title: hiPSC-derived HE cells Day2 UK5099

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Fastq files were created and reads counted using Cellranger v3.1
Count matricies were created in Seurat v3.1
Genome_build: hg19
Supplementary_files_format_and_content: Text file with gene names in the rows and cells in the columns. Each entry gives a raw count.

source_name: hiPSCs

growth_protocol: The RB9-CB1 human iPSC line was co-cultured with mouse embryonic fibroblasts (MEFs, Millipore), passaged every six days and processed to form embryoid bodies (EBs). The hematopoietic differentiation protocol used in this study was previously described by Ditadi and Sturgeon, 2016. On day 8 or 10, EBs were singularized with 5-6 rounds of 5-minute incubations with TryPLE Express (Thermo Fisher Scientific). CD34+ cells were selected using the human CD34 MicroBead kit (Miltenyi Biotec) and stained with CD34-FITC, CD73-PE, VECad-PerCPCy5.5, CD38-PC7, CD184-APC, CD45-AF700, CD43-APCH7, GPA-eF450, CD90-BV605 and the viability marker 7AAD in order to sort HE (CD34+CD43-CXCR4-CD73-CD90+VECad+), EHT(CD34+CD43intCXCR4-CD73-CD90+VECad+) and HSC-like (CD34+CD43+CD90+CD38-) cells.

extract_protocol:
On day 1 and 2 (as indicated), cells were washed twice with PBS 0.04% UltraPure BSA and collected after a 2-minute incubation at 37°C with StemPro Accutase Cell Dissociation Reagent. Cells were spun down, resuspended in PBS 0.04% UltraPure BSA, counted (yield between 8,000-18,000 cells).
Library preparation was conducted according to the Chromium Single Cell 3’ Reagent kit v3 instructions (10x Genomics). Sequencing was performed on a NOVASeq 6000 from Illumina with the run parameters (28-8-0-91) recommended by 10x Genomics with a final loading concentration of 300 pM of the pooled libraries.

treatment_protocol: Sorted HE, EHT and HSC-like cells as well magnetically selected (Miltenyi Biotec) cord blood CD34+ cells were plated onto Matrigel (16 μg/cm2, Corning)-coated 96-well flat bottom plates in HE medium26 with 1% penicillin-streptomycin and kept in a humidified incubator at 37ºC, 5% CO2, 4% O2 overnight. The following day (day 0), wells were washed twice with PBS and fresh HE medium was added, together with UK5099 (10 µM) or DCA (3 mM), where indicated.

value: hiPSC-derived HE cells

tag: subculture period

value: 2 days


title: Sample_8831

status: Public on Nov 25 2021

type: SRA

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 Bd Laurier

country: France

institute: Université Laval

description:
Whole Metagenome Shotgun
See "Protocol 2" in the protocol section
WGS_species_count.csv

library_source: genomic

data_processing:
HiSeq BaseCalling
Whole Metagenome Reads were trimmed with Trimmomatic v0.37 (ILLUMINACLIP:2:30:1, TRAILING:30 and MINLEN:36)
WMS Read were assembled using RayMeta v2.3.1 (kmer = 31)
Quantification of the contigs was performed using kallisto v0.43.0
Blastn v2.4.0 against nt was used to assign taxonomy to the contigs
CSV file, Species raw count table, WGS_species_count.csv

molecule: genomic DNA

organism: Mus musculus

source_name: stool

extract_protocol:
DNA was isolated from fecal samples using the DNeasy PowerSoil Kit (QIAGEN)
Protocols 1 and 3: 15ng of DNA was used for an initial PCR amplification step of 25 cycles with specific bacterial 16S rRNA (V3-341F and V4-785R) hypervariable region oligos using Q5 High-Fidelity DNA polymerase (New England Biolabs, Whitby, Ontario, Canada). After purification with AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA), a second PCR amplification step of 8 cycles was performed to incorporate specific index adaptors for multiplexing. This step was followed by a purification step using AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA). The quality of the final libraries was examined with a DNA screentape D1000 on a TapeStation 2200 (Agilent Technologies, Santa Clara, CA, USA) and the quantification was performed with Quant-it HS (ThermoFisher Scientific, Canada) on a Victor3 plate reader fluorometer (PerkinElmer, Waltham, MA, USA). Protocol 2: DNA was quantified using QuantiFluor dye (Promega). Sequencing libraries were prepared using the Nextera Sample Preparation Kit (Illumina, San Diego, CA, USA) with 50 ng of purified DNA. Dual indices were added during library preparation. Libraries were validated using Agilent Bioanalyzer 2100 high sensitivity DNA chips (Agilent Technologies, Santa Clara, CA, USA) and were re-quantified with QuBit (ThermoFisher Scientific).
Protocols 1 and 3: 16S rRNA gene V3-V4 region. Protocol 2: Whole-genome shotgun sequencing

