC was dissolved from lyophilised powder into culture-sterile DMSO to produce a 20 mM stock solution and stored as 15μl aliquots at -80°C. For each new experiment a fresh aliquot of AzaC was diluted in RPMI/20% FBS to produce a 2 mM working stock which was diluted directly onto cells in culture.

tag: cell line

value: Untreated


title: Untreated.3

description: RNA-Seq of Untreated AML3 cells


title: Untreated.1

description: RNA-Seq of Untreated AML3 cells


title: Treated.2

description: RNA-Seq of Aza treated AML3 cells

value: Aza Treated


title: lung tumor_continuous_biological rep1

description:
LungTum_Continuous_1
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with continuous selumetinib.

source_name: mouse KC158


title: Treated.3

description: RNA-Seq of Aza treated AML3 cells


title: Treated.1

description: RNA-Seq of Aza treated AML3 cells


title: Myers_Jurkat_2_None_UW

status: Public on Mar 01 2011

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description: Reduced Representation

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

source_name: Jurkat

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Jurkat_protocol.pdf UW_Stam:Jurkat_Stam_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeHaibMethylRrbs

tag: cell

value: Jurkat

tag: cell organism

value: Human

tag: cell description

value: T lymphoblastoid cell line derived from an acute T cell leukemia

tag: cell karyotype

value: cancer

tag: cell lineage

value: "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC

tag: cell sex

value: M

tag: replicate

tag: obtainedby

value: UW


title: Myers_Jurkat_1_None_UW

description: Reduced Representation


title: lung tumor_vehicle for pulsatile_biological rep3

description:
LungTum_Vehicle_Pul_3
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC515

value: KRASG12C GEMM

tag: tissue

value: Lung tumor

value: Vehicle for pulsatile selumetinib group

tag: genotype/variation


title: lung tumor_vehicle for pulsatile_biological rep2

description:
LungTum_Vehicle_Pul_2
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with vehicle at the same time with the pulsatile selumetinib treatment group.

source_name: mouse KC274

value: Tumor cells harbor an activating mutation of the human version of KRAS (KRASG12C/+) at the collagen I locus.


title: lung tumor_pulsatile_biological rep4

description:
LungTum_Pulsatile_4
Gene expression data from tumor lung FFPE tissue of a mouse that was treated with pulsatile selumetinib.

source_name: mouse KC244

value: Selumetinib, pulsatile


title: scRNA-seq, brain parenchyma leukocytes from C57BL/J mice 72h after transient middle cerebral artery occlusion

status: Public on Nov 26 2021

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

description:
stroke_cns_72h
single-cell RNA seq data of brain parenchyma leukocytes from C57BL/J mice 72h after transient middle cerebral artery occlusion

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v6.0)
Read alignments and transcript counting were done individually for each sample using the cellranger count pipeline with standard parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Standard cellranger output format

source_name: CD45iv-CD45+ leukocytes from brain parenchyma

extract_protocol:
Mice were injected (intravenously; iv) with fluorochrome coupled anti-mouse CD45 antibody (clone 30-11F, Biolegend, 3 µg/mouse). Five minutes later, animals were intracardially perfused with cold PBS with 10 U/ml heparin under deep ketamine/xylazine anesthesia. During perfusion, blood was collected and transferred into a tube. To separate different CNS compartments, the forebrain and cerebellum were dissected from mice. Under binoculars, the dura was dissected from the calvaria and the pia was dissected from the brain parenchyma. All choroid plexuses were removed from the ventricles of the brain. Brain tissue was cut into pieces and digested with collagenase D (2.5 mg/ml, Roche Diagnostics) and DNase I (0.05 mg/ml, Sigma) at 37 °C for 20 min. Pia, dura, and CP were digested in medium containing 1 mg/ml Collagenase D (Roche) for 45 min at 37°C. Afterwards, digested tissue was passed through a 70 μm cell strainer. The parenchyma was centrifuged on a 70%/37% percoll gradient. The interphase was removed, washed and re-suspended in PBS with 2% FCS. Cells extracted from the CNS, pia and dura were sorted for CD45+CD45iv- cells.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit with v2 and 3 chemistry (both from 10X Genomics, #1000128, #1000157). Sample processing and library preparation was performed according to manufacturer's instructions using AMPure beads (Beckman Coulter, A63881). Sequencing was carried out on a Illumina Novaseq using NovaSeq 6000 S4 Reagent Kit (300 Cycles, #20028312) the a 150-8-8-150 read setup.
scRNA-seq

value: brain parenchyma

tag: cell type

value: CD45iv-CD45+ tissue-resident leukocytes (TRL)

tag: condition

value: transient middle cerebral artery occlusion 72h


title: pool_2084

status: Public on Nov 11 2021

description: Pool of PCR products

data_processing:
CRISPResso Analysis of genome editing outcames
Genome_build: GRCm39/mm39
Supplementary_files_format_and_content: Quantification of editing frequency as determined by the percentage and number of unmodified and modified reads; fasta of amplicons used as reference; txt file of amplicone guides

source_name: liver

extract_protocol:
Genomic DNA was extracted from frozen retina and liver samples. 150 bp regions flanking the on target and off-target sites of mRho and mAlb gRNA were amplified by PCR, pooled and used for library construction.
10 ng of PCR products were used as input for the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina
OTHER: Amplicon sequencing

treatment_protocol: gRNA- and scramble-treated retina and liver.

tag: tissue.

value: liver

tag: genotype

value: wild type


title: pool_2067

description: Pool of PCR products

tag: strain


title: pool_5_50os

description: Pool of PCR products

source_name: retina

value: retina


title: Primed hiPSC well day 4 rep. 3

description: 3'DGE mRNA-seq

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.20.0.422)
Sequence reads were trimmed using bbduk software (bbmap suite 37.31)
Alignment was performed with STAR 2.6.0a.
The expression levels of genes were determined with HTseq-counts 0.9.1.
Differential expression analysis was performed using edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: HPD06 induced primed (isogenic, naïve hiPSCs-derived)

extract_protocol:
RNA was extracted with RNeasy Plus Micro Kit (Qiagen) following manufacturer instructions.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostics srl).

value: Human primed induced pluripotent stem cells

tag: culture system

value: Glass coverslip in standard plate

tag: culture conditions

value: On 2.5percent Matrigel growth factor reduced (MRF, Corning), cultured in Essential 8 medium (E8, Stemcell Technologies)

tag: time point

value: Day 4 after seeding


title: genomic DNA from eutopic endometrium Sample_712

status: Public on Sep 12 2023

type: genomic

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

country: Australia

institute: University of Queensland

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

hyb_protocol: All DNA samples were adjusted to the same volume and concentration for sodium bisulfite conversion followed by DNAm analysis on the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scan protocol was performed at the University of Southern California Epigenome Center.

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

label: Cy3 and Cy5

source_name: endometrium sample 712

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

value: Female

tag: sample type

value: endometrium

tag: disease state

value: Control

tag: cycle phase

value: ESE

tag: plate

tag: terminus

tag: batch

tag: euro

value: EUR

tag: recruiment

tag: age


title: genomic DNA from eutopic endometrium Sample_709

source_name: endometrium sample 709


title: genomic DNA from eutopic endometrium Sample_728

source_name: endometrium sample 728

value: PE