title: Non-Treated Apex sampled at day 5, Rep 2 [CAP6.2]


title: Non-Treated Apex sampled at day 4, Rep 3 [CAP5.3]

status: Public on Nov 22 2023

type: SRA

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

library_source: transcriptomic

data_processing:
Reads whose first 25 nucleotides had sequencing scores less than 30 were discarded.
Reads with at least 18 nt after removing the 3'-adapters were kept.
The unique sequences of the remaining reads were obtained and aligned to the miRNA sequences using the BLAST algorithm with the options of ``-S 1 -m 8 -e 0.01".
The abundances of miRNAs were calculated.
Assembly: Acomosus_321_v3 from Phytozome
Supplementary files format and content: Text file to show the names of unique miRNAs and their sequences.
Supplementary files format and content: MS Excel file to show the abundances of unique miRNAs.

molecule: total RNA

organism: Ananas comosus

source_name: Non-Treated Apex sampled at day 4

growth_protocol: A uniform plot with pineapple plants weighing 1.5 to 2 kg was selected in a commercial field (Cultivar 'MD1', PRI 73-50) at Dole Plantation, Wahiawa, Hawaii (21° 31’ 52.6 N; -158° 03’ 35.3 W) 6 weeks before commercial forcing.

extract_protocol:
Total RNA was extracted from the apex and leaf bases using the Qiagen RNeasy Plant Mini Kit (Qiagen, #74904) following the manufacturer's protocol. DNA was removed with the DNA-free DNA Removal Kit (Life Technologies, #AM1906M). Three biological replicates were sequenced for each sampling stage with three apices or leaf bases in each replication.
Total RNA (2 µg) was used for the preparation of the mRNA-Seq library using the TruSeq Stranded mRNA LT kit (Illumina, USA) according to the manufacturer’s protocol. The size of the RNA-Seq library was evaluated by electrophoresis (1 μl of sample + 1 μl of loading dye 6X, 1% Agarose, TBE 1X Buffer, 30 minutes, 60V) and 1 μl of sample was used for quantification with a Qubit Fluorometer (Invitrogen, USA) using the DNA HS assay kit.
The multiplexed pooled libraries were sequenced on Illumina HiSeq4000 with a 50 nt read length. Small RNA libraries were prepared from total RNA using the NEBNext Multiplex Small RNA Sample Kit for Illumina (E7300, NEB, Ipswich, MA) following the manufacturer’s protocol. The libraries were quantified by qPCR and sequenced in each lane with a read length of 50 nt.

treatment_protocol: The plot was divided into three replications with two treatments (control and treated) and ~50 plants in each treatment block. Water (10 ml) as control treatment or ethephon (50 mg ai in 10 ml) (Ethrel, Rhone-Poulenc, AG Company, North Carolina) as flower induction treatment was injected into the centre of the plant between 7:00 and 7:20 AM. At 8:30 to 8:45 am, three plants were harvested from each replication in the water control and ethephon-treated plants at each sampling time after treatment. Four grams of the "D" leaf base (most recently matured leaf) and the other leaves of the uprooted plants were trimmed in the field from the cut stem. The trimmed leaf bases and the trimmed stem were chilled and immediately returned to the laboratory on ice at 10 AM for further processing. The bases of the trimmed leaves were removed from the apex of the apex of the stem to expose the stem (Supplementary Figure SF1) and <1 g of the apex was taken from each stem and frozen in liquid nitrogen. This physical processing of the leaf bases and apex, especially the care needed to carefully remove the leaf bases from the shoot apex of the three control and treated plants of each of the three replications was completed by 2:00 PM and reported here 6 hours after ethephon or water control treatment. Subsequent leaf samples at the apex and ‘D’ were taken 1, 2, 3, 4, 5, 6 and 8 days after treatment between 8:00 and 8:30 AM and processed by noon in the laboratory. Leaf bases were included as a control to allow comparison with nonapex tissue, since leaf primordia remained on the excised apex. All samples were stored at -80 °C until ground into powder in liquid nitrogen for RNA extraction.

tag: tissue

value: Non-Treated Apex sampled at day 4

tag: treatment

value: water (10 ml) as control


title: Non-Treated Apex sampled at day 4, Rep 1 [CAP5.1]


title: Non-Treated Apex sampled at day 4, Rep 2 [CAP5.2]


title: Ethephon Treated Apex sampled at  day 1, Rep 1 [TAP2.1]

source_name: Ethephon Treated Apex sampled at  day 1

value: Ethephon Treated Apex sampled at  day 1

value: ethephon (50 mg ai in 10 mL) (Ethrel, Rhone-Poulenc, AG Company, North Carolina) as the flower induction treatment


title: Non-Treated Apex sampled at day 3, Rep 3 [CAP4.3]

source_name: Non-Treated Apex sampled at day 3

value: Non-Treated Apex sampled at day 3


title: Non-Treated Apex sampled at day 3, Rep 2 [CAP4.2]


title: Non-Treated Apex sampled at 6 hours Rep 3 [CAP1.3]

source_name: Non-Treated Apex sampled at 6 hours

value: Non-Treated Apex sampled at 6 hours


title: Non-Treated Apex sampled at day 1, Rep 3 [CAP2.3]

source_name: Non-Treated Apex sampled at  day 1

value: Non-Treated Apex sampled at  day 1


title: Non-Treated Apex sampled at day 2, Rep 2 [CAP3.2]

source_name: Non-Treated Apex sampled at day 2

value: Non-Treated Apex sampled at day 2


title: Non-Treated Apex sampled at 6 hours Rep 2 [CAP1.2]


title: Non-Treated Apex sampled at day 2, Rep 1 [CAP3.1]


title: Non-Treated Apex sampled at  day 1, Rep 1 [CAP2.1]


title: Non-Treated Apex sampled at day 3, Rep 1 [CAP4.1]


title: Non-Treated Apex sampled at 6 hours Rep 1 [CAP1.1]


title: Non-Treated Apex sampled at day 2, Rep 3 [CAP3.3]


title: Non-Treated Apex sampled at day 1, Rep 2 [CAP2.2]


title: Patient 36 organoids control

city: Brno

first: Core Facility

last: Bioinformatics

address: Kamenice 5

country: Czech Republic

institute: CEITEC - Masaryk University

data_processing:
Sequence reads were trimmed for low-quality sequence using Trimmomatic (parameter LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:5)
Trimmed sequence reads were mapped to Homo sapiens genome (GRCh38-p10) using STAR
Read count extraction was done using featureCount and normalization were performed using the R package DESeq2
Assembly: GRCh38-p10
Supplementary files format and content: TAB-delimited file with the read counts from featureCount.

molecule: polyA RNA

organism: Homo sapiens

source_name: Prostate

growth_protocol: 3D organoids culture. Cells isolated from patient-tissue after radical prostatectomy.

extract_protocol:
RNA was extracted using high pure RNA isolation kit from Roche
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq FWD kit, 75bp Directional RNA Library Prep Kit for Illumina and polyA selection. Sequencing was made at the CEITEC Core Facility Genomics (Brno, Czech Republic)

treatment_protocol: Organoids treated or not with TGF-B signalling pathway inhibitor (A 83-01)

value: Prostate

value: control


title: Non-Treated Apex sampled at day 6, Rep 1 [CAP7.1]

source_name: Non-Treated Apex sampled at day 6

value: Non-Treated Apex sampled at day 6


title: Patient 37 organoids control


title: Patient 35 organoids control


title: Patient 37 organoids treated with TGF-B signalling pathway inhibitor A 83-01


title: Patient 33 organoids control


title: Patient 35 organoids treated with TGF-B signalling pathway inhibitor A 83-01


title: Patient 36 organoids treated with TGF-B signalling pathway inhibitor A 83-01


title: Patient 33 organoids treated with TGF-B signalling pathway inhibitor A 83-01


title: WT E15 embryo Maxillary Molar

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

country: USA

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10X Genomics) was used to process reads into a barcode x count matrix by aligning to the mm10 mouse assembly and using the refdata-gex-mm10-2020-A annotation provided by 10X Genomics.
Assembly: mm10 transcriptome
Supplementary files format and content: barcode, features, and matrix output from cell ranger

organism: Mus musculus

source_name: Maxillary molar tooth organ

extract_protocol:
E15.5 embryos and P0/P1 mice pups (n=6) were used for single-cell dissociation. Mice embryos/pups were dissected out and transferred into ice-cold phosphate-buffered saline (PBS) in a 10 cm petri dish. Tooth organs were carefully dissected (maxillary and mandibular molars) of each respective stage and were collected in a 1.5 ml tube with 1X PBS with 0.04% bovine serum albumin (BSA) on ice. Samples were collected from mice embryos/pups in each respective age group. Harvested tooth organs were cut into small pieces in ice-cold 1X PBS with 0.04% BSA on ice. For isolating the single cells, Tissue pellets were then incubated in 1 ml of TrypLE express enzyme (Thermo Fisher Scientific, Waltham, MA) for 30 minutes at 37℃. Cells were collected by passing the suspension through a cell strainer, followed by centrifugation.
Libraries from isolated cells were prepared using the Chromium Next Single Cell 3’ Reagent Kit v3.1 (Dual Index -10x Genomics – protocol CG000315 Rev C), aiming for a total of 8,000 cells per sample. In brief, cell suspensions were loaded onto the Chromium Controller microfluidic device to be partitioned into bar code-containing Gel Bead-In-Emulsions (GEMs). Samples were incubated, and poly-adenylated mRNAs were reverse-transcribed into cDNAs containing a unique molecular identifier (UMI) and a cell barcode unique to each GEM. The GEMs were broken using a recovery agent to produce a bulk pool of barcoded molecules. Additional amplification of the cDNA was performed before proceeding to fragmentation, end repair, A-tailing, and ligation. A sample dual index PCR was performed in order to add the P5, i5, i7, and P7 sequences to the final scRNA-seq library. Finally, samples were pooled, and the library was sequenced using the Illumina NovaSeq 6000 with the SP reagent Kit v.1.5, resulting in 28x90 bp paired-end reads.

value: Maxillary molar tooth organ

tag: genotype

tag: age


title: C_K5_18_wt_my_2_S61880

city: Vienna

first: Isabelle

last: Weinhofer

address: Spitalgasse 4

country: Austria

institute: Medical University of Vienna

description: M-CSF-dependent differentiation of human blood-derived monocytes towards macrophages for 7 days in vitro

data_processing:
STAR
Mapping was done using STAR to hg38 genome.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

source_name: Blood

growth_protocol: Human peripheral blood-derived monocytes were differentiated using 50 ng/ml M-CSF and maintained in RPMI complemented with Penicillin /Streptavidin, 10% heat-inactivated FBS

extract_protocol:
Cells were lysed in TRIzol® following the manufacturer’s (Invitrogen) instructions and homogenized by passing through a QIAshredder spin column (Qiagen). The isolated total RNA fraction was purified using RNeasy® Mini Kit and RNase-free DNase digestion (Qiagen).3 µg total RNA was used for the generation of mRNA-focused libraries.
RNA libraries for RNA-seq were prepared using poly-A selection.

