title: KCM7

city: Leuven

first: Georg

last: Halder

address: Herestraat 49

department: VIB-KU Leuven Center for Cancer Biology

country: Belgium

institute: VIB-KU Leuven

description: macrophages from WT liver

data_processing:
Raw sequencing reads were cleaned for adapters using Trimmomatic v0.39 (REF Bolger).
Cleaned reads were mapped to the Mus Musculus 10 genome (GRCm38/mm10) and assigned to genes using HISAT2 v2.1.0.
The raw counts matrix was generated using Rsubread package v2.2.3.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file with sample infromation table

source_name: Liver

growth_protocol: Breeding protocol: Osteopontin-iCreERT2;Yapflox/flox;Tazflox/flox mice were generated by crossing Yapflox/flox;Tazflox/flox mice (generated by Erik Olson) to Opn-iCreERT2 mice (generated by Frédéric Lemaigre). Siblings with Yapflox/flox;Tazflox/flox, but lacking the Opn-iCreERT2 driver, were used as controls.

extract_protocol:
Single cell suspensions were obtained by dissociating the liver with pronase and collagenase by perfusion. Hepatocytes were distinguished from the non-parenchymal fraction by two 50G centrifugations. After incubation with red blood cell lysis buffer for 3 minutes, NPF was blocked with 1% bovine serum albumin and incubated with antibodies (Suppl.Table 1) for 15 minutes. After adding propidium iodide (Merck #P4864), we used FACS Ariall to isolate macrophages (F4/80+ CD45+ UV- PI-). Hepatocytes were obtained using a Percoll gradient and sorted by FACS, according to the absence of PI.
RNA libraries were prepared according to the QuantSeq 3’ mRNA-Seq Library Prep kit FWD (Lexogen). The resulting library (50bp, single stranded) was sequenced by the Illumina HiSeq4000.

treatment_protocol: Tamoxifen (Sanbio #13258) was intraperitoneally injected on five consecutive days (1,6mg/kg in oil) in mice of 7-8 weeks old, followed by a three-week washout period.  Half of the mice were intraperitoneally injected with CCl4 (1ml/kg) and samples were harvested 48h after that.

value: B6;129P; Mixed background

value: liver macrophage

tag: treatment

value: Tamoxifen

value: Yap fl/fl Taz fl/fl

tag: group


title: S0_CD71_low nascent RNA replicate 1

status: Public on Nov 02 2020

type: SRA

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

library_source: transcriptomic

data_processing:
Psuedo-aligned with Kallisto 0.43.0 to Ensembl transcriptome reference GRCm38.93 (command: "kallisto quant -i /path/to/index -o /path/to/output /path/to/fastq")
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene by sample counts matrix (comma separated values)

molecule: total RNA

organism: Mus musculus

source_name: Primary mouse erythroblasts (Lin-; CD71-; Ter119-)

growth_protocol: Fetal livers were freshly isolated at e12.5-e13.5 from C57BL/6 mouse embryos. Primary erythroid progenitors were purified by FACS sorting lineage-negative cells based on their expression of CD71 and Ter119 as previously described (Oudelaar, Beagrie et al. Nat. Comms 2020). FACS-purified cells were rested for six-hours post-sort in erythroid media (IMDM supplemented with 20% FCS and 0.001% β-mercaptoethanol).

extract_protocol:
Cells were  pelleted by centrifugation at 200G for 5 minutes and washed in PBS. The cell pellet was lysed in tri-reagent, and snap frozen on dry ice/ethanol. Total RNA was extracted from tri-reagent using a Direct-zol RNA kit (Zymo). 4sU labelled RNA was purified as previously described (Duffy et al. PMID 27925666). Briefly, 20-100µg of labelled total RNA was added to 50µl MTSEA-biotin-XX (0.1mg/ml in dimethylformamide) and 25μl of 10x Biotinylation buffer (100mM Tris pH 7.4 10mM EDTA) in a 250μl reaction and rotated for 30 minutes at room temperature. 400µl chloroform/isoamylalcohol (24:1) was added to the reaction and incubated for 3m. The aqueous phase was isolated using phase-lock gel tubes and purified by isopropanol precipitation. The RNA pellet was resuspended in 60µl RNase free water, denatured at 65°C for 10 min and cooled on ice for 5 min. RNA was incubated with 60µl µMacs streptavidin magnetic beads (Miltenyi) for 15 minutes at room temperature with rotation, applied to a MACS column in a magnetic stand and washed with 1ml MACS wash buffer (100mM Tris pH 7.5, 10mm EDTA, 1M NaCl, 0.1% Tween20) two times at 65°C and two times at room temperature. RNA was eluted from the column by applying 100 μL of freshly prepared 100 mM dithiothreitol (DTT), followed by a second elution round 5 min later, then purified using a Qiagen RNeasy RNA clean-up kit with on-column DNase digestion, eluting in 20μl of DEPC water.
Libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara Bio) following the manufacturer’s instructions with a fragmentation time of 3 minutes and 14 cycles of PCR amplification.

treatment_protocol: 500μM 4‐thiouridine (4sU) was added to liquid cultures for 45 minutes

tag: strain

tag: developmental stage

tag: tissue

value: fetal liver

tag: cell type

value: primary erythroblasts

tag: cell markers

tag: rna population

value: nascent RNA


title: S7_MM1S_BioRep2_Pd

type: RNA

city: Salamanca

first: Teresa

last: Paíno Gómez

state: Salamanca

address: Campus Miguel de Unamuno

country: Spain

institute: Centro de Investigación del Cáncer

hyb_protocol: Hybridization was performed on the Affymetrix Clariom S Human array as per the manufacturers protocol.

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Raw data were quantile normalized, background corrected and log2 transformed with the Robust Multi-array Average (RMA) algorithm using the oligo package (v.1.44.0) in R (v.3.5.0).  BrainArray custom CDF files (version 22 Ensembl) at  gene level were used as reference.
ClariomSHuman_Hs_ENSG.cdf

label: biotin

organism: Homo sapiens

source_name: MM.1S multiple myeloma cell line

label_protocol: As per manufacturer's instructions (Affymetrix)

growth_protocol: MM.1S cells were cultured in RPMI-1640 medium +  10% inactivated FBS.

extract_protocol: RNA and DNA were extracted using AllPrep DNA/RNA Mini Kit (Qiagen). RNA integrity was assessed using Agilent 2100 Bioanalyzer.

treatment_protocol: MM.1S cells were sub-lethally treated (% viability: 74-81%) with:  PIM (PIM447 100 nM, for 24 hours), Pd (pomalidomide 200 nM + dexamethasone 5 nM, for 15 hours) or PIM-Pd (PIM447 100 nM + pomalidomide 200 nM + dexamethasone 5 nM, for 10 hours). Untreated MM.1S cells were used as control.

value: Pomalidomide + Dexamethasone

tag: biological replicate (pairs)


title: S10_MM1S_BioRep3_PIM


title: S5_MM1S_BioRep2_Control

value: Control


title: S6_MM1S_BioRep2_PIM


title: KCM6

description: macrophages from WT liver

molecule: polyA RNA

tag: genotype


title: S12_MM1S_BioRep3_PIM-Pd

value: PIM447 + Pomalidomide + Dexamethasone


title: PyMT WT Tumor

city: Bengaluru

first: Mohamed Ashick

last: Mohamed Saleem

state: Karnataka

address: #1519/10, 8Th A Main, 'Akshaya', Sahakaranagar

country: India

institute: LifeBytes India Pvt Ltd

data_processing:
Data pre-processing was done using the standard cellranger pipeline. Basecalls and demultiplexing were performed with cellranger mkfastq, which uses bcl2fast2. Read trimming, alignment, UMI counting and cell barcode assignment were all performed using cellranger count, which uses STAR for read alignment and custom tools for the other steps.
Single-cell transcriptome sequencing raw reads were quality filtered using Fqtrim (v0.9.7) tool. Read 2 (non-barcode read) were trimmed and filtered for low quality bases, poly-A/T tails and N bases. UMItools (v0.5.4) was used to distinguish the reads per cell (barcode).
Clean and barcode classified reads were aligned against Mouse genome reference (GRCm38) using STAR aligner (v2.5.3a) and output was restricted to uniquely aligned reads. De-duplication (PCR duplicates with same UMI) were removed. Reads were assigned with position based annotation of genomic features using featureCounts module in the subread package (v1.6.0).
Gene expression matrix was filtered for cells with <500 genes expressed and <500 total UMI counts genes and >0.25 percentage of reads aligned to Mitochondrial genome using Monocle2 (v2.6.4) R package. Following cell-type specific markers were used for the cells classification, Basal cells: Krt14, Krt5, Snai2; Luminal Mature cells: Pgr, Prlr, Foxa1, Gpx3, Esr1; Luminal Progenitor cells; CD14, Kit, Lalba; Lumino-basal: Krt14, Krt8, CD14; EMT-like: Trim29, Vim, Cldn6, Sox4. We identified and classified cell-types using Monocle2’s classifyCells function. Transition of gene expression kinetics was performed by integrative Pseudotime analysis using Monocle2.
Genome_build: mm10
Supplementary_files_format_and_content: UMIcounts.txt.gz: Raw count matrix (genes in rows and cells in columns)
Supplementary_files_format_and_content: MetaData.tsv: Each cells additional processed information and cell type annotation [only for post-filtered cells]

source_name: Mammary

growth_protocol: All mice were maintained according to IACUC protocols until the time of sacrifice. Mice were anesthetized using isoflurane and surgery was carried out to resect mammary glands or tumors.

extract_protocol:
Following dissociation, cells were washed twice in PBS and filtered through a 70- and 40-μm cell strainer to obtain single-cell suspensions following which they were FACS sorted and sent for single cell library preparation and processing
Dissociated single cell suspensions were placed on ice and counted on a Luna automated cell counter. Cell concentrations from each sample were be normalized to 1000 cells/ul and loaded onto a Chromium Single Cell A Chip (10x Genomics Inc.) targeting a capture rate of 5,000 cells per sample. Single cell RNA-seq libraries were be prepared using the Chromium Single Cell 3’ v2 kit (10x Genomics) following the manufacturer’s protocol. Libraries were quantified by qubit and peak size determined on a fragment analyzer instrument. All libraries were pooled and sequenced on an Illumina NextSeq500 High Output 26bp x 98bp run to generate an average of 50,000 reads/cell.

treatment_protocol: For Mammary gland preparations (L21_263, L21_264) - Mouse mammary fat pads (no. 3 and 4) were harvested and digested with Collagenase A and Hyaluronidase for 2-3 hours at 37°C in a rotator, cells were treated with trypsin, and subsequently with dispase to aid dissociation. For Tumors (L21_279, L21_280) - tumors were resected and minced using a razor blade in DMEM containing 2 mg/mL collagenase and 100 U/mL hyaluronidase (Roche) in a rotator at 37°C for 30 minutes. Following incubation, tumors were minced further and re-incubated for another 30 minutes. Dissociated cells were washed twice in PBS and filtered through a 70- and 40-μm cell strainer to obtain single-cell suspensions.