treatment_protocol: Protocol 1: Mice were administered ampicillin (1 g/l) in their drinking water and neomycin (10 mg/ml), metronidazole (10 mg/ml) and vancomycin (5 mg/ml) via oral gavage twice daily for 1 week. Twenty-four hours following the last antibiotic administration, mice were transferred to new cages and deprived of chow. Mice were fasted for 2 hours prior to receiving 250 µl of Moviprep at 30-minute intervals for a total of 5 administrations. Mice were then fasted for 6 additional hours before oral administration of 200 µl of fecal solution (fresh fecal pellets homogenized in sterile PBS 1× at 70–120 mg/ml and passed through a 70-µm filter) prepared using fecal pellets from donor WT or sPLA2-IIATGN mice. The administration of fresh fecal solution was repeated on the two following days. Arthritis was induced two weeks later, and its severity was monitored daily for 9 days before mice were euthanized. Feces were collected on days 0, 15 and 21 for microbiota composition assessment. Protocol 2: Mice were housed in an SPF animal facility for 8 months before their fecal microbiota was sequenced. Protocol 3: Mice were housed for up to 14 months in an Elite SPF+ animal facility and their fecal microbiota was sequenced at approximately 14 weeks and 14 months of age.

tag: strain

tag: genotype


title: hiPSC-derived HE cells Day2 DCA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: treatment

value: 3mM DCA


title: hiPSC-derived HE cells Day2-ctrl


title: Sample9.Horse.203203210051_R03C02

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

country: USA

institute: University of California, Los Angeles

description: genomic DNA methylation from tissue=Blood species=Horse

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to the the Beadchip HorvathMammalMethylChip40 using standard Illumina protocol

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

data_processing: SeSaMe normalization as described in W. Zhou et al 2018. PMID: 30085201

label: Cy3 and Cy5

organism: Equus caballus

source_name: Blood

label_protocol: Standard Illumina Protocol

growth_protocol: DNA extracted from tissues

extract_protocol: genomic DNA was extracted

treatment_protocol: Standard Illumina Protocol

tag: tissue

value: Blood

tag: tissuedetailed

value: Blood -Buffy Coat


title: Sample_8826


title: CD34+ cells from cord blood

source_name: Cord blood

value: CD34+ cells from cord blood

value: 1 day


title: Tfpi Knockdown 8

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA).
mRNA abundance was expressed in reads per kb of exon per million reads mapped.
A false discovery rate of 0.05 was used as a cutoff for significant differential expression.
Functional patterns of transcript expression were analyzed using Ingenuity Pathway Analysis (Qiagen).
Genome_build: human reference genome (GRCh37)

source_name: human trophoblast stem cell

extract_protocol:
Total RNA was isolated from cells and tissues using TRIzol reagent (cat no. 15596018, Thermo Fisher, Waltham, MA).
Complementary DNA libraries from total RNA samples were prepared with Illumina TruSeq RNA preparation kits (Illumina, San Diego, CA). Barcoded cDNA libraries were multiplexed and sequenced with a HiSeq2000 DNA sequencer (100-bp paired-end reads) using a TruSeq 200-cycle SBS kit (Illumina) at the KUMC Genome Sequencing Facility. Reads from *.fastq files were mapped to the rat reference genome (Ensembl Rnor_5.0.78) using CLC Genomics Workbench 12.0 (Qiagen, Redwood City, CA). mRNA abundance was expressed in reads per kb of exon per million reads mapped.  A false discovery rate of 0.05 was used as a cutoff for significant differential expression (euglycemia vs hyperglycemia).