treatment_protocol: Foamy macrophages were generated by the presence of 20µg/mL murine brain-derived myelin for 7days during differentiation

value: Blood

tag: cell type

value: Monocyte-derived macrophages

value: Control

value: Myelin wt


title: C_K9_18_wt_my_3_S61885

description: M-CSF-dependent differentiation of human blood-derived monocytes towards macrophages for 7 days in presence of murine myelin in vitro


title: WT E15 embryo Mandibular Molar

source_name: Mandibular molar tooth organ

value: Mandibular molar tooth organ


title: WT P1 Maxillary Molar


title: WT P1 Mandibular Molar


title: C_K36_18_wt_my_9_S61901


title: C_K24_18_wt_my_7_S61907


title: C_K21_18_wt_my_6_S61915


title: C_K19_18_wt_my_5_S61910


title: HUVECs cells Biol Rep 1, siANGPTL4-XEN445 10 µM

city: New Haven

first: Bal Krishna

last: Chaube

state: CT

address: Amistad Research Building, Amistad St

department: Comparative Medicine

institute: Yale University

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
SI-X1_242_335_S105

data_processing:
Reads aligned to hg19 build of human genome with STAR
Quantified to hr19 RefSeq annotation model through Partek E/M
Genes were normalized as counts per million
Assembly: hg19
Supplementary files format and content: tab-delimited text file include cpm values for each Sample (raw gene count)

source_name: HUVEC

growth_protocol: HUVECs (Human umbilical vein endothelial cells, P2) were obtained from the Yale School of Medicine, Vascular Biology and Therapeutics Core facility and cultured in M199/EBSS medium supplemented with 20% fetal bovine serum (FBS), 2 mM Glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated from control cells using TrueSeq Small RNA Library preparation (Illumina)

treatment_protocol:
Expression of ANGPTL4 was silenced in HUVECs (60-70% confluent, P4) by using specific sets of siRNAs using RNAiMAX according to manufactures instructions.
36h post trasfections cells were treated with either CoCl2 (100uM) or appropriate vehical control (PBS) for aditional 24h. In another sets of experiment, 36h posttrasfection, cells were treated either XEN445 (10uM) or apropriate vehical control (DMSO) for aditional 24h.

tag: cell line

value: HUVEC

value: Primary Endothlelial Cell

value: ANGPTL4 knockdown

tag: time


title: C_K12_18_wt_my_4_S61924


title: Patient 32 organoids control


title: HUVECs cells Biol Rep 2,  siANGPTL4-XEN445 10 µM

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
SI-X2_230_347_S106


title: HUVECs cells Biol Rep 3, NS-XEN445 10 µM

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
NS-X3_195_382_S101

value: NS


title: HUVECs cells Biol Rep 2, NS-XEN445 10 µM

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
NS-X2_207_370_S100


title: HUVECs cells Biol Rep 3,  siANGPTL4 DMSO3

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
SI-D3_254_323_S104

value: Vehicle control (DMSO)


title: HUVECs cells Biol Rep 1, NS-XEN445 10 µM

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
NS-X1_219_358_S99


title: HUVECs cells Biol Rep 2,  siANGPTL4 DMSO2

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
SI-D2_266_311_S103


title: HUVECs cells Biol Rep 3, NS DMSO3

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
NS-D3_231_346_S98


title: HUVECs cells Biol Rep 1, siANGPTL4 DMSO1

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
SI-D1_278_299_S102


title: Patient 32 organoids treated with TGF-B signalling pathway inhibitor A 83-01


title: HUVECs cells Biol Rep 3,  siANGPTL4 CoCl2 100 µM

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
SI_H3_221_356_S83

value: Cobalt Chloride (CoCl2)


title: HUVECs cells Biol Rep 1, NS DMSO1

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
NS-D1_255_322_S96


title: HUVECs cells Biol Rep 2,  siANGPTL4 CoCl2 100 µM

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
SI_H2_233_344_S82


title: HUVECs cells Biol Rep 3, NS CoCl2 100 µM

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
NS_H3_257_320_S80


title: HUVECs cells Biol Rep 1, siANGPTL4 CoCl2 100 µM

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
SI_H1_245_332_S81


title: HUVECs cells Biol Rep 2, NS CoCl2 100 µM

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
NS_H2_269_308_S79


title: HUVECs cells Biol Reph 1, NS CoCl2 100 µM

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
NS_H1_281_296_S78


title: HUVECs cells Biol Rep 2, NS VC2

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
NS-VCtrl2_197_380_S85

value: Vehicle control (PBS)


title: HUVECs cells Biol Rep 3,  siANGPTL4 VC3

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
SI-VCtrl3_208_369_S92


title: C_K2_18_wt_my_1_S61892

description: M-CSF-dependent differentiation of human blood-derived monocytes towards macrophages for 7 days in presence of murine myelin in vitro


title: HUVECs cells Biol Rep 3, NS VC3

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
NS-VCtrl3_280_297_S86


title: HUVECs cells Biol Rep 3,  siANGPTL4

description:
NS-vs-siANG-Basal-Raw-gene-counts.txt
siANG-Ctrl3_267_310_S95

value: No treatment

value: 60h post transfection


title: HUVECs cells Biol Rep 3,  siANGPTL4-XEN445 10 µM

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
SI-X3_218_359_S107


title: HUVECs cells Biol Rep 2,  siANGPTL4

description:
NS-vs-siANG-Basal-Raw-gene-counts.txt
siANG-Ctrl2_279_298_S94


title: HUVECs cells Biol Rep 3, NS Control

description:
NS-vs-siANG-Basal-Raw-gene-counts.txt
NS-Ctrl3_244_333_S89


title: HUVECs cells Biol Rep 1, siANGPTL4

description:
NS-vs-siANG-Basal-Raw-gene-counts.txt
siANG-Ctrl1_196_381_S93


title: HUVECs cells Biol Rep 1, NS Control

description:
NS-vs-siANG-Basal-Raw-gene-counts.txt
NS-Ctrl1_268_309_S87


title: HUVECs cells Biol Rep 2, NS Control

description:
NS-vs-siANG-Basal-Raw-gene-counts.txt
NS-Ctrl2_256_321_S88


title: HUVECs cells Biol Rep 2, NS DMSO2

description:
NS-vs-siANGPTL4-XEN445-Raw-gene-counts.txt
NS-D2_243_334_S97


title: HBL-1_s_MeDIP-seq

city: Cologne

first: Christina

last: Grimm

address: Weyertal 115b

department: Translational Epigenetics

country: Germany

institute: University of Cologne, Medical Faculty and University Clinic Cologne

library_source: genomic

data_processing:
MeDIP sequencing reads were aligned to the GRCh38 reference genome using bwa Version 0.7.15-r1140.
Aligned reads were analyzed in 250 base windows using the R/bioconductor package QSEA with standard parameters.
Beta values (% methylation) for the 250 base windows where exported from QSEA as bigwig files
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

source_name: diffuse large B-cell lymphoma (ABC-DLBCL)

growth_protocol: Cell lines were grown at 37°C and 5% CO2 in medium supplemented with fetal bovine serum

extract_protocol:
genomic DNA was extracted from cell lines with the Dneasy blood and tissue kit (Cat No./ID: 69504; Qiagen, Hilden, GER), DNA was sheared by focused ultrasonication to a size of 100-300 bp using a Covaris E220 (Covaris Ltd., Brighton, UK)
libraries were prepared from 1.3 µg DNA using the TrueSeq DNA Sample Preparation Kit (Illumina, San Diego, USA) with unmethylated TrueSeq indexed adaptors according to the Illumina protocol. Libraries were denatured by 95°C for 10 min and subjected to methylated DNA immunoprecipitation (MeDIP) using 5 µg antibody targeting 5-methylcytidine (clone33D3). Following MeDIP enrichment, libraries were amplified using 10 PCR cycles and size selection was performed on a 2% agarose gel. 50 bp paired end reads were generated on a HiSeq2000 (Illumina).

treatment_protocol: Cell lines with aquired Venetoclax resistance were established by long-term increasing exposures with Venetoclax beginning with 1nM Venetoclax

tag: cell line name

tag: venetoclax resistance

value: no

tag: cellosaurus id

tag: antibody

value: 5-methylcytidine (clone 33D3, Eurogentec,#BI-MECY-1000, Lot:vt150601)


title: 697_s_MeDIP-seq

source_name: Precursor B-cell acute lymphoblastic leukemia


title: 697_r_MeDIP-seq

value: 697-VEN Resistant

value: aquired Venetoclax  resistance


title: OCI-LY-19_r_MeDIP-seq

source_name: diffuse large B-cell lymphoma (GCB-DLBCL)

value: OCI-LY-19-VEN Resistant


title: OCI-LY-19_s_MeDIP-seq


title: WSU-NHL_s_MeDIP-seq

source_name: Follicular lymphoma

value: WSU-NHL


title: WSU-NHL_r_MeDIP-seq

value: WSU-NHL-VEN Resistant


title: HBL-1_r_MeDIP-seq

value: HBL-1-VEN Resistant


title: P30-OH-KUBO_s_MeDIP-seq

source_name: B cell precursor acute lymphoblastic leukemia


title: KARPAS-422_r_MeDIP-seq

value: KARPAS-422-VEN Resistant


title: P30-OH-KUBO_r_MeDIP-seq

value: P30-OH-KUBO-VEN Resistant


title: KARPAS-422_s_MeDIP-seq


title: DB_r_MeDIP-seq

value: DB-VEN Resistant


title: HUVECs cells Biol Rep 1, siANGPTL4 VC1

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
SI-VCtrl1_232_345_S90

value: HUVEC

value: Primary Endothlelial Cell

value: ANGPTL4 knockdown


title: HUVECs cells Biol Rep 2,  siANGPTL4 VC2

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
SI-VCtrl2_220_357_S91

value: Vehicle control (PBS)


title: HUVECs cells Biol Rep 1, NS VC1

description:
NS-vs-siANGPTL4-Hypoxia-Raw-gene-counts.txt
NS-VCtrl1_209_368_S84

value: NS


title: DB_s_MeDIP-seq

value: DB


title: DOHH-2_r_MeDIP-seq

value: DOHH-2-VEN Resistant


title: ciprofloxacin-resistant Pseudomonas aeruginosa, G1 treated 2

city: Hefei

first: jian

last: cheng

address: JINZHAI ROAD 96

institute: USTC

data_processing:
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. To control for false positives in the analysis, the p-values of the differentially expressed genes were adjusted using the Benjamini and Hochberg approach. In this analysis, genes with an adjusted p-value (Padj) < 0.05 were considered significantly differentially expressed. The GOSeq package (v1.34.1) was used to identify Gene Ontology (GO) terms that annotate a list of enriched genes with a significant p-value less than 0.05.
Assembly: dgcA

organism: Bacteria

growth_protocol: Ciprofloxacin-resistant Pseudomonas aeruginosa cells were maintained with LB with 37 oC.

extract_protocol: The entire RNA was extracted using the TRIzol RNA Extraction Kit.

treatment_protocol: Ciprofloxacin-resistant Pseudomonas aeruginosa were mixed with PBS or G1, and then exposed to light to study the impact of NO release on bacterial gene expression through RNA sequencing.