value: Mammary

tag: age

value: 16-20 weeks

value: wild type

tag: cell line

value: MMTV-PyMT


title: S4_MM1S_BioRep1_PIM-Pd


title: S3_MM1S_BioRep1_Pd


title: S9_MM1S_BioRep3_Control


title: S1 nascent RNA replicate 1

source_name: Primary mouse erythroblasts (Lin-; CD71 high; Ter119-)

value: Lin-; CD71 high; Ter119-


title: S2_MM1S_BioRep1_PIM


title: PyMT PKA Tumor

value: PKA activated


title: KCM18

description: macrophages from KO liver + CCl4

value: Tamoxifen and CCl4 injection

value: Opn-CreERt2 Yapfl/fl Tazfl/fl


title: PyMT WT Hyperplasia

value: 8-9 weeks


title: KCM15

description: macrophages from WT liver + CCl4

value: B6;129P; Mixed background

value: liver macrophage


title: PyMT PKA Hyperplasia


title: KCM12

description: macrophages from WT liver + CCl4

value: Yap fl/fl Taz fl/fl


title: KCM14

description: macrophages from KO liver + CCl4


title: KCM4

description: macrophages from KO liver

value: Tamoxifen


title: HEPM19

description: Hepatocytes from WT liver

value: hepatocyte


title: PA14 ∆rclR+ HOSCN 2

city: London

first: Huw

middle: David

last: Williams

address: Imperial College Road

department: Department of Life Sciences

institute: Imperial College London

data_processing:
Reads were mapped using bowtie2 and aligned to the reference genome Pseudomonas aeruginosa UCBPP-PA14 (NC_008463.1)
Expression values in Reads Per Kilobase per Million mapped reads (RPKM) were calculated using FeatureCounts
RPKM values were normalised against the OD600 of the samples
Log2 fold change of WT+HOCl vs. WT untreated, WT+HOSCN vs. WT untreated, WT+HOCl vs. ∆rclR+HOCl and WT+HOSCN vs. ∆rclR+HOSCN was calculated
Genome_build: Pseudomonas aeruginosa UCBPP-PA14, complete genome (NC_008463.1)
Supplementary_files_format_and_content: Excel spreadsheet containing tab 1: expression data reads, RPKM values; tab 2: RPKM OD normalised values; tab 3: log2 fold change values of WT+HOCl vs. WT untreated, WT+HOSCN vs. WT untreated, WT+HOCl vs. ∆rclR+HOCl and WT+HOSCN vs. ∆rclR+HOSCN

organism: Pseudomonas aeruginosa

source_name: Bacterial cells

growth_protocol: PA14 WT and ∆rclR strains were grown overnight in LB broth at 37◦C on a shaking platform (two biological replicates of each strain). The four cultures were subcultured 1:50 in LB and grown to mid-exponential phase (37◦C, shaking, for 2.5 hours). These exponential phase cultures were subcultured, three separate times, 1:50 in LB and grown again for 2.5 hours. At this point, either HOCl was added to a final concentration of 2.2 mM, or HOSCN was added to a final concentration of 0.8 mM or nothing was added (untreated control). Cultures were incubated for a further 20 minutes before recording OD600, harvesting cells and extracting RNA.

extract_protocol:
After 20 minute incubation with HOCl or HOSCN, cells were harvested, washed and RNA preserved by addition of RNAlater (Ambion). Bacteria were lysed with lysozyme and proteinase K buffer and total RNA extracted using the RNeasy Protect Bacteria Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA samples were DNase treated using a TURBO DNA-free kit (Ambion), according to the manufacturer’s instructions, prior to sending RNA on dry ice to vertis Biotechnologie AG for preparation of cDNA libraries and Illumina sequencing.
rRNA was removed using the bacterial Ribo-Zero rRNA Removal Kit (Illumina), and then RNA fragmented by ultrasound. An oligonucleotide adapter was ligated to the 3’ end of the RNA and first-strand cDNA synthesis carried out with M-MLV reverse transcriptase. The cDNA was purified and a 5’ Illumina TruSeq sequencing adapter (with a TruSeq barcode sequence) was ligated to the 3’ end of the antisense cDNA. PCR amplification of the cDNA to about 10-20 ng/µl was carried out with a high-fidelity DNA polymerase for 11 or 12 cycles. The cDNA was purified and then pooled and size fractionated in the range of 200-500 bp. The cDNA pool was single-read sequenced on an Illumina NextSeq 500 system using a 75 bp read length.

treatment_protocol: The concentration of HOCl required was prepared by diluting sodium hypochlorite (NaOCl) solution with 10-15% available chlorine (Sigma) directly into LB. This was further diluted into the exponential phase cultures to a final concentration of 2.2 mM HOCl (0.015-0.0225% chlorine), and cultures were incubated for 20 minutes. HOSCN was prepared enzymatically by combining glucose, glucose oxidase (GO), potassium thiocyanate (KSCN) and lactoperoxidase (LPO) directly in LB. This was diluted in the exponential phase cultures to a final concentration of 0.8 mM HOSCN (0.01% glucose, 0.5 U/ml GO, 0.75 mM KSCN and 3 U/ml LPO), and cultures were incubated for 20 minutes.

tag: description

value: Pseudomonas aeruginosa UCBPP-PA14 strain

tag: background strain


title: Bacillus subtilis grown on surface of boiled soybeans

city: uji

first: HASHIMOTO

last: WATARU

address: gokasho

department: Division of Food Science and Biotechnology

country: Japan

institute: Graduate School of Agriculture, Kyoto University

description: B

data_processing:
Illumina HiSeq 2500 System User Guide Document # 15035786 v01 HCS 2.2.70
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Subsequently, the reads were mapped to the reference of B. subtilis BEST 195 whole genome using bowtie v0.11.2
Genome_build: Bacillus subtilis BEST 195
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Bacillus subtilis

source_name: cell

growth_protocol: B. subtilis NBRC 16449 cells were grown in liquid LB, LB solidified with agar, or on surface of boiled soybeas. B.subtilis NBRC 16449 cells were aerobically precultured in liquid LB at 37℃ for 1 day. The cells were harvested and resuspended in 0.85％ NaCl. The suspesion containing 3.6 ×107 cells was inoculated to liquid LB, LB solidified with agar, or on surface of boiled soybeans. After inoculation, the cells in each were grown to logarithmic growth phase.

extract_protocol:
Bacterial cells were centrifuged and suspended in 0.85% NaCl, and total RNAs were extracted by following Hot phenol method (Damm et al. 2015). Illumina (Hiseq2500)  was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Washing with 0.85% NaCl and harvesting by the centrifuge.

value: log phase


title: Bacillus subtilis grown in liquid LB

description: A


title: PA14 ∆rclR+ HOCl 2


title: KCM17

description: macrophages from KO liver + CCl4


title: KCM16

description: macrophages from WT liver + CCl4


title: KCM13

description: macrophages from KO liver + CCl4


title: Bacillus subtilis grown in LB solidified with agar

description: C


title: KCM9

description: macrophages from WT liver


title: KCM21

description: macrophages from KO liver


title: HEPM14

description: hepatocytes from KO liver + CCl4


title: HEPM10

description: hepatocytes from KO liver


title: KCM5

description: macrophages from KO liver


title: KCM20

description: macrophages from KO liver


title: HEPM9

description: hepatocytes from WT liver


title: HEPM13

description: hepatocytes from KO liver + CCl4


title: PA14 WT 2

value: WT


title: PA14 ∆rclR+ HOSCN 1


title: PA14 WT+ HOCl 1


title: PA14 WT+ HOSCN 1


title: PA14 WT 1


title: PA14 ∆rclR 1


title: HEPM4

description: hepatocytes from KO liver


title: PA14 ∆rclR+ HOCl 1


title: PA14 WT+ HOCl 2


title: PA14 WT+ HOSCN 2


title: day 14 pool 3 RVFV

city: Barcelona

first: Anna

last: Esteve-Codina

address: Carrer Baldiri Reixac 4-8

institute: CNAG-CRG

data_processing:
RNA-seq were mapped against the de novo assembled transcriptome with STAR 2.5.2a version
Quantified with RSEM version 1.2.28
Differential expression was performed with DESeq2 version 1.18
Genome_build: in house assembled transcriptome (ENA accession number: ERZ1264479)
Supplementary_files_format_and_content: COUNTS_genes_BUSQUESTS_04_newAnn.txt reports raw counts.txt

organism: Culex pipiens

source_name: pool of 4 mosquitoes

growth_protocol: Culex pipiens hybrid form mosquitoes used for RVFV infection were reared from a laboratory colony originally collected in Gavà in 2012 (Spain). Mosquitoes were reared at 26ºC during the day and 22ºC at night at 80% of relative humidity (HR). The photoperiod consisted in 14 h: 10 h (light: dark) with two crepuscular cycles of 30 min to simulate dawn and dusk. Mosquitoes were fed using 10% sucrose solution.

extract_protocol:
RNAeasy kit Qiagen
The RNASeq libraries were prepared from total RNA using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc., Rev. E, October 2013). Briefly, after poly-A based mRNA enrichment with oligo-dT magnetic beads of at least 0.52 μg of total RNA as input material, the mRNA was fragmented to 80-250 nt, with the major peak at 130 nt. The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.
The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76 bp using the TruSeq SBS Kit v4 (Illumina). Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of FASTQ sequence files by CASAVA.

value: whole mosquitoes

tag: time

value: 14 days post-exposure

tag: infection

value: RVFV


title: PA14 ∆rclR 2


title: day 14 pool 2 RVFV


title: HEPM17

description: hepatocytes from KO liver + CCl4


title: HEPM21

description: hepatocytes from KO liver


title: day 14 pool 1 RVFV


title: HEPM6

description: hepatocytes from WT liver


title: HEPM5

description: hepatocytes from KO liver


title: HEPM20

description: hepatocytes from KO liver


title: HEPM16

description: hepatocytes from WT liver + CCl4


title: HEPM18

description: hepatocytes from KO liver + CCl4


title: day 14 pool 3 CTRL

value: Control


title: S1_MM1S_BioRep1_Control


title: day 14 pool 1 CTRL


title: day 14 pool 2 CTRL


title: KCM11

description: macrophages from KO liver + CCl4


title: day 3 pool 3 RVFV

value: 3 days post-exposure


title: day 3 pool 2 RVFV


title: HEPM12

description: hepatocytes from WT liver + CCl4


title: day 3 pool 3 CTRL


title: KCM8

description: macrophages from WT liver


title: day 3 pool 1 CTRL


title: HEPM8

description: hepatocytes from WT liver


title: day 0 pool 2 RVFV

value: 2 hours post-exposure


title: day 0 pool 3 RVFV


title: HEPM15

description: hepatocytes from KO liver + CCl4

value: Tamoxifen and CCl4 injection


title: day 0 pool 1 RVFV


title: day 3 pool 2 CTRL


title: HEPM2

description: hepatocytes from WT liver


title: HEPM7

description: hepatocytes from WT liver


title: day 0 pool 2 CTRL


title: day 0 pool 3 CTRL


title: day 0 pool 1 CTRL


title: day 3 pool 1 RVFV


title: PATU-8902_tRNA_woSG2

city: New York

middle: S

last: Banh

state: NY

address: 522 First Avenue, Smilow 907

department: Radiation Oncology

country: USA

institute: New York University

description: tRNA (60-100nt)

data_processing:
tRNAs were analyzed as described by Evans, M.E., et al. Nucleic Acid. 2017.
https://github.com/Jessica-Pan/DM-tRNA-seq-ref-genomes
Cutadapt: -a CTGTAGGCACCATCAAT -m 13
Genome_build: hg19
Supplementary_files_format_and_content: tRNAs were analyzed as described by Evans, M.E., et al. Nucleic Acid. 2017.