value: WT

value: G1 with light


title: DOHH-2_s_MeDIP-seq

value: no

value: 5-methylcytidine (clone 33D3, Eurogentec,#BI-MECY-1000, Lot:vt150601)


title: ciprofloxacin-resistant Pseudomonas aeruginosa, G1 treated 3


title: ciprofloxacin-resistant Pseudomonas aeruginosa, G1 treated 1


title: ciprofloxacin-resistant Pseudomonas aeruginosa, PBS Control 3

value: PBS with light


title: 115C

type: genomic

city: Cape Coast

first: Nicholas

middle: Ekow

last: Thomford

state: Central

address: PMB, University of Cape Coast School of Medical Sciences, Coast Coast, Ghana

department: Dept. of Med. Biochem.,SMS, CoHAS,

country: Ghana

institute: University of Cape Coast, Ghana

scan_protocol: Plate is placed on the MassARRAY System.with Chip Prep Module or Mass ARRAY Nanodispenser and MAssARRAY analyzer

data_processing:
MassARRAY TyperAnalyzer is used to capture and process datasets.Post processing parameters are set and autolcuster used for cluster plots. PGx Reprot v3 is then generated after post processing using the software
Traffic Light pane with call rates of >/= 85% are good data calls and indcated as green

extract_protocol: DNA was extracted and used to undertake genotyping. Genomic DNA would be amplified using supplied PGx PCR primers in a final reaction volume of 5uL.

tag: population

value: Ghanaian

value: Blood


title: ciprofloxacin-resistant Pseudomonas aeruginosa, PBS Control 2


title: ciprofloxacin-resistant Pseudomonas aeruginosa, PBS Control 1


title: 054A

description: DNA was extracted and used to undertake genotyping


title: 070B


title: 0173D


title: 030B


title: 016A


title: 0173C


title: 0144C


title: SC, 4-5 months, rep6

city: Providence

first: Gregorio

last: Valdez

state: RI

address: 70 Ship St

institute: Brown University

data_processing:
Data were trimmed for both adaptor and quality using Trimmomatic v.0.36 and the Nextera paired-end adapter
Salmon v.0.11.3 was used to index, align, and quantify transcripts.
QC summary statistics were examined using FastQC v0.11.5 and MultiQC v1.0.
R statistical software v4.1.2 was used to generate lists of differentially expressed genes.
Assembly: Salmon: Mus-musculus.GRCm39
Supplementary files format and content: tab-delimited text files include normalized read counts for each sample

source_name: other Schwann cell

extract_protocol:
Cells collected by FACS. RNA isolation performed by Genewiz.
Illumina ultra-low input

value: other Schwann cell

tag: Sex

value: female

value: 4-5 months


title: SC, 4-5 months, rep5


title: PSC, 4-5 months, rep6

source_name: Perisynaptic Schwann cell

value: Perisynaptic Schwann cell


title: 0040E


title: M-109


title: 0041F


title: M-108


title: M-106


title: M-105


title: M-104


title: PSC, 4-5 months, rep5


title: M-103


title: PSC, 4-5 months, rep4


title: M-101


title: SC, 4-5 months, rep4


title: M-102


title: M-052


title: M-051


title: SC, 4-5 months, rep3


title: M-049


title: M-048


title: M-047


title: M-044


title: SC, 4-5 months, rep2


title: PSC, 4-5 months, rep2


title: M-042


title: M-040


title: M-046


title: SC, 4-5 months, rep1


title: M-038


title: M-039


title: M-041


title: M-036


title: SC, 23-24 months, rep6

value: 23-24 months


title: M-032


title: PSC, 4-5 months, rep1


title: M-035


title: M-033


title: PSC, 23-24 months, rep6


title: M-031


title: M-030


title: M-029


title: M-028


title: PSC, 4-5 months, rep3


title: SC, 23-24 months, rep5


title: PSC, 23-24 months, rep5


title: SC, 23-24 months, rep4


title: M-027


title: M-025


title: M-026


title: PSC, 23-24 months, rep4


title: M-023


title: M-021


title: SC, 23-24 months, rep3


title: M-020


title: PSC, 23-24 months, rep3


title: M-017


title: M-019


title: M-016


title: M-015


title: SC, 23-24 months, rep2


title: PSC, 23-24 months, rep2


title: M-014


title: H-075


title: SC, 23-24 months, rep1


title: M-011


title: H-074


title: H-073


title: PSC, 23-24 months, rep1


title: H-072


title: MGT_withEV_TBX20_CutTag 2

city: Birmingham

first: Changde

last: Cheng

state: Alabama

address: 1824 6th Ave S, WTI 510G

department: Department of Medicine - Hematology & Oncology

institute: The University of Alabama at Birmingham

data_processing:
Rawreads were subjected to adapter removal .
Sequencing reads were aligned against hg19 reference genome using bowtie2
Peaks were called by using SEACR 1.3.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: iCM fibroblasts

growth_protocol: H9Fs were cultured in DMEM medium supplement with 20% FBS and 1% Penstrep (HDF medium). HCFs were cultured with FBM2 bullet kit purchased from ATCC (HCF medium), and HFFs were cultured using IMDM with 10% FBS and 1% Pen-strep (HFF medium).

extract_protocol:
CUT&Tag DNA was prepared using CUTANA pAG-Tn5 for CUT&Tag (Epicypher), following the manufacturer’s instructions.
Library construction was performed using the NEBNext UltraII DNA Library Prep Kit from NEB (E7645S).

treatment_protocol: For reprogramming, pMXs-puro-hMGT8, pBabe-miR-133 plasmids15, pBabe-TBX20 or pBabe-EV (constructed in lab) were used for infection.

value: iCM fibroblasts

value: ESC H9 derived fibroblasts H9F

value: R&D systems     MAB8124-SP


title: H-071


title: MGT_withTBX20_TBX20_CutTag 2


title: MGT_withTBX20_TBX20_CutTag 1

value: Invitrogen      PA-40669


title: H-070


title: MGT_withEV_TBX20_CutTag 1


title: H-069


title: Kidney Medulla-Hi-C-Donor5

city: Freiburg

first: Stefan

last: Haug

address: Hugstetter Str. 49

institute: Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg

data_processing:
Please note that the available fastq raw-data files were all downsampled to an equal read depth for comparability reasons.
Following alignment and downsampling, contact matrices (.hic files) were generated and visualized using the Juicebox application (https://www.aidenlab.org/juicebox/).
Intrachromosomal interactions (loops) in cortex and medulla were inferred using Mustache (Roayaei Ardakany u.a. 2020) from the .hic files. We used a p-value threshold of 0.1 with a sparsity threshold of 0.7 for detecting intrachromosomal interactions and an fdr threshold of 0.2 to identify differential intrachromosomal interactions between cortex and medulla.
Assembly: GRCh38 (hg38)
Supplementary files format and content: .hic; Hi-C chromosomal contact matrices
Supplementary files format and content: .bedpe; Files with differential chromosomal interactions (loops)

source_name: Kidney Medulla

extract_protocol:
Approximately 0.5 cm3 of tissue was minced with a razor blade and fixed and nutated for 20 minutes in 10 mls of a 1:10 dilution of 10% neutral buffered formalin (Fisher). Following this, the formalin was quenched by direct addition of 0.1 g of glycine (Sigma) and nutation for another 15 minutes.
The tissue fragments were submitted to Phase Genomics for Hi-C library preparation using their Human Hi-C Kit and sequencing on an Illumina HiSeq 4000.

value: Kidney Medulla


title: H-068


title: H-067


title: 2500 ppm, replicate 3

type: RNA

city: Durham

first: Jian-Liang

last: Li

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description: Gene expression data

hyb_protocol: 12μg of amplified biotin-mRNAs were fragmented and 10μg hybridized to each array for 16 hr at 45°C in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. Array slides were stained with streptavidin/phycoerythrin utilizing a double antibody staining procedure and then washed for antibody amplification according to the GeneChip® Hybridization, Wash and Stain Kit and user manual.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000 and data was obtained using the GeneChip® Expression Console Software (AGCC; Version 1.2)

data_processing: Array data were pre-processing and normalized by the affy package.  The Robust Multichip Analysis (RMA) approach was applied for the normalization.

label: biotin

organism: Rattus norvegicus

source_name: rat brain cortical tissue

label_protocol: Gene expression analysis was conducted on 3 biological replicates using Affymetrix Rat Genome 230 2.0 GeneChip® arrays (Affymetrix, Santa Clara, CA). One hundred ng of total RNA was amplified as directed in the Affymetrix 3' IVT Express kit protocol, performing the IVT reaction for 16 hr.

growth_protocol: On postnatal day 4 (PND4; day of birth PND0) one pup per F2b litter (n=10) was selected. Following decapitation on PND4, brains were excised from the cranium, the cortical tissue dissected, rapidly frozen, and stored at -80oC.

extract_protocol: Total RNA was isolated using TRIzol® (Invitrogen), treated with 2.5L DNase I and 10L Buffer RDD (RNase-Free DNase Set; Qiagen, Hildon, Germany) (RT; 10 min), then column separation (RNeasy mini prep, Qiagen).

treatment_protocol: Male and female rats (F0) were randomly assigned to dose groups of 0, 750, or 2500 ppm and continuously exposed via the diet beginning 2-weeks prior to breeding cohabitation and throughout 3 successive pregnancies producing 3 successive litters in the F1 generation.

value: rat brain cortical tissue

value: 2500 ppm, 4-Methylimidazole

tag: developmental stage


title: H-066


title: Kidney Medulla-Hi-C-Donor4

data_processing:
Please note that the available fastq raw-data files were all downsampled to an equal read depth for comparability reasons.
Following alignment and downsampling, contact matrices (.hic files) were generated and visualized using the Juicebox application (https://www.aidenlab.org/juicebox/).
Intrachromosomal interactions (loops) in cortex and medulla were inferred using Mustache (Roayaei Ardakany u. a. 2020) from the .hic files. We used a p-value threshold of 0.1 with a sparsity threshold of 0.7 for detecting intrachromosomal interactions and an fdr threshold of 0.2 to identify differential intrachromosomal interactions between cortex and medulla.
Assembly: GRCh38 (hg38)
Supplementary files format and content: .hic; Hi-C chromosomal contact matrices
Supplementary files format and content: .bedpe; Files with differential chromosomal interactions (loops)

extract_protocol:
Approximately 0.5 cm^3 of tissue was minced with a razor blade and fixed and nutated for 20 minutes in 10 mls of a 1:10 dilution of 10% neutral buffered formalin (Fisher). Following this, the formalin was quenched by direct addition of 0.1 g of glycine (Sigma) and nutation for another 15 minutes.
The tissue fragments were submitted to Phase Genomics for Hi-C library preparation using their Human Hi-C Kit and sequencing on an Illumina HiSeq 4000.

tag: donor


title: Kidney Cortex-Hi-C-Donor4

source_name: Kidney Cortex

value: Kidney Cortex


title: 2500 ppm, replicate 1

description: Gene expression data


title: 2500 ppm, replicate 2

description: Gene expression data


title: H-063


title: Kidney Medulla-RNA-seq-Donor3 (medulla_3)

description:
RAM0015_Medulla_RNA
Sequencing by ActiveMotif, Configuration HiSeq 2x150 PE HO HiSeq 2x150bp

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Below are the statistics of mapping the reads to the reference genome.
Bedgraph files with genome coverage were computed with bedtools (v2.27.1) genomecov from .bam files and then converted to bigwig (.bw) files with UCSC BedGraphToBigWig.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted. A Space separated txt file conaining the hit counts was created.
Assembly: GRCh38 (hg38)
Supplementary files format and content: bigwig; RNA-seq reads
Supplementary files format and content: txt-file with raw gene counts (not normalized, space separated)

extract_protocol:
Kidney cortex and medulla tissues were stabilized overnight at 4°C in RNALater before long term storage at -80°C
RNA libraries were prepared for sequencing using standard Illumina protocols


title: U2OS

city: Tampa

first: Chia-Ho

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

data_processing:
Sequencing reads were subjected to a variety of pre- and post-alignment QC measures before mapped against reference genome hs37d5  , using TopHat 2.0.13.
Gene-level quantification was determined using HTSeq 0.6.1 by summation of raw counts of reads aligned to the region associated with each gene.
Gene expression data are provided as raw read counts and normalized read counts. Differential expression analysis is not performed as it’s not requested.
Assembly: hs37d5
Supplementary files format and content: tab-delimited text file includes raw count for each sample

source_name: osteosarcoma

extract_protocol:
Total RNA was prepared from each osteosarcoma cell line using the mirVana miRNA Isolation Kit (Cat# AM1560, Invitrogen, Thermo Fisher)
RNA-sequencing libraries were prepared using the Nugen Ovation Human FFPE RNA-seq Multiplex System according to the manufacturer’s protocol (Tecan Genomics, Inc, Redwood City, CA)

value: osteosarcoma


title: Kidney Medulla-RNA-seq-Donor3 (medulla_2)

description:
RAM0013_Medulla_RNA
Sequencing by ActiveMotif, Configuration HiSeq 2x150 PE HO HiSeq 2x150bp


title: U2OS

hyb_protocol: Samples were prepared and hybridized to the CytoScan HD Assay (Affymetrix, Santa Clara, CA, USA) according to Affymetrix specifications.

scan_protocol: standard protocol

data_processing:
The data generated from the assay were normalized, copy number status calculated, and the data reviewed for quality using the Chromosome Analysis Suite (ChAS) v3.0 (Thermo Fisher Scientific, Waltham, MA).
The resulting cychp files are generated by the Affymetrix Chromosome Analysis Suite (ChAS) v3.0

source_name: ostosarcoma cell line

extract_protocol: DNA was extracted using the Blood and Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany)

value: ostosarcoma cell line


title: 750 ppm, replicate 2

description: Gene expression data

value: 750 ppm, 4-Methylimidazole


title: H-062

value: Ghanaian

value: Blood


title: Control, replicate 3

description: Gene expression data

value: Control


title: 750 ppm, replicate 3

description: Gene expression data


title: MG-63

label_protocol: Samples were prepared and hybridized to the CytoScan HD Assay (Affymetrix, Santa Clara, CA, USA) according to Affymetrix specifications.


title: MG-63


title: OS252


title: MNNG

value: MNNG


title: Kidney Cortex-Hi-C-Donor5


title: Kidney Medulla-RNA-seq-Donor1 (medulla_1)

description:
RAM0012_Medulla_RNA
Sequencing by ActiveMotif, Configuration HiSeq 2x150 PE HO HiSeq 2x150bp


title: MNNG


title: Control, replicate 1

description: Gene expression data


title: OS252


title: SAOS2


title: H-057


title: 143B


title: 750 ppm, replicate 1

description: Gene expression data


title: Kidney Cortex-RNA-seq-Donor3  (cortex_3)

description:
RAM0015_Cortex_RNA
Sequencing by ActiveMotif, Configuration HiSeq 2x150 PE HO HiSeq 2x150bp


title: Kidney Cortex-RNA-seq-Donor1 (cortex_1)

description:
RAM0012_Cortex_RNA
Sequencing by ActiveMotif, Configuration HiSeq 2x150 PE HO HiSeq 2x150bp


title: SAOS2


title: Kidney Cortex-RNA-seq-Donor2  (cortex_2)

description:
RAM0013_Cortex_RNA
Sequencing by ActiveMotif, Configuration HiSeq 2x150 PE HO HiSeq 2x150bp


title: H-054


title: Cal51_Ran-D

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description: protein:RNA complexes ~90-300kDa, large RNA fraction (CLIP-tag RNA inserts >120nt).

data_processing:
HITS-CLIP libraries were sequenced on an Illumina NextSeq machine to produce 85 bp single-ended reads to a depth of ~3.5-5.8 million reads.
Raw reads were adapter trimmed and filtered using cutadapt v2.10 (Martin, 2011) using an adapter sequence of AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, an error rate of 0.2, and an overlap of 5 and a minimum length of 28.
Reads derived from PCR duplication were collapsed using Unique Molecular Identifiers (UMIs) using UMI-tools (v1.0.1; Smith et al., 2017) by first using the ‘extract’ method with default parameters to cut 10 bp UMIs from the 3’ end of each read and place it in the read header.
Reads were then mapped against the human reference genome (hg19) using the STAR spliced alignment algorithm (v2.7.7a, Dobin et al., 2013) with default parameters and setting --chimSegmentMin 20, --twopassMode Basic and --chimOutType Junctions for backsplice identification.
UMIs were used to collapse PCR duplicate reads using the UMI-tools ‘dedup’ method with default parameters and alignments were quality filtered using samtools (-bq 10, Li et al., 2009).
Enrichment of HITS-CLIP reads in various regions was analysed using UCSC gene annotation and scripting in python using the pyreference (https://pypi.org/project/pyreference/) and HTSeq (Putri et al., 2021) libraries. For the most abundant 250 circRNAs in the cytoplasm, we counted the number of reads which a) mapped to exons within the circRNA (excluding in 3’-UTRs), b) mapped to exons in the same gene but outside of the circRNA (excluding in 3’-UTRs), c) mapped to introns in the gene outside of the circRNA, and d) mapped to 3’-UTR regions.
Assembly: Human genome, build hg19
Supplementary files format and content: For the top 250 circRNAs, a table of counts of reads which a) mapped to exons within the circRNA (excluding in 3’-UTRs), b) mapped to exons in the same gene but outside of the circRNA (excluding in 3’-UTRs), c) mapped to introns in the gene outside of the circRNA, and d) mapped to 3’-UTR regions, csv format.

growth_protocol: CAL51 cells were grown at 37°C with 5% CO2 and maintained in DMEM media + 10% FBS

extract_protocol:
Cells grown to 80% confluency in 150mm dishes were rinsed with ice-cold PBS and UV irradiated with 250 mJ/cm2, 254 nm, in ice-cold PBS using a Spectrolinker XL1500 (Spectro-UV). Cells were lysed in the dish with 1ml 1 X PXL [1 X PBS, 0.1% SDS, 0.5% deoxycholate, 0.5% Igepal] + EDTA-free Complete protease inhibitor cocktail (PIC; Roche), & lysate collected by scraping.
3' adapter NEBNext 3’SR adaptor for Illumina; /5rApp/AGA TCG GAA GAG CAC ACG TCT /3AmMO/. 5' adapter /5AmMC6/GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNNNN. RT primer 5'-AGACGTGTGCTCTTCCGA-3'. PCR amplification with a common forward primer (NEBNext SR primer for Illumina) and barcoded reverse primers for each sample (NEBNext Index primers for Illumina).

value: Triple negative breast cancer (TNBC) cell line.

value: WT

value: HITS-CLIP using anti-Ran antibody (BD Transduction Laboratories Cat#610341) on wt CAL51 cells grown in DMEM +10% FCS.


title: H-061


title: 143B


title: H-053


title: Cal51_Ran-C

description: protein:RNA complexes ~90-300kDa, small RNA fraction (CLIP-tag RNA inserts <120nt).


title: H-060


title: SKMES_shZNF714_rep3 [S4_3]

city: Poznan

first: Marta

last: Machnik

state: Wielkopolska

address: Rokietnicka 8

department: Chair of Medical Biotechnology

country: Poland

institute: Poznan University of Medical Sciences

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Methylation EPIC BeadChIP using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.  Background intensity computed from a set of negative controls was subtracted from each analytical data point.  The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100). Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Methylatioin Module v1.9.0).  The ß-value reflects the methylation level of each CpG site.  A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.
matrix processed value definition: Average Beta

label: not provided

source_name: lung squamous cell carcinoma cell line, knocked-down ZNF714 expression

label_protocol: Standard Illumina Protocol

growth_protocol: Lung cancer cells received DMEM F-12 medium (Biowest, Nuaillé, France) with 10% FBS (EURx, Gdansk, Poland) and 1% penicillin-streptomycin (Biowest, Nuaillé, France). The cells were cultured in a suitable incubator at 37°C in 5% CO2. Trypsin (Biowest, Nuaillé, France) at the appropriate concentration was used to detach the cells during passaging.

extract_protocol: DNA from 3 biological replicates of H2073 and SKMES cells (WT, shLUC, shZNF714) was isolated with Cell Culture DNA Purification Kit (EurXEURx, Gdansk, Poland) according to the manufacturer’s protocol.

treatment_protocol: shZNF714 and shLUC cancer cells were transduced with lentiviral vectors carrying shRNA sequences complementary to ZNF714 mRNA or complementary to luciferase (5’-CAGCGATGACGAAATTCTTAG-3’) as a control (respectively). We used a mix of two different shZNF714 sequences (5’-ACACCTACATCAACATAAAAG-3’; 5’-CAAATGTGGTTGAGTGTAAGG-3’) to obtain the most efficient level of gene knockdown (shZNF714). Lentiviral particles were prepared by 2nd generation system in HEK-293T cells, using psPAX2 and pMD2.G packaging plasmid and pLV-THEM-GP transfer vector.

value: SKMES

tag: histopathological subtype

value: squamous cell carcinoma


title: SKMES_shZNF714_rep2 [S4_2]


title: SKMES_shZNF714_rep1 [S4_1]


title: "D" leaf from treated plants at d.a.t. 5 replicate 2

city: Urbana

first: Dessiree

middle: Patricia

last: Zerpa Catanho

state: Illinois

address: 1201 W. Gregory Dr, 279 ERML

institute: University of Illinois at Urbana-Champaign

data_processing:
FastQC (Version 0.10.1) for raw read quality evaluation
Trimmomatic-0.36 (Version 3, 29 June 2007) for adapters and low-quality reads removal (ILLUMINACLIP:Adapters.fa:2:30:10 HEADCROP:10 LEADING:28 TRAILING:28 MINLEN:30)
Hisat2 (Version 2.0.5) for alignment
SAM files to BAM files converted with Samtools (Tools for alignments in the SAM format) Version: 1.2 (using htslib 1.2.1)
Aligned reads were counted using featureCounts (Version 1.6.0) and summarized per gene ID
Assembly: Acomosus_321_v3.fa.gz
Supplementary files format and content: Processed data files (Text documents) contain raw read counts (not normalized) for each "Geneid" for each of the samples. Processed FASTA file contains the sequences for each "Geneid" identifier used in the processed data files (see Acomosus_321_v3.transcript.fa.gz).

source_name: "D" Leaf

growth_protocol: Plants growing on a commercial pineapple field (Ananas comosus, cultivar 'MD2', PRI 73-50) at Dole Plantation, Wahiawa, Hawaii were selected for the experiment one month before commercial forcing.

extract_protocol:
TRIzol Reagent (Ambion USA)
2 µg of total RNA were used for RNA-Seqlibrarypreparation. Low Sample Protocol with TruSeq® Stranded mRNA LT kit (Illumina USA) was follow to build the libraries.

treatment_protocol: 10 ml of either water (untreated or "control") or ethephon (50 mg) was applied into the center of the plants.