growth_protocol: PATU-8902 cells were passaged in DMEM (no pyruvate) + 10% FBS + 1% Pen/Strep. 25,000,000 cells were seeded into a 15cm plate and allowed to adhere overnight.

extract_protocol: tRNAs were purified as described by Evans, M.E., et al. Nucleic Acid. 2017.

treatment_protocol: Cells were washed once with PBS  and media was changed to DMEM (2.78mM glucose, 4mM glutamine, 1mM pyruvate) + 10% dialyzed FBS with or without 400uM serine and 400uM glycine for 24 hours.

value: Pancreatic Ductal Adenocarcinoma Cell Line

value: -Ser/Gly


title: PATU-8902_tRNA_wSG3

description: tRNA (60-100nt)

value: +Ser/Gly


title: PATU-8902_tRNA_woSG3

description: tRNA (60-100nt)


title: PATU-8902_tRNA_wSG2

description: tRNA (60-100nt)


title: SUDHL5_GSK126_rep1

city: Bethesda

first: Devin

last: Dersh

state: MD

address: 33 North Drive

institute: NIH

description:
AB3872-L1_HGJLCBGXB_S22
AB3872-L1_HGMGVBGXB_S22

data_processing:
Demultiplexing with bcl2fastq
Trimming with CLC Genomics Workbench v12.0
Aligning with CLC Genomics Workbench v12.0
Mapping to hg38 genome with CLC Genomics Workbench v12.0
Log2 of total exon counts normalized by upper quartile scaling and ANOVA statistics computed using JMP/Genomics v9.1
Genome_build: hg38
Supplementary_files_format_and_content: L2FC_GSK126.xlsx contains log2-fold change values and associated adjusted p-values for the comparison of GSK126-treated cells to their DMSO-treated controls.

growth_protocol: Cells were cultured at 37°C in 5% CO2-containing humidified incubators in complete growth medium: Advanced RPMI, 5% fetal bovine serum, penicillin/streptomycin, and Glutamax.

extract_protocol:
Qiagen RNeasy miniprep, with on-column DNase I treatment.
New Englad Biolabs NEBNext polyA mRNA magnetic isolation module.  NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.  NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set 1)

treatment_protocol: Cells were treated with DMSO or GSK126 for 4 days prior to collection. HBL1: 4µM; WSUDLCL2: 4µM; SUDHL4: 4µM; SUDHL5: 1.5µM. Cells were expanded with fresh medium containing DMSO or GSK126 on days 2 and 3.

tag: cell of origin subtype

value: Germinal-center B cell like

tag: ezh2 genotype

value: wild type (Y641)

tag: drug treatment


title: SUDHL5_DMSO_rep3

description:
AB3871-L1_HGJLCBGXB_S21
AB3871-L1_HGMGVBGXB_S21

value: DMSO


title: SUDHL5_DMSO_rep2

description:
AB3870-L1_HGJLCBGXB_S20
AB3870-L1_HGMGVBGXB_S20


title: SUDHL5_GSK126_rep2

description:
AB3873-L1_HGJLCBGXB_S23
AB3873-L1_HGMGVBGXB_S23


title: SUDHL4_GSK126_rep3

description:
AB3868-L1_HGJLCBGXB_S18
AB3868-L1_HGMGVBGXB_S18

value: mutant (Y641S)


title: PATU-8902_tRNA_wSG1

description: tRNA (60-100nt)

tag: treatment


title: SUDHL4_GSK126_rep2

description:
AB3867-L1_HGJLCBGXB_S17
AB3867-L1_HGMGVBGXB_S17


title: SUDHL5_DMSO_rep1

description:
AB3869-L1_HGJLCBGXB_S19
AB3869-L1_HGMGVBGXB_S19


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 5

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
adapter trimming of fastq files with the tool TrimGalore v0.4.5 with parameters "illumina --paired --phred33 --clip_r1 3 --three_prime_clip_r2 3”
we used STAR to align the paired-end reads to the human reference genome (build 38) with parameter “quantMode GeneCounts”
We used Picard Tools to de-duplicate and sort the alignments.
The feature-Count tool was used to count how many reads have mapped to each human gene (using the Gencode v29 basic annotation schema).
The DESeq2 algorithm was used to determine significant differences in expression (counts) between the different experimental conditions.
Genome_build: GRCh38
Supplementary_files_format_and_content: count matrix generated with feature-Count

source_name: B cells

extract_protocol:
RNA was isolated from B cells using the TriPure isolation reagent
Libraries were prepared according to SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio)
Paired-end sequencing was performed on an Illumina HighSeq 4000 instrument (Illumina Inc.)

treatment_protocol: Total RNA from B cells, isolated from PBMCs after treatment with iRBCs and uRBCs for 48 h, was sequenced

value: B cells

value: Treatment with lysates of RBC infected with P. falciparum (iRBC)


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 4

value: BAFF_var (Hom.)


title: SUDHL5_GSK126_rep3

description:
AB3874-L1_HGJLCBGXB_S24
AB3874-L1_HGMGVBGXB_S24


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 5

value: WT

value: Treatment with lysates of RBC uninfected  (uRBC)


title: SUDHL4_DMSO_rep3

description:
AB3865-L1_HGJLCBGXB_S15
AB3865-L1_HGMGVBGXB_S15


title: SUDHL4_DMSO_rep2

description:
AB3864-L1_HGJLCBGXB_S14
AB3864-L1_HGMGVBGXB_S14


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 8


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 8


title: PATU-8902_tRNA_woSG1

description: tRNA (60-100nt)


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 11


title: SUDHL4_GSK126_rep1

description:
AB3866-L1_HGJLCBGXB_S16
AB3866-L1_HGMGVBGXB_S16


title: WSUDLCL2_GSK126_rep2

description:
AB3861-L1_HGJLCBGXB_S11
AB3861-L1_HGMGVBGXB_S11

value: mutant (Y641F)


title: WSUDLCL2_GSK126_rep1

description:
AB3860-L1_HGJLCBGXB_S10
AB3860-L1_HGMGVBGXB_S10


title: WSUDLCL2_GSK126_rep3

description:
AB3862-L1_HGJLCBGXB_S12
AB3862-L1_HGMGVBGXB_S12


title: SUDHL4_DMSO_rep1

description:
AB3863-L1_HGJLCBGXB_S13
AB3863-L1_HGMGVBGXB_S13


title: WSUDLCL2_DMSO_rep3

description:
AB3859-L1_HGJLCBGXB_S9
AB3859-L1_HGMGVBGXB_S9


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 4


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 4


title: DOHH2_TRA_POS

city: Okayama city

first: Katsuyoshi

last: Takata

address: 2-5-1, Kita-ku, Shikata-cho

department: Pathology

institute: Okayama University

description: gene expression of sorted sample

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2600D Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DOHH2, TRA-1-60, positive population

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: RNA was extracted using miRN easy mini kit (Qiagen, Valencia, CA).

treatment_protocol: cell lines were treated with rituximab and IgG for 24hr at 37ºC, then TRA-1-60 population was sorted using FACS Aria.

tag: cell population

value: TRA-1-60 positive

tag: status

value: drug-resistant


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 10

tag: cell type


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 4


title: DOHH2_TRA_NEG

description: gene expression of sorted sample

source_name: DOHH2, TRA-1-60, negative population

value: TRA-1-60 negative

value: drug-sensitive


title: FL18_TRA_POS

description: gene expression of sorted sample

source_name: FL18,TRA-1-60, positive population


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 10


title: WSUDLCL2_DMSO_rep1

description:
AB3857-L1_HGJLCBGXB_S7
AB3857-L1_HGMGVBGXB_S7


title: FL18_TRA_NEG

description: gene expression of sorted sample

source_name: FL18,TRA-1-60, negative population


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 6


title: WSUDLCL2_DMSO_rep2

description:
AB3858-L1_HGJLCBGXB_S8
AB3858-L1_HGMGVBGXB_S8


title: HBL1_GSK126_rep1

description:
AB3854-L1_HGJLCBGXB_S4
AB3854-L1_HGMGVBGXB_S4

value: Activated B cell like


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 6


title: HBL1_GSK126_rep2

description:
AB3855-L1_HGJLCBGXB_S5
AB3855-L1_HGMGVBGXB_S5


title: HBL1_GSK126_rep3

description:
AB3856-L1_HGJLCBGXB_S6
AB3856-L1_HGMGVBGXB_S6


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 2


title: HBL1_DMSO_rep2

description:
AB3852-L1_HGJLCBGXB_S2
AB3852-L1_HGMGVBGXB_S2


title: HBL1_DMSO_rep3

description:
AB3853-L1_HGJLCBGXB_S3
AB3853-L1_HGMGVBGXB_S3


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 9


title: HBL1_DMSO_rep1

description:
AB3851-L1_HGJLCBGXB_S1
AB3851-L1_HGMGVBGXB_S1


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 2


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 11


title: TMD8 rep2

data_processing:
Demultiplexing bcl2fastq v2.17
Trimming adapters and low-quality bases with Trimmomatic v0.36
Aligned to human hg38 reference genome and Gencode v30 using STAR v2.6.1c
RSEM v1.3.2 to generate gene-level raw counts and covert to FPKM
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq_FPKM.xlsx contains FPKM values for each gene, for all cell samples analyzed

extract_protocol:
Trizol extraction of total RNA
polyA selection via Illumina TruSeq Stranded Library protocol as described by manufacturer.