value: "D" Leaf

tag: replicate

value: biol rep 2

tag: days after_treatment

value: Cultivar 'MD1', PRI 73-50

value: Ethephon


title: Cal51_Ran-B

description: protein:RNA complexes ~45-90kDa

tag: treatment


title: "D" leaf from treated plants at d.a.t. 5 replicate 3

tag: tissue

value: biol rep 3

tag: genotype


title: H-056

source_name: Blood


title: Control, replicate 2

description: Gene expression data

value: rat brain cortical tissue


title: H-052


title: "D" leaf from treated plants at d.a.t. 4 replicate 3


title: Ctrl-FLAG_HMLE_rep2

description: Replicate 2

data_processing:
Raw reads were adapter trimmed and filtered using cutadapt v2.8 (Martin, 2011) using an adapter sequence of AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, error rate of 0.2, and overlap of 5 and minimum length of 28.
Reads derived from PCR duplication were collapsed using Unique Molecular Identifiers (UMIs) using UMI-tools (v0.5.3; Smith et al., 2017) by first using the ‘extract’ method with default parameters to cut the 10 bp UMIs from the 3’ end of the reads.
Reads were then mapped against the human reference genome (hg19) using the STAR (v2.7.2c) spliced alignment algorithm (Dobin et al.) with parameters --twopassMode basic and --quantMode GeneCounts and otherwise default parameters, at an alignment rate of ~82-97%.
Subsequently, unique molecular identifiers (UMIs) were used to collapse PCR duplicate reads using the UMI-tools ‘dedup’ method with default parameters.
To identify enriched regions of the genome, replicate samples were pooled using the Picard Tools function MergeSamFiles (Broad Institute, 2019) and quality filtered using samtools (-q 10, Li et al., 2009).
For the endogenous ESRP1, N-terminal FLAG-tagged inducible ESRP1 and C-terminal FLAG-tagged inducible ESRP1, peak calling was then performed separately for each strand using MACS2 peak caller (version 2.1.1; (Zhang et al., 2008) using the combination of the IgG and FLAG control samples as the control. The following settings were used (-f BAM -g hs --keep-dup all --nomodel --extsize 50 -B --call-summits --slocal 0 --llocal 0 --fe-cutoff 3 -q 0.05) and the resulting peak files from each strand were merged.
Assembly: Human reference genome (build hg19/b37)
Supplementary files format and content: Bed format peak files.

source_name: HMLE

growth_protocol: HMLE cells were grown at 37°C with 5% CO2 and maintained in HUMEC basal serum free media

extract_protocol:
Cells grown to 80% confluency in 150mm dishes were rinsed with ice-cold PBS and UV irradiated twice with 300 mJ/cm2, 254 nm, in ice-cold PBS using a Spectrolinker XL1500 (Spectro-UV). Cells were lysed in the dish with 750µl 1 X PXL [1 X PBS, 0.1% SDS, 0.5% deoxycholate, 0.5% Igepal] + EDTA-free Complete protease inhibitor cocktail (PIC; Roche), & lysate collected by scraping.
3' adapter NEBNext 3’SR adaptor for Illumina; /5rApp/AGA TCG GAA GAG CAC ACG TCT /3AmMO/. 5' adapter /5AmMC6/GUUCAGAGUUCUACAGUCCGACGAUCNNNNNNNNNN. RT primer 5'-AGACGTGTGCTCTTCCGA-3'. PCR amplification with a common forward primer (NEBNext SR primer for Illumina) and barcoded reverse primers for each sample (NEBNext Index primers for Illumina).
CLIP-seq

treatment_protocol: 3XFLAG-tagged ESRP1 expressing cell lines were treated with 1 µg/ml doxycycline for 72 hours prior to harvest.

value: HMLE

tag: cell type

value: epithelial

value: HITS-CLIP negative control using anti-FLAG antibody (Sigma Cat# F1804) on wt HMLE cells grown in HuMEC basal serum free media (Thermo Fisher).


title: "D" leaf from treated plants at d.a.t. 5 replicate 1

value: biol rep 1


title: H-051

value: Ghanaian

value: Blood


title: Ctrl-FLAG_HMLE_rep1

description: Replicate 1

tag: cell line


title: SKMES_shLUC_rep2 [K4_2]

source_name: lung squamous cell carcinoma cell line, control shRNA sequence

value: shLUC


title: "D" leaf from treated plants at d.a.t. 4 replicate 2


title: FLAG_iESRP1-Cterm_rep2

description: Replicate 2

value: HMLE-iESRP1-FLAG (C-term)

value: HITS-CLIP using anti-FLAG antibody (Sigma Cat# F1804) on HMLE cells stably transduced to express C-terminally 3XFLAG-tagged ESRP1. HMLE-iFLAG-ESRP1 cells were grown in HuMEC basal serum free media (Thermo Fisher) and FLAG-ESRP expression induced with 1 ug/ml doxycycline for 72 hours.


title: Y_012A


title: FLAG_iESRP1-Cterm_rep1

description: Replicate 1


title: T1


title: SKMES_WT_rep3 [K3_3]

source_name: lung squamous cell carcinoma cell line, unmodified

value: SKMES

value: WT


title: SKMES_shLUC_rep3 [K4_3]

value: squamous cell carcinoma


title: MH-120


title: SKMES_WT_rep2 [K3_2]


title: Y_077A


title: SKMES_WT_rep1 [K3_1]


title: FLAG_iESRP1-Nterm_rep2

description: Replicate 2

value: HMLE-iFLAG-ESRP1 (N-term)

value: HITS-CLIP using anti-FLAG antibody (Sigma Cat# F1804) on HMLE cells stably transduced to express N-terminally 3XFLAG-tagged ESRP1. HMLE-i-ESRP1_FLAG cells were grown in HuMEC basal serum free media (Thermo Fisher) and ESRP-FLAG expression induced with 1 ug/ml doxycycline for 72 hours.


title: MH-064


title: H2073_shZNF714_rep2 [S2_2]

source_name: lung adenocarcinoma cell line, knocked-down ZNF714 expression

value: adenocarcinoma


title: MH-077


title: "D" leaf from treated plants at d.a.t. 3 replicate 2

value: "D" Leaf

value: biol rep 2

value: Cultivar 'MD1', PRI 73-50

value: Ethephon


title: Ctrl-IgG_HMLE_rep2

description: Replicate 2

value: HMLE

value: epithelial

value: HITS-CLIP negative control using rabbit IgG control antibody (ThermoFisher Cat# 02-6102) on wt HMLE cells grown in HuMEC basal serum free media (Thermo Fisher).


title: H2073_shZNF714_rep1 [S2_1]


title: FLAG_iESRP1-Nterm_rep1

description: Replicate 1


title: "D" leaf from treated plants at d.a.t. 2 replicate 3

value: biol rep 3


title: "D" leaf from treated plants at d.a.t. 4 replicate 1

value: biol rep 1


title: ESRP1_HMLE_rep2

description: Replicate 2

value: HITS-CLIP using anti-ESRP1 antibody (Proteintech Cat# 21045-1-AP) on wt HMLE cells grown in HuMEC basal serum free media (Thermo Fisher).


title: "D" leaf from treated plants at d.a.t. 3 replicate 3


title: MH-076

value: Ghanaian

value: Blood


title: SKMES_shLUC_rep1 [K4_1]

value: SKMES

value: shLUC


title: Ctrl-IgG_HMLE_rep1

description: Replicate 1

value: WT


title: "D" leaf from treated plants at d.a.t. 2 replicate 2


title: H2073_shLUC_rep3 [K2_3]

source_name: lung adenocarcinoma cell line, control shRNA sequence


title: MH-050


title: MH-014


title: "D" leaf from treated plants at d.a.t. 1 replicate 3


title: H2073_shZNF714_rep3 [S2_3]


title: "D" leaf from treated plants at d.a.t. 3 replicate 1


title: H2073_shLUC_rep2 [K2_2]


title: "D" leaf from treated plants at d.a.t. 1 replicate 2


title: ESRP1_HMLE_rep3

description: Replicate 3


title: D13 EB, replicate 2, scRNAseq

city: Paris

first: Laurence

last: Guyonneau-Harmand

address: 27 rue Chaligny

country: France

institute: Etablissement Français du Sang

description:
10x Genomics
TJ22B_hg19

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Matrix (.mtx), features (.tsv) and barcodes (.tsv) output files from CellRanger
Supplementary files format and content: Metadata files (.tsv) with UMAP coordinates and cell identities

source_name: Embroid Body

extract_protocol:
EBs were dissociated in 0.1% collagenase B (Roche Diagnostics, Laval, QC, Canada) for 1 hour at 37°C. They were then treated with 0.25% trypsin for 3 minutes and digested by gentle mechanical shaking.
Mice were killed at week 20, and the femurs and tibias were removed. Bone marrow was flushed, single-cell suspensions were prepared by gently pipeting up and down several times followed by  rinsing and filtration on 40 μm cell strainers (Nylon mesh).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Embroid Body

value: PCI-CAU

value: iPS

tag: time

value: 13 days of culture

tag: assembly

tag: cellranger software_version

tag: chromium 10x_technology


title: H2073_shLUC_rep1 [K2_1]

value: adenocarcinoma


title: MH-003


title: H2073_WT_rep3 [K1_3]

source_name: lung adenocarcinoma cell line, unmodified


title: MH-005


title: H-015


title: KG001


title: "D" leaf from treated plants at d.a.t. 2 replicate 1

value: "D" Leaf

value: Cultivar 'MD1', PRI 73-50

value: Ethephon


title: H2073_WT_rep2 [K1_2]


title: D13 EB, replicate 1, scRNAseq

description:
10x Genomics
TJ22A_hg19


title: Stem apex from treated plants at d.a.t. 8 replicate 3

source_name: Stem apex

value: Stem apex


title: D17 EB, replicate 2, scRNAseq

description:
10x Genomics
TJ18T_hg19

value: 17 days of culture


title: H2073_WT_rep1 [K1_1]


title: Stem apex from treated plants at d.a.t. 8 replicate 2

value: biol rep 2


title: H-013


title: D17 EB, replicate 1, scRNAseq

description:
10x Genomics
TJ18D_hg19


title: ESRP1_HMLE_rep1

description: Replicate 1

value: HMLE

value: epithelial

value: HITS-CLIP using anti-ESRP1 antibody (Proteintech Cat# 21045-1-AP) on wt HMLE cells grown in HuMEC basal serum free media (Thermo Fisher).


title: Salmonella, ΔSEN1990::frt, rep 3

city: Santiago

first: Susan

last: Bueno

state: Región Metropolitana

address: Avda. Libertador Bernardo O’Higgins #340

department: Departamento de Genetica Molecular y Microbiología

country: Chile

institute: Pontificia Universidad Católica de Chile

description: 150 bp paired-end

data_processing:
Quality control of raw reads was carried out using FastQC v0.11.9. Adapters and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6. and the trimmed reads were aligned to the reference genome using STAR v2.6.1d. BAM file filtering and indexing was carried out using SAMtools. RNAseq library quality control was implemented using RSeQC v4.0.0 and QualiMap v2.2.2-dev. Duplicate reads were marked using Picard tools v2.23.9. Library complexity was estimated using Preseq v2.0.3. Duplication rate quality control was performed using dupRadar v1.18.0. Reads overlapping with coding sequences were assigned to genes using featureCounts v2.0.1. Classification of rRNA genes and their reads were based on annotations and RepeatMasker rRNA tracks from the UCSC genome browser when applicable. Differential gene transcription analysis was completed using DESeq2 v1.28.0. Functional enrichment analysis was achieved using g:Profiler python API v1.0.0. Quality control and analysis results plots were visualized using MultiQC v1.9. BAM indexing and read coverage plots were done with IGV 2.16.0.
Assembly: NC_011294
Supplementary files format and content: Wild_Type_vs_SEN1990_DESeq_results

organism: Salmonella enterica subsp. enterica serovar Enteritidis

growth_protocol: Overnight cultures were diluted in LB broth to OD600 = 0.01 and grown at 37°C and shaking until OD600 = 0.6.

extract_protocol:
The cultures were centrifugated at 8,000g for 8 min, the supernatant was discarded, and RNA was isolated using TRizol and chloroform. Samples were further purified from salts using drop dialysis in MF-Millipore™ membranes (0.025µm pore diameter) in nuclease-free water for 4 h on ice.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit and sequenced on an Illumina NovaSeq platform to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample.

tag: strain


title: H-012

tag: population

value: Ghanaian

value: Blood


title: D19 EB, replicate 1, scRNAseq

description:
10x Genomics
TJ16A_hg19

value: 19 days of culture


title: D19 EB, replicate 2, scRNAseq

description:
10x Genomics
TJ16B_hg19

value: Embroid Body


title: H-011


title: "D" leaf from treated plants at d.a.t. 1 replicate 1

value: biol rep 1


title: Stem apex from treated plants at d.a.t. 7 replicate 2


title: Salmonella, ΔSEN1990::frt, rep 2

description: 150 bp paired-end


title: D15 EB, replicate 2, scRNAseq

description:
10x Genomics
TJ4_hg19

value: PCI-CAU

value: iPS

value: 15 days of culture


title: Salmonella, ΔSEN1990::frt, rep 1

description: 150 bp paired-end


title: H-009


title: H-010


title: Stem apex from treated plants at d.a.t. 7 replicate 1


title: Stem apex from treated plants at d.a.t. 8 replicate 1


title: Stem apex from treated plants at d.a.t. 6 replicate 2


title: Salmonella, Wild-Type, rep 3

description: 150 bp paired-end

value: Wild-Type


title: D15 EB, replicate 1, scRNAseq

description:
10x Genomics
TJ3_hg19


title: Stem apex from treated plants at d.a.t. 6 replicate 3

value: biol rep 3

value: Cultivar 'MD1', PRI 73-50


title: Kidney Medulla-ATAC-seq-Donor3 (medulla_3)

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings (“bwa mem”). Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Only properly aligned read pairs with a mapping quality >= 40 aligning to the same chromosome were selected with samtools 1.13 (H. Li u. a. 2009). Read duplicates were removed with picard 2.25.5, reads located within the ENCODE blacklist regions were removed with deepTools alignmentsieve 3.5.1 (Ramírez u. a. 2016). Accessible regions (ARs, peaks) for each sample were called with MACS 2.1.0  (Zhang u. a. 2008) at a cutoff q-value of 0.01 without control file and the –nomodel, -shift -100 and –extsize 200 options. Then a masterlist of ARs across all samples was created using bedops –m (bedops 2.4.35 (Neph u. a. 2012)), and exported as .bed file.
BAM files were filtered applying filter settings used for peak-calling (see above). Files were then additionally normalized for read depth  by random down sampling to the sample with lowest coverage. Then MACS 2.1.0  (Zhang u. a. 2008) was used to generate read coverage tracks (.bw files.)
The read-counts for all master list ARs for all samples were determined with bedops bedmap –count from the read-depth normalized .bam files and then stored as a space separated table (.txt).
Assembly: GRCh38 (hg38)
Supplementary files format and content: bw; MACS2 read coverage for each sample  (normalized to lowest read depth across all samples)
Supplementary files format and content: bed; Masterlist of accessible regions across all samples (merged MACS2 peaks)
Supplementary files format and content: txt; number of ATAC-seq reads for each accessible region in the master list for all samples

extract_protocol:
Snap frozen tissue
Tn5 transposition and ATAC-seq was performed by ActiveMotif (Carlsbad, CA)

value: Kidney Medulla


title: H-008


title: H-007


title: Kidney Medulla-ATAC-seq-Donor1 (medulla_1)


title: Stem apex from treated plants at d.a.t. 7 replicate 3

value: Stem apex

value: Ethephon


title: Stem apex from treated plants at d.a.t. 6 replicate 1


title: Salmonella, Wild-Type, rep 1

description: 150 bp paired-end


title: H-006


title: Kidney Cortex-ATAC-seq-Donor3  (cortex_3)

value: Kidney Cortex


title: H-004


title: Stem apex from treated plants at d.a.t. 5 replicate 3


title: Stem apex from treated plants at d.a.t. 5 replicate 2

value: biol rep 2


title: Salmonella, Wild-Type, rep 2

description: 150 bp paired-end


title: Kidney Cortex-ATAC-seq-Donor2  (cortex_2)


title: Kidney Medulla-ATAC-seq-Donor3 (medulla_2)


title: Stem apex from treated plants at d.a.t. 5 replicate 1


title: H-002


title: Kidney Cortex-ATAC-seq-Donor1 (cortex_1)


title: root, EXPA1 line (8-4), Dex 7 days, replicate 4

city: Brno

first: Core Facility

address: Kamenice 5

institute: CEITEC - Masaryk University

data_processing:
Sequence reads were trimmed for low-quality sequence using Trimmomatic (parameter LEADING: 3 TRAILING: 3 SLIDINGWINDOW: 4:5)
Trimmed sequence reads were mapped to Arabidopsis thaliana genome (TAIR10) using STAR
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: TAIR10
Supplementary files format and content: BAM file of aligned reads against A. thaliana genome.
Supplementary files format and content: TAB-delimited file with the read counts from featureCount.
Supplementary files format and content: TAB-delimited file with the read counts from RSEM.

organism: Arabidopsis thaliana

source_name: root

extract_protocol:
RNA was harvested using Rneasy plant mini kit (Qiagen). 10 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NextSeq2000 P3 50bp Directional RNA Library Prep Kit for Illumina and polyA selection. Sequencing was made at GeneCore (EMBL Heidelberg, Germany).

treatment_protocol: Roots of 7-day old Arabidopsis seedlings of WT and EXPA1 overexpressing line (8-4) that were either grown on MS media +/- Dex or induced with Dex for 3 h.

value: root

value: EXPA1 line (8-4)

value: Dex 7 days


title: 167A

data_processing:
MassARRAY TyperAnalyzer is used to capture and process datasets.Post processing parameters are set and autolcuster used for cluster plots. PGx Reprot v3 is then generated after post processing using the software
Traffic Light pane with call rates of >/= 85% are good data calls and indcated as green

extract_protocol: DNA was extracted and used to undertake genotyping. Genomic DNA would be amplified using supplied PGx PCR primers in a final reaction volume of 5uL.

value: Ghanaian

value: Blood


title: Stem apex from treated plants at d.a.t. 4 replicate 3


title: 084A


title: root, EXPA1 line (8-4), Dex 7 days, replicate 3


title: seedlings, tmt2 1/2 MS+1% Suc, rep3

city: Xi'an

first: Yanting

last: Cao

state: Shaanxi

address: Beilin district, North Taibai Road

institute: Yanting Cao

description: 5 days

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Tair10.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Shoot of seedings

extract_protocol:
RNA was harvested using RNAprep Pure Plant kit (Tiangen, China). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Shoot of seedings

tag: cultivar

value: TMT2 knockout

value: 1% sucrose


title: Stem apex from treated plants at d.a.t. 4 replicate 2


title: seedlings, tmt2 1/2 MS+1% Suc, rep2

description: 5 days


title: root, EXPA1 line (8-4), Dex 7 days, replicate 2

last: Bioinformatics


title: 039A


title: 022E


title: Stem apex from treated plants at d.a.t. 3 replicate 3


title: Pichia pastoris GS115, hour48 [S2]

city: Hangzhou

first: Qi

last: Shen

state: Zhejiang

address: Chaowang road 118

institute: Zhejiang university of technology

data_processing:
Consensus Assessment of Sequence And Variation (CASAVA) v 1.6
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data using CLC Genomics Workbench v 20.0.4
Clean reads were mapped to the reference genome sequence of Pichia pastoris using Hisat2 tools software v 2.1.0.
Read count extraction and normalization were performed using StingTie v 2.1.5
Assembly: GCA_000027005.1
Supplementary files format and content: Microsoft excel file includes RPKM valuses for each sample

organism: Komagataella pastoris

source_name: Pichia pastoris

growth_protocol: Cells were cultured for indicated times in YPD medium

extract_protocol:
The cells cultured at 24, 36, and 48 hours were subjected to cell lysis using BeadBug prefilled tube (Sigma-Aldrich), followed by total RNA extraction using the RNAprep Pure Cell/Bacteria Kit. Subsequently, mRNA extraction was performed using RNeasy Pure mRNA Bead Kit (Tiangen Biotech). 1 ug of total RNA was used for the construction of sequencing libraies.
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina following manufacture’s protocol.

value: Pichia pastoris

value: Fungi

value: Wild-type

value: Cells were cultured for 48 hours


title: Pichia pastoris GS115, hour24 [D1]

value: Cells were cultured for 24 hours


title: seedlings, tmt2 1/2 MS, rep3

description: 7 days

value: No sucrose


title: root, EXPA1 line (8-4), Dex 7 days, replicate 1


title: Pichia pastoris GS115, hour36 [S1]

value: Cells were cultured for 36 hours


title: root, EXPA1 line (8-4), Dex 3 hours, replicate 4

value: Dex 3 hours


title: Stem apex from treated plants at d.a.t. 4 replicate 1

value: Stem apex

value: biol rep 1

value: Cultivar 'MD1', PRI 73-50

value: Ethephon


title: seedlings, tmt2 1/2 MS+1% Suc, rep1

description: 5 days


title: Stem apex from treated plants at d.a.t. 3 replicate 2

value: biol rep 2


title: 0070C

value: Ghanaian

value: Blood


title: Stem apex from treated plants at d.a.t. 3 replicate 1


title: 0042B


title: seedlings, tmt2 1/2 MS, rep1

description: 7 days

value: Shoot of seedings

value: TMT2 knockout


title: root, EXPA1 line (8-4), Dex 3 hours, replicate 3

value: root

value: EXPA1 line (8-4)


title: root, EXPA1 line (8-4), Dex 3 hours, replicate 2


title: seedlings, tmt2 1/2 MS, rep2

description: 7 days


title: root, EXPA1 line (8-4), Dex 3 hours, replicate 1


title: seedlings, WT 1/2 MS+1% Suc, rep3

description: 5 days

value: WT

value: 1% sucrose


title: seedlings, WT 1/2 MS+1% Suc, rep2

description: 5 days


title: PDF-exposed mice + S.epidermidis peritonitis

city: Cardiff

first: Anne-Catherine

last: Raby

state: Cardiff

address: Heath Park, Academic Avenue

country: United Kingdom

institute: Cardiff University

description: i.p. catheted fitter, daily PDF administration + S. epidermidis i.p. injection

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software: https://geneglobe.qiagen.com/us/analyze
For the normalization, average of a combination of automatically selected housekeeping genes (out of 5 tested Actb,B2m, Gapdh, Gusb, Hsp90ab1) were used
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where ΔCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-changes are 2^-ΔΔCt, where ΔΔCt = (ΔCt_Test Group - ΔCt_Control group)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes Actb, B2m, Gusb).
Fold Change worksheet reports S.epidermidis/Control, PDF/Control or PDF + S.epidermidis ratios.