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 7


title: TMD8 rep1


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 9


title: SUDHL4 rep2


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 8


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 8


title: HBL1 rep2


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 7


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 10


title: DOHH2 rep1


title: HBL1 rep1


title: Suit2-OE-3

city: Birmingham

first: Susan

middle: L

last: Bellis

state: ALABAMA

address: MCLM 350, 1918 University Boulevard

institute: University of Alabama at Birmingham

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequences were alinged using STAR version 2.7.3a with parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate; --outSAMattributes All
Transcript abundances was calculated from the aligned BAM file using HTSeq-Count version 0.11.3 with parameters -r pos; -t exon; -i gene_id; -a 10; -s no; -f bam
Normalization and differential expression on the transcript abundances was calculated using DESeq2 version 1.26.0 following their vignette
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: tab-delimited Excel file containing transcript abundances for each gene in each sample

source_name: ST6GAL1-OE in Suit2 cells - rep.3

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

treatment_protocol: Gene expression was compared in parental, poorly-metastatic Suit2  pancreatic cancer cells and two Suit2-derived highly metastatic subclones.  In addition, gene expression was assessed in Suit2 cells with forced overexpression of the ST6GAL1 gene..

value: pancreatic cancer + ST6GAL1-OE


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 9


title: DOHH2 rep2


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 9


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 3


title: Suit2-OE-1

source_name: ST6GAL1-OE in Suit2 cells - rep.1


title: Suit2-OE-2

source_name: ST6GAL1-OE in Suit2 cells - rep.2


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 7


title: Suit2-3

source_name: Suit2 parental line - rep.3

value: pancreatic cancer line


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 10


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 6


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 7


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 3


title: S2-LM7AA-3

source_name: Suit2 LM7 subclone - rep.3

value: metastatic pancreatic cancer


title: Suit2-1

source_name: Suit2 parental line - rep.1


title: SUDHL4 rep1

value: Germinal-center B cell like


title: S2-LM7AA-2

source_name: Suit2 LM7 subclone - rep.2


title: S2-LM7AA-1

source_name: Suit2 LM7 subclone - rep.1


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 6


title: S2-013-3

source_name: Suit2 013 subclone - rep.3


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 1


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 1


title: S2-013-1

source_name: Suit2 013 subclone - rep.1


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 1


title: DOX-2

city: Bristol

first: Keith

middle: William

last: Brown

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

institute: University of Bristol

description:
MXE.MATS.JC_v2.xlsx
RI.MATS.JC_v2.xlsx
SE.MATS.JC_v2.xlsx

data_processing:
NextSeq Control Software Version 2.0.0 and RTA v2.4.6 were used for instrument control and primary analysis respectively
Reads from the four samples were mapped to the human genome using the new Tuxedo Suite of programs (HISAT2, StringTie, Ballgown; https://www.ncbi.nlm.nih.gov/pubmed/?term=27560171)
To identify RNA splicing alterations, the four BAM files generated by HISAT2 were used as input for rMATS ( replicate Multivariate Analysis of Transcript Splicing; http://rnaseq-mats.sourceforge.net/user_guide.htm)
Genome_build: hg38
Supplementary_files_format_and_content: The output of rMATS gives Excel spreadsheets covering three types of alternative splicing (AS) that showed significant changes between control cells (DMSO) and ESRP2-induced cells (DOX): MXE = Mutually Exclusive Exons; RI = Retained Intron; SE = Skipped Exon. Individual files are produced where AS is supported by: JC = only reads that span splicing junctions.  Only results with an FDR<0.05 are shown.  COLUMN NAMES: ID, Gene ID and Gene Symbol: Entrez gene ID, Ensembl gene ID and gene name, Chr: Chromosome, Strand: + or – strand, exonStart and exonEnd: Start and end coordinates of the alternatively spliced exon, upstreamES, upstreamEE, downstreamES, downstreamEE: The start (ES) and end (EE) coordinates of the exons flanking the alternatively spliced exon, ID: Entrez gene ID, IJC_SAMPLE_DMSO_1/DMSO_2/DOX_1/DOX_2: The number of reads mapped to the exon inclusion isoform in each sample, SJC_SAMPLE_1_DMSO_1/DMSO_2/DOX_1/DOX_2: The number of reads mapped to the exon skipping isoform in each sample, IncFormLen: Effective length of the exon inclusion isoform, SkipFormLen: Effective length of the exon skipping isoform, PValue: p value, FDR: False discovery rate, IncLevel_DMSO_1/DMSO_2/DOX_1/DOX_2: Fraction of normalized read counts in the neighbourhood of the respective exon in each sample, indicating a splicing event where the exon was included in the final processed mRNA transcripts, IncLevelDifference: Average of (IncLevel_DMSO_1 and IncLevel_DMSO_2) minus Average of (IncLevel_DOX_1 and IncLevel_DOX_2).

source_name: Wilms tumor cell line E200L

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS), 100U/ml penicillin, 0.1mg/ml streptomycin and 2mM L-glutamine, at 37°C in 5% CO2

extract_protocol:
RNA was extracted using an RNAeasy kit (Qiagen), then DNase treated, and quality confirmed using an Agilent Screen tape RNA assay
Sequencing libraries were prepared from total RNA (500ng) using the TruSeq Stranded mRNA Library Preparation kit (Illumina, Inc.) and uniquely barcoded adapters (RNA LT adapters, Illumina, Inc)

treatment_protocol: Cell were treated for 96hrs with 2µg/ml Doxycycline (DOX) or control solvent (DMSO)

value: Wilms tumor cell line

tag: cell line variant

value: DOX=doxycycline treated (ESRP2 expression induced)


title: B cells purified from PBMCs treated with iRBC genotype BAFF_WT, replicate 3

value: B cells


title: Suit2-2

source_name: Suit2 parental line - rep.2


title: DOX-1


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 5

source_name: B cells


title: DMSO-1

value: DMSO=control (no ESRP2 expression)


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 5

value: BAFF_var (Hom.)

value: Treatment with lysates of RBC infected with P. falciparum (iRBC)


title: B cells purified from PBMCs treated with iRBC genotype BAFF_var, replicate 2


title: B cells purified from PBMCs treated with uRBC genotype BAFF_var, replicate 2

value: Treatment with lysates of RBC uninfected  (uRBC)


title: Endocard_CtrlE

city: Toronto

first: Gordon

last: Keller

state: Ontario

address: 101 College street

department: McEwen Stem Cell Institute

country: Canada

institute: University Health Network

description:
One sample was sequenced (one run).  However, the sample consisted of two populations labeled with two different sets of hashtag antibodies.
Bulk endocardial cells labeled with TotalSeq-A0255 anti-human Hashtag 5 antibody (BioLegend). Bulk control endothelial cells labeled with TotalSeq-A0254 anti-human Hashtag 4 antibody (Biolegend) prior to sequencing.

data_processing:
Raw data consisted of CellRanger-processed, filtered feature matrices
Datasets were read in and concatenated using scanpy.read_10x_mtx
Genome_build: hg19
Supplementary_files_format_and_content: Standard for 10x Prepreprocessing pipeline (Cell Ranger 3.1)

source_name: human embryonic stem cells (HES2-WT line)

growth_protocol: Endocardial and control endothelial cells were differentiated from day 3 ventricular cardiogenic mesoderm (Keller lab protocol), specified with 5ng/ml BMP4, 5ng/mlbFGF and 4ng/ml ActivinA from HES2-WT-hPSCs.

extract_protocol:
Day 9 endocardial and control endothelial bulk populations were isolated by FACS to eliminate dead cells. Endocardial and control endothelial populations were labeled with two different sets of Hashgtag antibodies prior sequencing. Endocardial cells with TotalSeq-A0255 anti-human Hashtag 5 antibody (BioLegend), control endothelial cells labeled with TotalSeq-A0254 anti-human Hashtag 4 antibody (Biolegend). Cells were mixed (85%-to-15% ratio respectively) and sequenced as one sample.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To generate endocardial cells day 3 mesodermal cells were treated with  bFGF (50ng/ml, day 3 - day 9) and BMP10 (10ng/ml, day 5 - day 9). To generate control endothelial cells day 3 mesodermal cells were treated with  bFGF (50ng/ml, day 3 - day 9) and VEGF (100ng/ml, day 3 - day 9).

value: ES-derived endocardial and control endothelial cells mixed in ratio 85%-to-15%, respectively

value: Day 9 differentiation cultures


title: RNAseq_Ctrl2_forHNRNPA3

city: Evanston

first: Xiaomin

last: Bao

state: IL

address: 633 Clark Street

department: Molecular Biosciences

institute: Northwestern University

description:
RNAseq in undifferentiated keratinocytes
RNAseq_HNRNPA3.csv

data_processing:
3'READS+ : 5' adapters were removed using CutAdapt. Four random nucleotides were removed from 5' end. T tails were removed and saved from 5' ends. Reads > 22 nucleotides were aligned using bowtie2 in end-to-end mode. Reads with a MAPQ score lower than 10 were filtered out. Reads with at least 2 unmappable Ts in their T tails were considered Poly-A supporting reads. Poly-A sites were merged by 24bp. A table of counts was generated for total reads in each PolyA site window. To identify differential usage of poly-A sites, the sum of counts at each gene was calculated. The relative percent usage was then calculated as counts at each site divided by the total counts at the gene associated with that site. EdgeR was used to assess differential usage based on the relative percent usage.
RNA-seq: Reads were aligned using HiSat2. Number of Raw reads at each gene was calculated using htseq-count, and DESeq2 was used for differential expression analysis in R
Genome_build: hg19
Supplementary_files_format_and_content: 3'READS+ processed data is in format of table with each PolyA-site containing counts. RNA-seq data is in format of table containing counts at each gene and DESeq output information.

source_name: human keratinoctyes

growth_protocol: neonatal keratinocyte were isolated from discarded foreskin, cultured in KSF and 154 keratinocyte medium

extract_protocol:
For both 3'READS+ and RNA-seq, RNA were extracted using Quick-RNA™ MiniPrep (Zymo Research), and mRNA were enriched using NEBNext® rRNA Depletion Kit (NEB) or NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB).
For 3'READS+, sequencing libraries were constructed using a modified version of the 3'READS+ protocol.  For RNA-seq, NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina (NEB) was used for library construction.

treatment_protocol: To induce differentiaiton, keratinocytes were seeded in confluence and cultured with the addition of 1.2mM of calcium to growth medium. 10 uM of siRNA for each target were nucleofected (Lonza to keratinocytes)

value: primary human neonatal keratinocytes

value: control


title: RNAseq_HNRNPA3sh1


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 1

value: WT


title: RNAseq_Ctrl1_forHNRNPA3


title: Ery_d13_UPID26_tech2

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

description: Genome-wide library of transposed fragments

library_source: genomic

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg19
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : DEEPtools bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above)from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

molecule: genomic DNA

source_name: Erythroid culture day 13

growth_protocol: Fresh blood was sourced from patients and diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or differentiated immediately. Cells were differentiated under a three-phase in vitro protocol adapted from that used for the BEL-A cell line (Trakarnsanga et al 2017). Briefly, for differentiation 0.5-2.5x105 cells were resuspended on day 0 in Phase I media at 105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x105 cells ml-1. Cells were counted on day 9 and diluted to 3x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. ATAC-seq was performed on days 7,10,11 and 13.