label: SYBR green

source_name: aortas

label_protocol: RT: Qiagen RT2 first strand kit, qPCR on QuantStudio12 flex

extract_protocol: Total RNA extracted with RNeasy Fibrous Tissue Mini Kit

tag: Sex

value: Female


title: Stem apex from treated plants at d.a.t. 2 replicate 1


title: Stem apex from treated plants at d.a.t. 2 replicate 2


title: Non infected PDF-exposed mice (i.p. catheter fitter, daily PDF administration)

description: i.p. catheted fitter, daily PDF administration


title: 0201B


title: root, EXPA1 line (8-4), control, replicate 4

value: control


title: seedlings, WT 1/2 MS+1% Suc, rep1

description: 5 days


title: root, EXPA1 line (8-4), control, replicate 3


title: seedlings, WT 1/2 MS, rep3

description: 5 days

value: No sucrose


title: Non-infected Control mice

description: i.p. catheter fitted, daily PBS administration for 36 days


title: seedlings, WT 1/2 MS, rep1

description: 5 days


title: seedlings, WT 1/2 MS, rep2

description: 5 days


title: Stem apex from treated plants at d.a.t. 1 replicate 2


title: S.epidermidis-injected mice with Paquinimod treatment

description:
Live S.epidermidis i.p. administration + Paquinimod weekly i.p.
AAN + Paquinimod

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software: https://geneglobe.qiagen.com/us/analyze
For the normalization, average of a combination of automatically selected housekeeping genes (out of 5 tested Actb,B2m, Gapdh, Gusb, Hsp90ab1) were used
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where ΔCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold-changes are 2^-ΔΔCt, where ΔΔCt = (ΔCt_Test Group - ΔCt_Control group)]
Matrix normalized worksheet reports normalized signal (against housekeeping genes Actb, B2m, Gusb).
Fold Change worksheet reports S.epidermidis/Control or S.epidermidis + Paquinimod/Control ratios.


title: Control + S.epidermidis peritonitis

description: i.p. catheted fitter, daily PBS administration + S. epidermidis i.p. injection


title: "D" leaf from untreated plants at d.a.t. 5 replicate 3

value: "D" Leaf

value: biol rep 3

value: Water


title: Stem apex from treated plants at d.a.t. 2 replicate 3

value: Stem apex

value: Cultivar 'MD1', PRI 73-50


title: S.epidermidis-injected mice

description:
Live S.epidermidis i.p. administration
AAN


title: root, wild type, Dex 7 days, replicate 3

value: Dex 7 days


title: root, EXPA1 line (8-4), control, replicate 2


title: Stem apex from treated plants at d.a.t. 1 replicate 3

value: Ethephon


title: root, EXPA1 line (8-4), control, replicate 1


title: root, wild type, Dex 7 days, replicate 4


title: Stem apex from treated plants at d.a.t. 1 replicate 1

value: biol rep 1


title: "D" leaf from untreated plants at d.a.t. 5 replicate 2

value: biol rep 2


title: root, wild type, Dex 7 days, replicate 1


title: Kasumi_5mark_o2_H3K4me3

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

institute: Peking University

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 20 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Assembly: hg19
Supplementary files format and content: The processed files were aggregate bigwig files.

source_name: Kasumi

extract_protocol:
Following uCoTarget protocol.
After PCR enrichment, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Cells were collocted by centrifugation at 300g for 3 minutes

value: Kasumi

tag: cell statement

value: Fixed by Formaldehyde

tag: chip antibody


title: Control mice sample

description:
PBS i.p. administration
Control


title: root, wild type, Dex 7 days, replicate 2

value: root


title: Kasumi_5mark_o2_H3K4me1


title: root, wild type, Dex 3 hours, replicate 3

value: WT

value: Dex 3 hours


title: "D" leaf from untreated plants at d.a.t. 5 replicate 1

tag: replicate


title: "D" leaf from untreated plants at d.a.t. 4 replicate 2

tag: days after_treatment


title: root, wild type, Dex 3 hours, replicate 2

tag: treatment


title: K562_5mark_o2_H3K4me3


title: "D" leaf from untreated plants at d.a.t. 3 replicate 3

tag: tissue


title: Kasumi_5mark_o2_H3K36me3


title: Mature_IFN_NoSFV_003

city: Parkville

first: Nagaraj

middle: Sundara

last: Moily

state: Victoria

address: Bio21 Institute, The University of Melbourne,

department: Biochemistry and Molecular Biology

institute: The University of Melbourne

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 mm10 whole genome using Salmon aligner as per default parameters
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Cultured neurons were dissociated and RNA was harvested using Rneasy Mini Kit(Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neurons were mock or pre treated with IFNβ for 12 hours prior to infection with SFV

value: Cortical neurons

tag: age

tag: genotype

value: wild type

value: IFNBeta treated


title: Mature_NoIFN_NoSFV_003

value: Untreated


title: K562_5mark_o2_H3K36me3


title: "D" leaf from untreated plants at d.a.t. 3 replicate 2

value: "D" Leaf


title: "D" leaf from untreated plants at d.a.t. 3 replicate 1

value: Water


title: Kasumi_5mark_o2_H3K27me3


title: Mature_IFN_SFV_003

value: IFNBeta treated and SFV infected


title: root, wild type, control, replicate 4

value: control


title: root, wild type, control, replicate 3


title: "D" leaf from untreated plants at d.a.t. 2 replicate 3

value: biol rep 3

value: Cultivar 'MD1', PRI 73-50


title: K562_5mark_o2_H3K27me3


title: "D" leaf from untreated plants at d.a.t. 4 replicate 3


title: Mature_NoIFN_SFV_003

value: Infected with SFV


title: Kasumi_5mark_o2_H3K27ac


title: root, wild type, Dex 3 hours, replicate 4


title: root, wild type, control, replicate 2


title: "D" leaf from untreated plants at d.a.t. 2 replicate 2

value: biol rep 2


title: Immature_IFN_NoSFV_003


title: K562_5mark_o2_H3K4me1


title: "D" leaf from untreated plants at d.a.t. 4 replicate 1

value: biol rep 1


title: "D" leaf from untreated plants at d.a.t. 2 replicate 1


title: K562_5mark_o2_H3K27ac

value: Fixed by Formaldehyde


title: root, wild type, Dex 3 hours, replicate 1

value: root


title: Immature_NoIFN_NoSFV_003


title: "D" leaf from untreated plants at d.a.t. 1 replicate 3


title: Kasumi_5mark_H3K4me3

value: Kasumi


title: BIU87_NC3

city: Shenyang

first: Shutao

last: Tan

address: No.36 Sanhao Street

institute: Shengjing Hospital of China Medical University

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.(Parameters: ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing by Unique Molecular Identifier(UMI).
The de-duplicated consensus sequences were mapped to the GRCh38 using STAR software (version 2.5.3a) with default parameters.(Parameters: --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}）
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).(Parameters: pvalue<0.05 |log2foldchang|>1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: BIU-87 cells were maintained in DMEM supplemented with 10% Fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was collected by TRIzol method. 2 μg total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit(Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's instruction.

treatment_protocol: Then BIU-87 cells were transfected with 50 nM concentration of si_AATF and si_nc, respectively, using riboFECTTM CP transfection kit method (C10511-05, RiboBio) for 48 hours according to the instructions.

tag: cell line

tag: cell type

value: Bladder cancer cells

value: WT


title: root, wild type, control, replicate 1


title: BIU87_NC2


title: "D" leaf from untreated plants at d.a.t. 1 replicate 2


title: BIU87_NC1


title: K562_5mark_H3K4me3


title: Immature_IFN_SFV_003

value: Cortical neurons

value: wild type


title: Immature_NoIFN_SFV_003


title: "D" leaf from untreated plants at d.a.t. 1 replicate 1


title: Kasumi_5mark_H3K4me1


title: Mature_IFN_NoSFV_002

value: IFNBeta treated


title: BIU87_AATF3

value: AATF silence


title: Stem apex from untreated plants at d.a.t. 8 replicate 3

value: Stem apex

value: Water


title: Mature_NoIFN_NoSFV_002

value: Untreated


title: K562_5mark_H3K4me1


title: BIU87_AATF2


title: BIU87_AATF1


title: Mature_IFN_SFV_002

value: IFNBeta treated and SFV infected


title: Kasumi_5mark_H3K36me3


title: Stem apex from untreated plants at d.a.t. 8 replicate 1

value: Cultivar 'MD1', PRI 73-50


title: K562_5mark_H3K36me3


title: Kasumi_5mark_H3K27me3


title: HaCaT cells, si-eIF4E+M5 3

city: Jinan

first: Wang

last: Ruijie

address: Jinan, China

institute: Qilu Hospital of Shandong University, Jinan, China

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Homo_sapiens.GRCh38.V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HaCaT cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HaCaT cells


title: Mature_NoIFN_SFV_002

value: Infected with SFV


title: HaCaT cells, si-eIF4E+M5 2


title: Stem apex from untreated plants at d.a.t. 7 replicate 2

value: biol rep 2


title: Immature_IFN_NoSFV_002


title: Stem apex from untreated plants at d.a.t. 7 replicate 3

value: biol rep 3


title: K562_5mark_H3K27me3

value: Fixed by Formaldehyde


title: Kasumi_5mark_H3K27ac

value: Kasumi


title: HaCaT cells, si-NC+M5 3


title: Stem apex from untreated plants at d.a.t. 6 replicate 3


title: K562_5mark_H3K27ac


title: HaCaT cells, si-NC+M5 2


title: Immature_IFN_SFV_002


title: Stem apex from untreated plants at d.a.t. 8 replicate 2


title: HaCaT cells, si-eIF4E+M5 1


title: Stem apex from untreated plants at d.a.t. 7 replicate 1

value: biol rep 1


title: HaCaT cells, si-NC+M5 1


title: Mature_IFN_NoSFV_001


title: Tg-C6

city: New York

first: Kelechi

last: Ndukwe

state: NY

address: 695 Park Ave, New York, NY 10065

department: Biology

institute: Hunter College City University of New York Graduate Center

description: Female, TgF-344AD transgenic rat, DZ/DIB chow

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.
reads were first mapped to the latest UCSC transcript (RGSC 6.0/rn6) set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15[2]. TMM (trimmed mean of M-values) was used to normalize the gene expression.
Differentially expressed genes were identified using the edgeR program[3].
Assembly: rn6
Supplementary files format and content: rsem_count.txt => Expected read count produced by RSEM for each gene in each sample.
Supplementary files format and content: TMM_normalized_reads_count_per_million.txt => Normalized gene expression data by TMM method

source_name: Left Hippocampus Brain

extract_protocol:
RNA was isolated by RNeasy Mini Kit from Qiagen
Kapa Stranded mRNA Kit (Roche, cat. KK8421) to generate strand-specific RNA-seq libraries

value: Left Hippocampus Brain

value: Tg-AD

value: DIB/DZ


title: Tg-C5


title: Stem apex from untreated plants at d.a.t. 6 replicate 1


title: H9 cells, KO_METTL3_3

city: Shanghai

first: Li

last: Jianguo

address: 1239 Siping Road

institute: Tongji University

data_processing:
First, cutadapt (V1.18) was used to remove adaptor sequences, low-quality bases and reads shorter than 50 bases.
Next, the trimmed clean data were mapped to the mouse reference genome (GEN-CODE GRCm38) using HISAT2 (V2.1.0) with the parameters “--rna-strandness RF --dta-cufflinks --no-discordant”.
After that, gene expression levels were quantified as FPKM by stringtie (V1.3.4d) with the parameter “-e --rf”. Genes with FPKM <0.1 in all samples were filtered, and FPKM values of replicates were averaged.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file includes FPKM values for each Sample

extract_protocol:
Total RNAs were extracted from METTL3-SMASh tagged hNPCs (treated with or without ASV) using TRIzol Reagent (Invitrogen, 15596026). DNA digestion was car-ried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quan-tified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina® (Wuhan Seqhealth, DR08402) following the manufacturer’s instruction. PCR products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumi-na) with PE150 model.

value: hESC-derived NPC cell

value: METTL3 KO


title: Stem apex from untreated plants at d.a.t. 5 replicate 3

data_processing:
FastQC (Version 0.10.1) for raw read quality evaluation
Trimmomatic-0.36 (Version 3, 29 June 2007) for adapters and low-quality reads removal (ILLUMINACLIP:Adapters.fa:2:30:10 HEADCROP:10 LEADING:28 TRAILING:28 MINLEN:30)
Hisat2 (Version 2.0.5) for alignment
SAM files to BAM files converted with Samtools (Tools for alignments in the SAM format) Version: 1.2 (using htslib 1.2.1)
Aligned reads were counted using featureCounts (Version 1.6.0) and summarized per gene ID
Assembly: Acomosus_321_v3.fa.gz
Supplementary files format and content: Processed data files (Text documents) contain raw read counts (not normalized) for each "Geneid" for each of the samples. Processed FASTA file contains the sequences for each "Geneid" identifier used in the processed data files (see Acomosus_321_v3.transcript.fa.gz).

value: Stem apex


title: Tg-C4


title: H9 cells, KO_METTL3_2


title: Mature_IFN_SFV_001

value: Cortical neurons

value: wild type


title: Immature_NoIFN_SFV_002


title: Stem apex from untreated plants at d.a.t. 6 replicate 2

value: Water


title: Stem apex from untreated plants at d.a.t. 5 replicate 1

value: Cultivar 'MD1', PRI 73-50


title: H9 cells, KO_METTL3_1


title: Immature_NoIFN_NoSFV_002

value: Untreated


title: H9 cells, Ctrl_3

value: Ctrl


title: Mature_NoIFN_NoSFV_001


title: Tg-C1


title: Immature_NoIFN_NoSFV_001


title: Stem apex from untreated plants at d.a.t. 4 replicate 3


title: Stem apex from untreated plants at d.a.t. 5 replicate 2

value: biol rep 2


title: Stem apex from untreated plants at d.a.t. 4 replicate 1


title: Stem apex from untreated plants at d.a.t. 4 replicate 2


title: Immature_IFN_SFV_001

value: IFNBeta treated and SFV infected


title: Tg-C3


title: Stem apex from untreated plants at d.a.t. 3 replicate 3

value: biol rep 3


title: Tg-2

description: Female, TgF-344AD transgenic rat, rodent chow

value: No Treatment


title: Mature_NoIFN_SFV_001

value: Infected with SFV


title: Tg-C2

value: Left Hippocampus Brain


title: Immature_IFN_NoSFV_001

value: IFNBeta treated


title: Tg4

value: Tg-AD


title: Tg-4


title: H9 cells, Ctrl_2

value: hESC-derived NPC cell


title: Tg3


title: H9 cells, Ctrl_1


title: H9 cells, Ctrl_m6A_Input

data_processing:
First, cutadapt (V1.18) was used to remove adaptor sequences, low-quality bases and reads shorter than 50 bases.
After quality control, the clean data were mapped to the mouse reference genome (GENCODE GRCh38) by bowtie2 (V2.3.5.1) with the following parameters: -N 1 -X 2000 -q -t -L 25 --no-mixed --no-discordant. The unmapped reads, nonuniquely mapped reads and PCR duplicates were removed.
The read counts were normalized to RPKM (reads per kilobase per million) in 100-bp bins for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: bigWig files for each Sample

extract_protocol:
Total RNAs were extracted from METTL3-SMASh tagged hNPCs (treated with or without ASV) using TRIzol Reagent (Invitrogen, 15596026). DNA digestion was car-ried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quan-tified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies, Q10210).
50 μg total RNAs were used for polyadenylated RNA enrichment by VAHTS mRNA Capture Beads（VAHTS, N401-01/02）. 20mM ZnCl2 was added to mRNA and incu-bated at 95℃ for 5min-10min until the RNA fragments were mainly distributed in 100-200 nt. Then 10% RNA fragments were saved as “Input” and the rest was used for m6A immunoprecipitation（IP）.The specific anti-m6A antibody (Synaptic Systems, 202203, 2.5 μg / IP) was applied for m6A immunoprecipitation. RNA samples of both input and IP were prepared using TRIzol reagent (Invitrogen, 15596026). The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Wuhan Seqhealth, DR08502) following the manufacturer’s in-struction. The kit eliminated duplication bias in PCR and sequencing steps, by using unique mo-lecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and fi-nally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
MeRIP-seq

tag: fraction

value: Input


title: Tg-3


title: Immature_NoIFN_SFV_001


title: H9 cells, METTL3_IP

extract_protocol:
RIP assay was performed on METTL3-SMASh tagged hNPCs by SeqHealth (Wu-han, China). The cells were treated with cell lysis buffer. The 10% lysis sample was stored and named “input”, and 80% was used in immunoprecipitation reactions with METTL3 antibody（Abcam, ab195352, 10 μg / IP）and named “IP”, and 10% was in-cubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”, respectively. The RNA of input and IP was extracted using TRIzol reagent (Invitrogen, 15596026).
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina (Wuhan Seqhealth, DR08502) following the man-ufacturer’s instruction. The kit eliminated duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: IP


title: WT5

description: Female, Wild-Type rat, rodent chow

value: Wild Type


title: H9 cells, METTL3_Input


title: RB170 cells, Cef8mM-1

city: Bangkok

first: Rossukon

last: Kaewkhaw

address: 270 Rama VI Road Ratchathewi

country: Thailand

institute: Mahidol University

data_processing:
Prune and trim poor quality reads using Trimmomatic tool
Quantify gene expression data using Kallisto on Ensembl V82
Assembly: HG38
Supplementary files format and content: Tab delimited file of transcript abundance as generated by Kallisto

growth_protocol: RB170 cells were culture in Neurobasal™-A Medium supplemented with 2.5% fetal bovine serum (FBS), 2.5% knock out bovine serum (KSR), 20pg/ml epidermal growth factor (EGF), 10pg/ml basic fibroblast growth factor (bFGF), 2mM of glutamax, 1mM of sodium pyruvate, 0.25ng/ml of fungizone, and antibiotics (complete media) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by TriPure Isolation reagent (Roche Applied Science, Penzberg, Germany).
RNA Libraries were constructed by using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc.)

treatment_protocol: RB170 was treated with ceftriaxone for 2 day in complete Neurobasal-A media

value: Retinoblastomas

value: MYCN amplified

value: Ceftriaxone (8mM)


title: Stem apex from untreated plants at d.a.t. 3 replicate 2

extract_protocol:
TRIzol Reagent (Ambion USA)
2 µg of total RNA were used for RNA-Seqlibrarypreparation. Low Sample Protocol with TruSeq® Stranded mRNA LT kit (Illumina USA) was follow to build the libraries.

value: Stem apex

value: Cultivar 'MD1', PRI 73-50

value: Water


title: WT3

description: Female, Wild-Type rat, rodent chow


title: Tg-1


title: Tg5


title: RB170 cells, Cef2mM-1

value: Ceftriaxone (2mM)


title: H9 cells, KO_m6A_IP

value: METTL3 KO


title: WT2

description: Female, Wild-Type rat, rodent chow

value: No Treatment


title: Stem apex from untreated plants at d.a.t. 3 replicate 1

value: biol rep 1


title: H9 cells, KO_m6A_Input


title: Stem apex from untreated plants at d.a.t. 2 replicate 3

value: biol rep 3


title: H9 cells, Ctrl_m6A_IP

value: Ctrl


title: ΔUBR4,  sgTIMM8A, isrib 200nM 16h, biol rep3

city: Berkeley

first: Diane

middle: L

last: Haakonsen

state: CA

address: 1951 Oxford St

department: MCB

institute: UC Berkeley

description:
D4T8AISR3
All_samples_TPM_counts.csv

data_processing:
To obtain transcript abundance counts, RNA-seq reads were mapped to the human reference transcriptome (GRch38, Ensembl Release 96) using Kallisto 0.48.0
Gene-level count estimates were obtained by summing counts or TPMs across all transcripts from a given gene
Assembly: GRCh38.96
Supplementary files format and content: CSV file containing TPM and estimated counts for each sample

growth_protocol: HEK29T WT and ΔUBR4  cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from cells using the NucleoSpin RNA kit (Macherey-Nagel)
mRNA was purified from total RNA using polyT oliog attached magnetic beads. mRNA was fragmented and first strand synthesis was performed with random hexamers followed by second strand cDNA synthesis. This was followed by end repair, A-tailling, adapter ligation, size selection, amplification and purification.

treatment_protocol: Cells were either untreated or treated with sodium arsenite 5uM or isrib 200nM for 16 hours

value: Human embryonic kidney cells

value: {delta}UBR4 sgTIMM8A

value: Isrib 200nM, 16 hours


title: Stem apex from untreated plants at d.a.t. 2 replicate 2

value: biol rep 2


title: Stem apex from untreated plants at d.a.t. 2 replicate 1


title: Tg2

value: Left Hippocampus Brain

value: Tg-AD


title: RB170 cells, Cef8mM-2

value: Retinoblastomas

value: MYCN amplified


title: Stem apex from untreated plants at d.a.t. 1 replicate 3

value: Stem apex


title: Single cell VEGFaR84_3

first: Vilas

last: Menon

department: Neurology

institute: Columbia University Medical Center

data_processing:
Bulk RNA-seq: Pseudoalignment of RNAseq reads was performed to a kallisto index created from transcriptome Ensembl v96, Mouse:GRCm38.p6 using kallisto (0.44.0).
Single-cell RNA-seq: Raw fastq (sequencing files) were processed using the Cellranger v3.0 analysis pipeline to align reads to the GRCm38.p6 mouse genome and generate feature-barcode matrices.
Assembly: GRCm38.p6
Supplementary files format and content: bulk_r84_est_counts_gene_kallisto
Supplementary files format and content: h5

source_name: Spinal cord

extract_protocol:
The neural dissociation kit (P) was used to dissociate the spinal cords into a single cell suspension. Following myelin removal using Miltenyi Biotec Myelin Removal Beads II, the samples were stained with CD31-APC and PI, and live endothelial cells were FACS sorted for single cell RNA sequencing
Bulk RNA-seq: mRNA was enriched from total RNA samples after sorting cells (see extract protocol) using poly-A pull down and cDNA libraries were prepared using Illumina Truseq chemistry, followed by sequencing using Illumina NovaSeq 6000. Single cell RNA-seq: Single cells were processed on the 10x Genomics Chromium platform (v3 chemistry), and cDNA libraries were sequenced on the Illumina NovaSeq6000

value: Spinal cord

value: Endothelial cell

value: Complete Freund's adjuvant + Pertussis Toxin + 5 mg/kg r84


title: ΔUBR4,  sgTIMM8A, isrib 200nM 16h, biol rep2

description:
D4T8AISR2
All_samples_TPM_counts.csv


title: RB170 cells, Cef0mM-2

value: Sterile water


title: Single cell VEGFaR84_2


title: ΔUBR4,  sgTIMM8A, Sodium arsenite 5uM 16h, biol rep3

description:
D4T8ASA3
All_samples_TPM_counts.csv

value: Sodium arsenite 5uM, 16 hours