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: Differentiated CD34+ HPSC

tag: gender

value: Female


title: Ery_d13_UPID27_tech1


title: Ery_d13_UPID27_tech2


title: Ery_d13_UPID26_tech1


title: Ery_d13_UPID25_tech2


title: RNAseq_HNRNPA3sh2


title: Ery_d13_UPID25_tech1


title: N_76

city: Taiyuan

first: Yongyan

last: Wu

state: Shanxi

address: No.85 South Jiefang Road, Taiyuan, Shanxi, China

department: Department of Otolaryngology Head & Neck Surgery, The First Hospital

country: China

institute: Shanxi Medical University

data_processing:
Basecalls performed using Perl package developed by Novogene.
Contaminant reads were filtered from the fq file and get the final clean reads. And then summarize the length distribution of these clean reads.
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using bowtie2 v2.2.8 and paired-end clean reads were aligned to the reference genome using HISAT2(Langmead, B.et al) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’, other parameters were set as default. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Then coding potential analysis was performed with CNCI, CPC, Pfam-sca, and phyloCSF, Transcripts predicted with coding potential by either/all of the four tools above were filtered out, and those without coding potential were candidate set of lncRNAs. Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Genome_build: hg19
Supplementary_files_format_and_content: txt file

source_name: adjacent normal mucosa tissue

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life  technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent  Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LSCC tissues and adjacent mormal mucosa tissues excised from LSCC patients after surgery were stored with RNAlater  (Cat#AM7020，Life  technologies, Carlsbad, CA, US) immediately following the manufacturer’s instructions.

tag: tissue

value: adjacent normal mucosa tissue

tag: tumor stage

value: Not Applicable

tag: tobacco smoking

tag: alcohol consumption


title: N_77


title: S2-013-2

source_name: Suit2 013 subclone - rep.2

value: metastatic pancreatic cancer


title: Ery_d13_UPID22_tech1


title: B cells purified from PBMCs treated with uRBC genotype BAFF_WT, replicate 3

tag: genotype


title: DMSO-2

tag: cell line

value: Wilms tumor cell line


title: N_74


title: Ery_d13_UPID20_tech1

value: Male


title: N_73


title: Ery_d13_UPID16_tech1


title: N_75


title: Ery_d11_UPID27_tech2

source_name: Erythroid culture day 11


title: N_64


title: N_65


title: Ery_d11_UPID27_tech1


title: N_63


title: Ery_d11_UPID26_tech2


title: N_62


title: N_61


title: N_58


title: N_66


title: Ery_d11_UPID25_tech2


title: Ery_d10_UPID27_tech2

source_name: Erythroid culture day 10


title: Ery_d11_UPID25_tech1


title: Ery_d11_UPID26_tech1


title: N_57


title: N_56


title: N_55


title: Ery_d13_UPID06_tech1


title: Ery_d10_UPID25_tech2


title: Ery_d10_UPID26_tech1


title: Ery_d10_UPID25_tech1


title: N_53


title: N_52


title: N_51


title: Ery_d10_UPID22_tech1


title: N_50


title: N_46


title: Ery_d10_UPID20_tech1


title: Ery_d10_UPID16_tech1


title: Ery_d10_UPID06_tech1


title: Ery_d10_UPID27_tech1


title: N_36


title: Ery_d07_UPID27_tech2

source_name: Erythroid culture day 7


title: Ery_d07_UPID27_tech1


title: N_35


title: Ery_d07_UPID26_tech2


title: N_31


title: Ery_d10_UPID26_tech2


title: N_34


title: N_54


title: Ery_d07_UPID25_tech2


title: Ery_d07_UPID26_tech1


title: N_29


title: N_28


title: N_27


title: Ery_d07_UPID25_tech1


title: N_25


title: N_26


title: N_24


title: N_37


title: LNCaP95_DMSO

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: LNCaP cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum. LNCaP95 cells were cultured in phenol red-free RPMI-1640 containing penicillin-streptomycin, supplemented with10% charcoal/dextran-treated FBS

extract_protocol:
Total RNA was collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Before hormone treatment, cells were incubated in phenol red-free RPMI-1640 containing penicillin-streptomycin, supplemented with5% charcoal/dextran-treated FBS. Cells were treated with 10nM DHT or the equivalent EtOH for 1.5, 3, 6, 12, 24h. LNCaP95 cells were transfected with pLKO lentivirus vectors for non-target, AR-V7#1, and AR-V7#2 using Lipofectamine 3000, and they were exposed to puromycin for 4 days for selection.  LNCaP95 cells were transfected with each siRNA  using Lipofectamine and RNAiMAX. LNCaP95 cells were treated with 50uM JPH203 or the equivalent DMSO for 2 days.

tag: agent

value: DMSO


title: LNCaP95_siLAT1

tag: vector


title: LNCaP95_sicontrol_2


title: LNCaP95_JPH203


title: LNCaP95_siSLC3A2


title: N_23


title: N_22


title: LNCaP95_sicontrol_1


title: N_20


title: N_30


title: LNCaP95_shNoN

value: shNon

tag: selective drug

value: puromycin


title: LNCaP95_shAR-V7#2


title: N_18


title: N_19


title: N_15


title: LNCaP95_shAR-V7#1


title: LNCaP95_10nM_DHT_H3K27ac

data_processing:
BCL2FASTQ version1.8.4 software was used for basecalling.
ChIP-seq reads were aligned to hg19 reference human genome, using bowtie.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format. Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

extract_protocol:
For ChIP-seq, sonicated nuclear fraction was incubated with each antibody and histone-DNA complexes were isolated.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) following the manufacturer’s protocol.Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: Before hormone treatment, cells were incubated in phenol red-free RPMI-1640 containing penicillin-streptomycin, supplemented with5% charcoal/dextran-treated FBS for 3 days. Cells were treated with 10nM DHT or the equivalent EtOH for 12h. LNCaP95 cells were transfected with pLKO lentivirus vectors for non-target, AR-V7#1, and AR-V7#2 using Lipofectamine 3000, and they were exposed to puromycin for 4 days for selection.

tag: chip antibody

value: H3K27ac (#39159, Active Motif)


title: N_13


title: LNCaP95_shNoN_H3K27ac

tag: shRNA

value: shNoN


title: SPL7 Sparc-/-

city: Palermo

first: Claudio

last: Tripodo

address: Corso Tukory 211

department: Department of Health Sciences

country: Italy

institute: University of Palermo School of Medicine

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14
Reads were aligned to ENSEMBL mouse genome assembly BALB_cJ_v1 using STAR
Absolute gene counts were obtained by counting the number of reads per gene using HTSeq-count
Genome_build: BALB_cJ_v1
Supplementary_files_format_and_content: The tab-delimited text files contain the gene raw counts obtained with HTSeq-count

extract_protocol:
Total RNA samples were isolated using RNeasy Mini Kit (Qiagen). DNA was removed with a DNase treatment in all the samples. rRNA removal was performed using the RiboMinus™ Eukaryote Kit for  RNA-Seq (Invitrogen).
Illumina TruSeq Stranded Total RNA Library preparation kit with Ribo-Zero

treatment_protocol: A20 cell lines were injected i.v.(5*10^5 cells) in recipient mice. Following 5 weeks of injection, mice were sacrificed and the A20 cells recovered from the bone marrow, spleen, and liver tissues through flow cytometry sorting.

tag: recipient strain background

value: Balb/c

tag: genotype/variation

value: Sparc-/-

tag: treatment

value: injected with A20 lymphoma cells

value: Spleen


title: LNCaP95_shAR-V7#2_H3K27ac


title: LNCaP95_shAR-V7#1_H3K27ac


title: N_14


title: SPL6 Sparc-/-


title: N_12


title: SPL5 Sparc-/-


title: LNCaP95_EtOH_H3K27ac

value: EtOH


title: SPL4 Sparc-/-


title: N_11


title: SPL3 Sparc-/-


title: LI7 Sparc-/-

value: Liver


title: LNCaP_10nM_DHT_H3K27ac

source_name: LNCaP

value: LNCaP


title: N_10

value: adjacent normal mucosa tissue


title: N_16

value: Not Applicable


title: N_8


title: N_7


title: LI4 Sparc-/-


title: LI2 Sparc-/-


title: LNCaP_10nM_DHT_H3K4me1

value: H3K4me1 (#ab8895, Abcam)


title: N_6


title: LNCaP95_EtOH_H3K4me1


title: BM4 Sparc-/-

source_name: Sparc-/-_A20_Bone marrow

value: Bone marrow


title: LNCaP_EtOH_H3K4me1


title: N_5


title: BM2 Sparc-/-


title: BM3 Sparc-/-


title: BM1 Sparc-/-


title: LNCaP95_10nM_DHT_H3K4me3

value: H3K4me3 (#ab7766, Abcam)


title: N_4


title: LNCaP_EtOH_H3K27ac


title: SPL11 Balb/c

source_name: wild type_A20_Spleen

value: wild type


title: N_3


title: SPL4 Balb/c


title: SPL10 Balb/c


title: SPL7 Balb/c


title: LNCaP95_EtOH_H3K4me3


title: N_2


title: LNCaP95_10nM_DHT_H3K4me1


title: LI5 Sparc-/-


title: LI6 Sparc-/-


title: BM5 Sparc-/-


title: LI5 Balb/c

source_name: wild type_A20_Liver


title: LNCaP_EtOH_H3K4me3


title: N_1


title: LI2 Balb/c


title: LI1 Balb/c


title: C_77

source_name: LSCC tissue

value: LSCC tissue

value: Yes

value: No


title: LNCaP_EtOH_AR

value: AR (#6-680 Millipore)


title: LNCaP95_10nM_DHT_AR


title: LI3 Balb/c

value: Balb/c


title: BM3 Balb/c

source_name: wild type_A20_Bone marrow


title: C_76


title: SPL3 Balb/c


title: C_75


title: BM2 Balb/c


title: BM5 Balb/c


title: LNCaP_10nM_DHT_H3K4me3


title: hESC_rep4

description:
DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown
Human_Capture.txt

data_processing:
Library strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg19
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: H1 hESC (WiCell)

growth_protocol: Fresh blood was sourced either as 100 ml whole blood collected from three healthy donors (two males, one female) using EDTA Vacuettes (Becton Dickson) or 5 ml leukocyte cones (NHS Blood & Transport). Whole cell counts were performed on a Pentra ES60 (Horiba) for donor blood to ensure clinically healthy red blood cell counts. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through two LS Columns (Miltenyi Biotec) with three MACs buffer washes. Counting of cells was performed on a Luna FL (Logos) after staining with acridine orange (AO) and propidium iodide (PI). CD34+ cells were either stored in freezing buffer (90% FBS, 10% DMSO) or resuspended in Phase I mediumfor a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 0.5-2.5x10^5 cells were resuspended on day 0 in Phase I media at 10^5 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 10^5 cells ml-1. On day 7, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase II media at 3x10^5 cells ml-1. Cells were counted on day 9 and diluted to 3x10^5 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (400 rcf, 5 min, RT) and resuspended in Phase III media at 10^6 cells ml-1. Cells were counted on days 13 and 15 and diluted to 10^6 cells ml-1 in Phase III media. Reproducibility between differentiations was confirmed morphologically with cytospins and immunologically with six FACS cell surface markers (CD34, CD36/Fatty acid translocase, CD71/Transferrin receptor, CD235a/Glycophorin A, CD49d/α-Integrin, CD233/Band). Human ESC line H1 (H1-hESC; WiCell) was grown on Matrigel (Corning) coated plates in mTeSR1 medium (StemCell technologies). Cells were harvested as a single cell suspension using Accutase (EDM Millipore); Fixation were carried out in mTeSR1 medium.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies)
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

tag: cell type

value: H1 hESC

tag: day of differentiation

tag: Sex

value: Male


title: C_74

tag: tissue


title: BM1 Balb/c

value: injected with A20 lymphoma cells


title: hESC_rep2


title: LI4 Balb/c


title: hESC_rep1


title: hESC_rep3


title: C_73

tag: tumor stage


title: Ery_Don003

source_name: CD34 Culture

value: Erythroid

value: Day 10


title: C_66

tag: tobacco smoking


title: Ery_Don002


title: C_65

tag: alcohol consumption


title: BM4 Balb/c


title: LNCaP95_10nM_DHT_12hr

tag: time point


title: Ery_Don001

value: Female


title: LNCaP95_10nM_DHT_24hr

tag: cell line


title: C_64


title: C_63


title: C_62


title: LNCaP95_10nM_DHT_1.5hr

tag: agent


title: LNCaP_10nM_DHT_24hr

value: LNCaP


title: LNCaP95_10nM_DHT_3hr


title: LNCaP95_EtOH_0hr

value: EtOH


title: C_61


title: HT29 T0 vs T6 rep2

city: Jouy en Josas

first: Florian

last: Chain

address: Domaine de Vilvert

department: Institut Micalis

country: France

institute: INRA

hyb_protocol: 825ng of Cy3-labelled cRNA from a specific treatment was mixed with the same amount of Cy5-labelled cRNA from another treatment. cRNAs were hybridized to the Agilent 4x44K Whole Human Genome Microarray (Agilent Technologies, France) at 65°C, for 17 hours in a rotating incubator. After hybridization, slides were washed and then scanned by using an Agilent G2565CA scanner (Agilent Technologies, France).

scan_protocol: Raw data were then extracted using Feature Extraction Software version 10.5.1.1 (Agilent Technologies, France).

data_processing: The R 3.0.2 software and the LIMMA package were used to analyse the microarray data (within-array normalization by loess method followed by between-arrays normalization by quantile method) and to generate lists of differentially expressed genes. Gene lists were created by filtering on adjusted p-value using0.05 threshold with Benjamini and Hochberg false discovery rate as multiple testing correction, followed by filtering on expression level (|Fold Change|>1.5 as a cut-off). Results for comparisons between treatments are given in separate files (1 file per comparison).

source_name: non stimulated HT29 cells at T=0 hour

label_protocol: For labeling, 100 ng of total RNA was reverse transcribed and then stained with Cy3 or Cy5 using the Two Color Low Input Quick Amp Gene Expression Labeling Kit (Agilent Technologies, France) according to the manufacturer's instructions. The CyDye-labelled cRNAs were then purified using the RNeasy Mini Kit (Qiagen, France). cRNA quantity was determined by Nanodrop and quality was checked on Agilent 2100 expert Bioanalyzer. Yield and specific activity were determined by referring to the manufacturer's instructions.

growth_protocol:
Faecalibacterium prausnitzii A2-165 strain (DSMZ collection, Braunschweig, Germany) (DSM N°17677) was grown in LYBHI medium (brain-heart infusion medium with 0.5% yeast extract) (Difco, Detroit, USA) supplemented with 1 mg/ml cellobiose (Sigma-Aldrich Chemie GmbH, Buchs, Switzerland), 1 mg/ml maltose (Sigma-Aldrich), and 0.5 mg/ml cysteine (Sigma-Aldrich) at 37°C in an anaerobic chamber. F. prausnitzii supernatant (SN) was recovered by centrifugation, filtered with 0.45 µm filters (VWR, Haasrode, Belgium) and stored at -80°C until further use.
The human colon carcinoma cell line HT-29 was seeded in 24-well culture plates (Nunc) in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS)-1% glutamine at 37°C in a 10% CO2-air atmosphere.  Medium was changed every day. Experiments were initiated on day 7 after seeding, when cells were at confluence (approx. 1.83X10^6 cells/well). Twenty-four hours before co-culture with F. prausnitzii SN (day6), the culture medium was changed for a medium with 5% heat-inactivated FCS and 1% glutamine .

extract_protocol: After co-incubation with LYBHI or F. prausnitzii SN HT-29 cells were collected and RNA was purified for DNA microarray hybridization. Total RNA was extracted from cells using the RNeasy Mini Kit (Qiagen, USA) and purified by on-column digestion of DNA with DNase I as recommended by the manufacturer to eliminate residual genomic DNA. RNA concentration was determined by Nanodrop quantification (Thermo Fisher Scientific Inc., France). RNA quality was checked on an Agilent 2100 expert Bioanalyzer (Agilent Technologies, France). Only RNAs with a RIN above 8  were  used for microarray and qRT-PCR experiments.

treatment_protocol: On the day of co-culture, either SN or LYBHI medium were added at a concentration of 10% (v/v) in a total volume of 500µl. Cells were stimulated simultaneously with recombinant human TNF-a (5 ng/ml; Peprotech, NJ, USA) for 6 h at 37°C in 10% CO2.   Treatments are coded as follows : T6 = HT29 at 6h (= reference) ; TNF = TNF-alpha stimulated HT29 cells at 6 hours; BHI = HT29 cells co-incubated with BHI at 6hours; SN = HT29 cells co-incubated with F.prausnitzii supernatant at 6 hours; BHI_TNF = HT29 cells stimulated with TNF-alpha and co-incubated with BHI at 6 hours; SN_TNF = HT29 cells stimulated with TNF-alpha and co-incubated with  F.prausnitzii supernatant at 6 hours; T0 = HT29 cells at T=0 hour.

tag: time

value: time = 0 hours

source_name: non stimulated HT29 cells at T=6 hours

value: time = 6 hours


title: HT29 T6 vs SN_TNF rep2

source_name: HT29 cells co-incubated with SN and stimulated with TNF at T=6 hours


title: HT29 SN_TNF vs T6 rep2


title: HT29 SN_TNF vs T6 rep1


title: C_58


title: LNCaP_10nM_DHT_6hr


title: LNCaP_10nM_DHT_3hr


title: LNCaP_10nM_DHT_12hr


title: HT29 T0 vs T6 rep1


title: LNCaP_10nM_DHT_1.5hr


title: HT29 T6 vs T0 rep1


title: HT29 T6 vs T0 rep2


title: C_57


title: LNCaP_EtOH_0hr


title: C_56


title: LNCaP95_10nM_DHT_6hr


title: LNCaP95_EtOH_AR


title: LNCaP_10nM_DHT_AR


title: HT29 T6 vs BHI_TNF rep1

source_name: HT29 cells co-incubated with BHI and stimulated with TNF at T=6 hours


title: C_55


title: HT29 BHI_TNF vs T6 rep1


title: C_54


title: HT29 T6 vs BHI rep1

source_name: HT29 cells co-incubated with BHI at T=6 hours

value: BHI


title: HT29 T6 vs SN_TNF rep1


title: C_53


title: HT29 T6 vs BHI_TNF rep2


title: HT29 BHI vs T6 rep1


title: C_52


title: C_50


title: C_51


title: C_46


title: C_37


title: Rat 6_hypothalamus_Ozone_Male

city: Research Triangle Park

first: Brian

last: Chorley

state: NC

address: US EPA, 109 TW Alexander Dr

institute: US EPA

description:
GRC333-24_S3
RNAseq_24_Normalized_counts_Male.txt

data_processing:
FASTQ files were demultiplexed, and adapters and low-quality bases were removed using Partek Flow NGS analysis software (Build 6.0.17.0403; St. Louis, MO).
Remaining sequences of 25 bp or greater were retained and trimmed from the 3’ ends if the Phred quality score was less than 25.
Trimmed reads were aligned to the rat genome (rn6) using STAR 2.5.3a using all default setting within Partek Flow.
Aligned sequences were then annotated to rn6 - RefSeq Transcripts 83 (2017-11-01) with the Partek E/M (expectation maximum) algorithm. Male and female samples were separated for later analyses.
Raw counts were normalized by counts per million (CPM), adding 0.0001 to all normalized counts. Geometric mean of normalized read counts ≤ 1.0 were removed and log 2 transformed.
Differentially expressed genes (DEGs) were determined through Gene-Specific Analysis (GSA) using a multimodel approach. P-value ≤ 0.05 and log2(fold change) ≤ -1.3 or ≥ 1.3 cutoffs were applied to identify DEGs.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited files contains CPM normalized count values for all samples and mapped featues (excluding features <1 of geometric mean across samples). Males and Female samples have separate files.

organism: Rattus norvegicus

extract_protocol:
Fetal and placental endpoints were collected for assessment at GD 21. Dams and fetuses were euthanized using a lethal intraperitoneal dose of pentobarbital (> 400 mg/kg). For a subset of fetuses in each litter (1st and 2nd fetus on the ovarian side of each horn), the hypothalamus was dissected, quick frozen in liquid nitrogen,and stored at -80ºC until use. Total RNA was isolated from fetal whole hypothalamus using Trizol with the Direct-Zol RNA Purification Kit (Zymo Research). Isolated RNAs were quantified by the Qubit fluorometer (ThermoFisher) and quality checked by Bioanalyzer (Beckman Coulter, Inc.; Santa Clara, CA). All samples had a RIN at or above 9.
Hypothalamic RNA samples (n = 6/sex/group from the same subset of selected fetuses, 1 μg each) were processed on Apollo324 system (Takara Bio USA, Inc.; Mountain View, CA) using PrepXTM mRNA selection and mRNA-seq library prep for Illumina. The products from library preparation were amplified by PCR with the sequencing index primers. The PCR products were purified on Apollo324 and assessed for quality using Bioanalyzer. The library concentrations were verified by Qubit.

treatment_protocol: Dams were randomly assigned by body weight using an in-house excel macro to be exposed to either filtered air or 0.8 ppm ozone for 4 hours in the mornings (0700 – 1100) during implantation receptivity (gestation day, GD, 5 and 6) in Long-Evans rats. Control rats were exposed to filtered air. At GD 21, placental and fetal tissues were obtained for metabolic and genomic assessments.

tag: strain

value: Long-Evans

tag: age

value: GD 21

tag: exposure

value: 0.8 ppm ozone


title: Rat 5_hypothalamus_Ozone_Male

description:
GRC333-23_S9
RNAseq_24_Normalized_counts_Male.txt


title: Rat 4_hypothalamus_Ozone_Male

description:
GRC333-22_S15
RNAseq_24_Normalized_counts_Male.txt


title: HT29 BHI_TNF vs T6 rep2


title: siP1 #3_2

city: Seoul

first: Do Young

last: Hyeon

state: Select State

address: 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: Gene expression in wild type A549 cells transfected with siPIERCE1 #3 [rep2]

hyb_protocol: According to the standard Agilent protocols, the RNA was reverse-transcribed, amplified and then hybridized onto the array.

scan_protocol: Agilent Technologies G2600D SG13094295

data_processing: Scanned signal intensity was log2-transformed. The log2-transformed data for four conditions (siP1 #1, siP1 #2, siP1 #3, and siControl) were then quantile-normalized. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011a).

source_name: A549 cells, wild type, transfected with siPIERCE1 #3, replicate 2

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: A549 cells were maintained in the DMEM and RPMI (HyClone) supplemented with Penicillin/streptomycin (Gibco) and 10% of FBS (HyClone) at 37℃ with 5% CO2 in a humidified chamber.

extract_protocol: Total RNA was isolated from A549 cells using WelPrepTM (Welgene, Daegu, Korea), and the integrity of the total RNA was checked using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: A549 cells were transfected with one of three difference sequences of siPIERCE1 or siControl.

tag: genotype

value: wild type

value: transfected with siPIERCE1 #3


title: siControl_1

description: Gene expression in wild type A549 cells transfected with siControl [rep1]

source_name: A549 cells, wild type, transfected with siControl, replicate 1

value: transfected with siControl


title: C_36

value: LSCC tissue

value: No

value: Yes


title: Rat 3_hypothalamus_Ozone_Male

description:
GRC333-21_S20
RNAseq_24_Normalized_counts_Male.txt

value: Male


title: HT29 T6 vs SN rep2

source_name: HT29 cells co-incubated with SN at T=6 hours

value: SN


title: siP1 #2_1

description: Gene expression in wild type A549 cells transfected with siPIERCE1 #2 [rep1]

source_name: A549 cells, wild type, transfected with siPIERCE1 #2, replicate 1

value: transfected with siPIERCE1 #2


title: siP1 #3_1

description: Gene expression in wild type A549 cells transfected with siPIERCE1 #3 [rep1]

source_name: A549 cells, wild type, transfected with siPIERCE1 #3, replicate 1


title: HT29 T6 vs BHI rep2


title: siControl_2

description: Gene expression in wild type A549 cells transfected with siControl [rep2]

source_name: A549 cells, wild type, transfected with siControl, replicate 2


title: siP1 #1_2

description: Gene expression in wild type A549 cells transfected with siPIERCE1 #1 [rep2]

source_name: A549 cells, wild type, transfected with siPIERCE1 #1, replicate 2

value: transfected with siPIERCE1 #1


title: siP1 #2_2

description: Gene expression in wild type A549 cells transfected with siPIERCE1 #2 [rep2]

source_name: A549 cells, wild type, transfected with siPIERCE1 #2, replicate 2


title: HT29 SN vs T6 rep2


title: K171R_2 (array)

description: Gene expression in SNU484 cells harboring RUNX3 K171R mutation 8 hours after exposure to hypoxia [rep2]

data_processing: Scanned signal intensity was log2-transformed. The log2-transformed data for two comparisons (K129R versus WT, K171R versus WT) were then quantile-normalized. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011a).

source_name: SNU484 cells, RUNX3 K171R mutant, 8h after exposure to hypoxia, replicate 2

growth_protocol: SNU484 cells were passaged in our laboratory according to Korean Cell Line Bank (KCLB, Seoul, Korea) protocol.

extract_protocol: Total RNA was isolated from SNU484 cells using WelPrepTM (Welgene, Daegu, Korea), and the integrity of the total RNA was checked using a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA).

treatment_protocol: SNU484 cells were maintained and exposed to hypoxic conditions as described elsewhere.

value: RUNX3 K171R mutant

value: 8h after the exposure to hypoxia


title: HT29 TNF vs T6 rep2

source_name: HT29 cells stimulated with TNF

value: TNF

value: time = 6 hours


title: HT29 SN vs T6 rep1


title: K129R_2 (array)

description: Gene expression in SNU484 cells harboring RUNX3 K129R mutation 8 hours after exposure to hypoxia [rep2]

source_name: SNU484 cells, RUNX3 K129R mutant, 8h after exposure to hypoxia, replicate 2

value: RUNX3 K129R mutant


title: Rat 1_hypothalamus_Ozone_Male

description:
GRC333-19_S4
RNAseq_24_Normalized_counts_Male.txt

value: Long-Evans

value: GD 21


title: Rat 2_hypothalamus_Ozone_Male

description:
GRC333-20_S11
RNAseq_24_Normalized_counts_Male.txt

value: 0.8 ppm ozone


title: HT29 BHI vs T6 rep2

value: BHI


title: K171R_1 (array)

description: Gene expression in SNU484 cells harboring RUNX3 K171R mutation 8 hours after exposure to hypoxia [rep1]

source_name: SNU484 cells, RUNX3 K171R mutant, 8h after exposure to hypoxia, replicate 1


title: WT_2 (array)

description: Gene expression in wild type SNU484 cells 8 hours after exposure to hypoxia [rep2]

source_name: SNU484 cells, wild type, 8h after exposure to hypoxia, replicate 2

value: wild type


title: siP1 #1_1

description: Gene expression in wild type A549 cells transfected with siPIERCE1 #1 [rep1]

source_name: A549 cells, wild type, transfected with siPIERCE1 #1, replicate 1


title: K129R_1 (array)

description: Gene expression in SNU484 cells harboring RUNX3 K129R mutation 8 hours after exposure to hypoxia [rep1]

source_name: SNU484 cells, RUNX3 K129R mutant, 8h after exposure to hypoxia, replicate 1


title: C_34

source_name: LSCC tissue

value: LSCC tissue


title: Rat 6_hypothalamus_Air_Male

description:
GRC333-18_S16
RNAseq_24_Normalized_counts_Male.txt

value: Air


title: Rat 5_hypothalamus_Air_Male

description:
GRC333-17_S23
RNAseq_24_Normalized_counts_Male.txt


title: Rat 4_hypothalamus_Air_Male

description:
GRC333-16_S21
RNAseq_24_Normalized_counts_Male.txt


title: Rat 3_hypothalamus_Air_Male

description:
GRC333-15_S22
RNAseq_24_Normalized_counts_Male.txt


title: HT29 T6 vs TNF rep1

source_name: non stimulated HT29 cells at T=6 hours

source_name: HT29 cells stimulated with TNF at T=6 hours


title: HT29 T6 vs TNF rep2


title: Rat 5_hypothalamus_Ozone_Female

description:
GRC333-11_S19
RNAseq_24_Normalized_counts_Female.txt

value: Female


title: Rat 6_hypothalamus_Ozone_Female

description:
GRC333-12_S13
RNAseq_24_Normalized_counts_Female.txt


title: HT29 T6 vs SN rep1


title: C_29

value: Yes


title: C_31


title: WT_1 (array)

description: Gene expression in wild type SNU484 cells 8 hours after exposure to hypoxia [rep1]

source_name: SNU484 cells, wild type, 8h after exposure to hypoxia, replicate 1


title: C_30


title: HT29 TNF vs T6 rep1


title: Rat 4_hypothalamus_Ozone_Female

description:
GRC333-10_S8
RNAseq_24_Normalized_counts_Female.txt


title: C_35


title: Rat 3_hypothalamus_Ozone_Female

description:
GRC333-9_S17
RNAseq_24_Normalized_counts_Female.txt


title: C_28


title: C_27


title: Rat 2_hypothalamus_Ozone_Female

description:
GRC333-8_S6
RNAseq_24_Normalized_counts_Female.txt


title: Rat 1_hypothalamus_Ozone_Female

description:
GRC333-7_S24
RNAseq_24_Normalized_counts_Female.txt


title: Rat 6_hypothalamus_Air_Female

description:
GRC333-6_S12
RNAseq_24_Normalized_counts_Female.txt


title: Rat 5_hypothalamus_Air_Female

description:
GRC333-5_S2
RNAseq_24_Normalized_counts_Female.txt


title: C_26


title: Rat 3_hypothalamus_Air_Female

description:
GRC333-3_S14
RNAseq_24_Normalized_counts_Female.txt


title: Rat 2_hypothalamus_Air_Female

description:
GRC333-2_S18
RNAseq_24_Normalized_counts_Female.txt


title: Rat 1_hypothalamus_Air_Female

description:
GRC333-1_S7
RNAseq_24_Normalized_counts_Female.txt


title: Rat 2_hypothalamus_Air_Male

description:
GRC333-14_S1
RNAseq_24_Normalized_counts_Male.txt

value: Male


title: C_24


title: C_23


title: C_22


title: C_20


title: C_19

value: No


title: C_18


title: Rat 4_hypothalamus_Air_Female

description:
GRC333-4_S10
RNAseq_24_Normalized_counts_Female.txt


title: C_16


title: C_25


title: C_14


title: C_13


title: C_12


title: C_11


title: C_15


title: C_10


title: C_8


title: C_7


title: Rat 1_hypothalamus_Air_Male

description:
GRC333-13_S5
RNAseq_24_Normalized_counts_Male.txt


title: MMR1350T3

type: genomic

city: Christchurch

first: Andrew

last: Dodgshun

address: 2 Riccarton Avenue

department: Children’s Haematology/Oncology Centre

country: New Zealand

institute: Christchurch Hospital

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: CHaMP package, R language

label: Cy3 and Cy5

source_name: Tumour tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using commercially available kits (differing by source of tissue) according to standard protocols

tag: age at diagnosis

tag: tissue source

value: FFPE

tag: histology

value: AO

tag: primary (p) or recurrent (r)

value: R

value: M


title: MMR128T16

value: Fresh Frozen

value: GBM

value: P

tag: Sex

value: F


title: WT005

value: PXA

value: U


title: MMR1282T1

value: HGG


title: MMR1273T25


title: C_6

tag: tissue

value: LSCC tissue


title: MMR1273T26


title: MUT034

value: Anaplastic PXA


title: MD0190T2


title: MD1307T1


title: MD0029T1


title: C_4

tag: tumor stage


title: MD0005T1


title: MMR0134T10


title: MD1273T3


title: C_3

tag: tobacco smoking


title: MD0139T1


title: MMR0139T2

value: AA


title: MMR0140T7


title: MMR0134T12


title: C_2

value: Yes

tag: alcohol consumption


title: MD1277T1


title: MD1293T1


title: CTL-36 hrs_rep 2

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization within lumi package in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HCT116 cells were cultured in DMEM/F12 with 5% Horse serum, at 37oC, 5%CO2.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: SUNO1 was depleted by using siRNA. Control siRNA was used as control in HCT116 cells. We performed the microarray in biologicl duplicates. We used to two time points (36 hrs and 72 hrs post siRNA treatment) to identify the gene sets that showed differential expression during early and late time points post SUNO1 depletion.

tag: sirna

value: Control

tag: time point


title: SUNO1 siRNA-36hrs-rep 1

tag: cell line

value: SUNO1 siRNA


title: MMR1260T8


title: MMR0128T10


title: CTL-36 hrs_rep 1


title: SUNO1 siRNA-36hrs-rep 2


title: C_5


title: MD0002T16

value: FFPE


title: SUNO1 siRNA-72hrs-rep 2


title: C_1


title: MD1260T1


title: SUNO1 siRNA-72hrs-rep 1


title: PATU-8902_RPF_woSG3

first: Robert

last: Banh

address: 522 First Avenue, Smilow 907

institute: New York University

description: Ribosome Protected Fragment (RPF)

data_processing:
Library strategy: Ribo-seq
Total and ribosome protected fragments (RPFs) were analyzed as described by Darnell A.M., et al. Molecular Cell. 2018.
Cutadapt: -a CTGTAGGCACCATCAAT -m 13
Genome_build: hg38
Supplementary_files_format_and_content: total and ribosome protected fragments (RPFs) were analyzed as described by Darnell A.M., et al. Molecular Cell. 2018.

extract_protocol: Total and ribosome protected fragments (RPFs) were purified as described by Ingolia N.T., et al. Nature protocols. 2012.

treatment_protocol: Cells were washed once with PBS  and media was changed to DMEM (2.78mM glucose, 4mM glutamine, 1mM pyruvate) + 10% dialyzed FBS with or without 400uM serine and 400uM glycine for 24 hours.

tag: cell type

value: Pancreactic Ductal Adenocarcinoma Cell Line

tag: treatment

value: -Ser/Gly


title: MD0052T1

value: AO

value: M


title: W1L_rep3

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

country: Germany

data_processing:
library strategy: Y-shaped Adapter-ligated MAture tRNA sequencing (YAMAT-seq)
Sorted into 27 samples using the unique, 6-bp Illumina indices. 0 mismatches allowed.
Per sample: reads between 80 and 151 bp were extracted (in Geneious v11.1.4)
Per sample: 80-151 bp reads were aligned to a set of 42 reference tRNA sequences (all unique primary sequences predicted in the SBW25 genome by GtRNAdb). This was done using Geneious version 11.1.4 (assembly parameters: up to 10% mismatches or gaps of <3 bp per read, up to 5 ambiguities per read, no assignment of reads that map equally well to more than one reference sequence, and no iterations)
Per sample: read numbers for the 42 contigs were used in pairwise comparisons with DESeq2 (in R version 3.6.0)
Genome_build: The 42 tRNA sequence reference file was derived from the SBW25 genome sequence (NCBI accession number: NC_012660.1) using GtRNAdb (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/bacteria/Pseu_fluo_SBW25/pseuFluo_SBW25-tRNAs.fa)
Supplementary_files_format_and_content: 27 text files: the raw read numbers aligned to the 42 reference sequences. One file per sample.
Supplementary_files_format_and_content: "aligned_reads.xlsx" contains a summary of the data for all 27 samples, plus a spreadsheet for each of the 9 strains listing the of the number of reads aligned to each reference sequence in each replicate. "deseq2_comparisons.xlsx"  contains the DESeq2 output for pairwise comparisons between strains of interest.

organism: Pseudomonas fluorescens

source_name: W1L_liquid cell culture

growth_protocol: Samples were grown from single colonies in liquid culture overnight (28˚C, shaking). A small volume of grown culture was inoculated into fresh medium and grown to mid-exponential phase (approx. 5-7 hours, 28˚C, shaking).

extract_protocol:
Per sample: 1.5 ml aliquots of mid-exponential phase culture were taken, and total RNA extracted (TRIzol Max Bacterial RNA isolation kit; Life Technologies).
The YAMAT-seq method is an adaptation of that published for human cell lines (Shigematsu et al., 2017). For each sample, 5 ug total RNA was subjected to tRNA deacylation treatment by exposure to hydrochloric acid. Hybrid DNA/RNA Y-shaped adapters (Eurofins) were ligated to exposed 5'-CCA-3' tRNA ends using T4 RNA ligase 2 (New England Biolabs). Ligation products were reverse transcribed into cDNA (SuperScript III reverse transcriptase; Thermo Fisher), and amplified PCR (Phusion; Thermo Fisher). One of 27 sample-specific indices (Illumina) was added to each of the 27 reactions. The quality and quantity of each PCR product was checked using an Agilent DNA 7500 kit on a Bioanalyzer (Agilent), and samples combined in equimolar amounts into a single tube. The mixture was run on a 5 % polyacrylaminde gel (Bio-Rad Laboratories), and the group of bands ranging between 180 bp and 250 bp excised. DNA was extracted in deionized water overnight, and agarose removed by centrifugation through filter paper. DNA quality and quantity was checked with a Quant-iT dsDNA BR Assay kit (Invitrogen) on a Fluorescence Nanodrop.High throughput sequencing was performed at the Max Planck Institute for Evolutionary Biology (Ploen, Germany). Single-end, 150 bp reads were generated with a NextSeq 550 Output v2.5 kit (Illumina).

tag: strain type

value: evolved

tag: evolution day

tag: molecule subtype

value: mature tRNA


title: M4L_rep3

institute: Max Planck Institute for Evolutionary Biology

source_name: M4L_liquid cell culture

value: engineered then evolved

tag: genotype


title: CTL-72 hrs_rep 2


title: PATU-8902_RPF_woSG2

city: New York

description: Ribosome Protected Fragment (RPF)


title: MMR0134T13

tag: age at diagnosis

tag: tissue source

value: Fresh Frozen

value: GBM

value: R


title: MD1281T1

tag: histology

value: GBM/MB

tag: primary (p) or recurrent (r)

value: P

value: F


title: PATU-8902_RPF_woSG1

description: Ribosome Protected Fragment (RPF)


title: MD0043T1

tag: Sex


title: M2Lop_rep3

source_name: M2Lop_liquid cell culture


title: MMR0101T11


title: M1L_rep3

source_name: M1L_liquid cell culture


title: delSercga1_rep3

source_name: delSercga1_liquid cell culture

value: engineered


title: delSercga2_rep3

source_name: delSercga2_liquid cell culture


title: PATU-8902_RPF_wSG2

description: Ribosome Protected Fragment (RPF)

value: +Ser/Gly


title: SBW25_rep3

source_name: SBW25_liquid cell culture

value: SBW25 (wild type)


title: W1L_rep2


title: PATU-8902_RPF_wSG1

description: Ribosome Protected Fragment (RPF)


title: MMR0134T11


title: PATU-8902_RPF_wSG3

description: Ribosome Protected Fragment (RPF)


title: M3L_rep2

source_name: M3L_liquid cell culture


title: PATU-8902_Total_woSG3

description: Total RNA


title: M2L_rep2

source_name: M2L_liquid cell culture


title: M2Lop_rep2


title: PATU-8902_Total_woSG2

description: Total RNA


title: delSercga2_rep2


title: PATU-8902_Total_woSG1

description: Total RNA


title: SBW25_rep2


title: Abcb4(-/-)/IL13(-/-) vs. IL13-/-

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

institute: Max-Planck-Institute for Infection Biology

hyb_protocol: Whole mouse genome 8x60K microarrays were done according to the supplier’s protocol (Agilent Technologies)

scan_protocol: Scanning of microarrays was performed with 3 µm resolution using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware)

source_name: double knock out (double KO)

label_protocol: RNA labeling was performed with the low input Quick Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Generation and characteristics of knockout lineages C.FVB(129P2)-Abcb4tm1Bor (Abcb4-/-) and BALB/c-ll13tm2Anjm (IL-13) have been described previously. Abcb4-/-- and IL-13-/- mice were crossed to raise double-knockout hybrids C.Cg-ll13tm2Anjm-Abcb4tm1Bor (Abcb4-/-IL-13-/-).

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: Mice at  8 weeks of age were used.

tag: strain

tag: tissue

value: liver

source_name: knock out (KO)


title: PATU-8902_Total_wSG3

description: Total RNA

value: Pancreactic Ductal Adenocarcinoma Cell Line


title: MD1268T2

value: AA


title: M1L_rep2


title: W1L_rep1


title: M4L_rep2


title: MD0138T1

value: FFPE


title: M3L_rep1


title: PATU-8902_Total_wSG2

description: Total RNA


title: MD0143T1

value: M


title: Abcb4(-/-)/IL13(-/-) vs. Abcb4-/-


title: IL13-/- vs. Abcb4(-/-)/IL13(-/-)


title: MD1294T1


title: M4L_rep1


title: delSercga1_rep2


title: M2L_rep1


title: PATU-8902_Total_wSG1

description: Total RNA


title: Abcb4-/- vs. Abcb4(-/-)/IL13(-/-)


title: M2Lop_rep1


title: M1L_rep1


title: Wild-Type vs. IL13-/-

source_name: wildtype

value: Wild-Type

value: BALB/c


title: Abcb4-/- vs. Wild-Type

value: FVB/N


title: 3READS_CPSFsi

data_processing:
3'READS+ : 5' adapters were removed using CutAdapt. Four random nucleotides were removed from 5' end. T tails were removed and saved from 5' ends. Reads > 22 nucleotides were aligned using bowtie2 in end-to-end mode. Reads with a MAPQ score lower than 10 were filtered out. Reads with at least 2 unmappable Ts in their T tails were considered Poly-A supporting reads. Poly-A sites were merged by 24bp. A table of counts was generated for total reads in each PolyA site window. To identify differential usage of poly-A sites, the sum of counts at each gene was calculated. The relative percent usage was then calculated as counts at each site divided by the total counts at the gene associated with that site. EdgeR was used to assess differential usage based on the relative percent usage.
RNA-seq : Reads were aligned using Tophat2. Number of Raw reads at each gene was calculated using in house generated script, and DESeq was used for differential expression analysis in R
Genome_build: hg19
Supplementary_files_format_and_content: 3'READS+ processed data is in format of table with each PolyA-site containing counts. RNA-seq data is in format of table containing counts at each gene and DESeq output information.

source_name: human keratinoctyes

value: primary human neonatal keratinocytes

value: 3'READS+ in undifferentiated keratinocytes with CPSF1 siRNA


title: IL13-/- vs. Wild-Type


title: Colon_Control_004

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mus musculus Sure Print GE 4x44 v2 microarrays with oligonucleotide 45,220 probes (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Colon, control_replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Mouse colon and ileum samples were homogenized using the FastPrep instrument (MP Biomedicals), total RNA was isolated using RNAspin columns (Macherey-Nagel).

treatment_protocol: Three groups of mice (n=4) were randomized to receive distinct doses of ZnCl2 solutions (Sigma–Aldrich, St. Quentin–Fallavier, France) administered in the drinking water (Zn: 250 mg per kg body weight (mg/kg), 50 or 12 mg/kg) while a control group consisted in standard uncontaminated drinking water (n=4). Zn concentration is negligible in drinking water and its concentration is 25 mg/kg in standard chow (Diet A04C-10, Scientific Animal Food and Engineering, Augy, France). After 15 days of Zn treatment, mice are sacrificed and sections (0.5 /1cm in length) from the median colon and terminal ileum were collected and processed with RNA stabilization solution (RNA-later, Ambion, Life Technologies).

value: colon

tag: gender

value: female

tag: age

value: 7 weeks

tag: diet

value: 15 days of standard uncontaminated drinking water consumption


title: delSercga2_rep1

value: engineered

value: mature tRNA


title: Colon_Control_003

source_name: Colon, control_replicate 3


title: delSercga1_rep1