value: human trophoblast stem cell

tag: shRNA

value: Tfpi shRNA


title: hippocampus cr biological rep1

type: RNA

city: Madison

first: Jamie

last: Barger

state: WI

address: 510 Charmany Drive, Suite 263

institute: LifeGen Technologies, LLC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on the Affymetrix Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: hippocampus, Calorie Restricted diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix)

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

tag: gender

value: male

tag: diet

value: calorie restricted


title: hiPSC-derived HSC-like cells

value: hiPSC-derived HSC-like cells


title: Sample8.Horse.203203210051_R02C02


title: Sample_8818

value: WT


title: Sample_8816


title: hippocampus cr biological rep4


title: hippocampus cr biological rep3


title: hiPSC-derived EHT cells

value: hiPSC-derived EHT cells


title: Sample7.Horse.203203210051_R01C02


title: Sample6.Horse.203203210051_R06C01


title: Sample_8815


title: hippocampus control biological rep4

source_name: hippocampus, Control diet

value: control


title: hippocampus cr biological rep2


title: Sample10.Horse.203203210051_R04C02


title: hiPSC-derived HE cells


title: hippocampus control biological rep5


title: hippocampus cr biological rep5


title: Sample5.Horse.203203210051_R05C01


title: hippocampus control biological rep3


title: Sample3.Horse.203203210051_R03C01


title: hippocampus control biological rep2


title: Sample4.Horse.203203210051_R04C01


title: hippocampus control biological rep1


title: Sample1.Horse.203203210051_R01C01


title: FG1907_06

status: Public on Nov 24 2021

city: Innsbruck

first: Gabriel

last: Schneebauer

address: Technikerstrasse 25

country: Austria

institute: University of Innsbruck

data_processing:
Illumina NovaSeq6000 RTA3 software used for basecalling: version 3.4.4
For comparison between the experimental groups, all forward reads were trimmed to a final size of 50 nt using fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit/index.html)
Reads were aligned to the draft genome sequence of the European eel (Henkel et al., 2012) FASTA with transcript sequences is available on the series record. using TopHat (version 2.0.13) (Trapnell et al., 2009)
The resulting files were filtered using SAMtools (version 1.2) (Li et al., 2009) to exclude secondary alignment of reads
Aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.6.1p1) (Anders et al., 2015)
As a correction scaling factor, library size estimates, determined using the R/Bioconductor (release3.3.2) package DESeq (Anders and Huber, 2010), were employed.
Genome_build: Anguilla_anguilla_genome_v1_09_nov_10 (GCA_000695075.1) (Henkel et al., 2012) FASTA with transcript sequences is available on the series record.
Supplementary_files_format_and_content: Microsoft Office Excel file (.xlsx) with the following columns: id; Name; Best hit; Description; Alternate description; Min e-value; Similarity; GO molecular function; GO biological process; GO cellular component; baseMean; baseMeanA; baseMeanB; foldChange; log2FoldChange; pval; padj; sample x; sample y; sample z

organism: Anguilla anguilla

source_name: rete mirabile tissue

growth_protocol: European eels were caught in Lake Constance by local fishermen and kept in freshwater for a few days.

extract_protocol:
Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 0.5 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep.

treatment_protocol: Eels were anesthetized with 2-phenoxyethanol (1 ml*L^-1), and subsequently decerebrated and spinally pithed. The body wall was opened ventrally, the swimbladder was exposed and carefully freed from connective tissue. Artery and vein at the heart pole of the retia mirabilia were carefully separated and occlusively cannulated using PE50 and PE60 catheters, respectively. Rete vessels were perfused with heparinized (100 i.u*mL^-1) saline solution containing (in mmol*L^-1) NaCl, 129; KC1, 5; MgSO4, 0.9; CaCl2, 1.1; glucose, 15. Perfusion of rete vessels was controlled by continuous binocular inspection and both retia mirabilia were dissected immediately after total clearance of blood cells. Half of the tissue was blotted dry on absorbent paper, shock frozen in liquid nitrogen and stored at -80°C until further use for analysis of protein expression. The second half was transferred into 1 ml RNAlater™ solution and immediately shock frozen in liquid nitrogen for analysis of the transcriptome.

tag: developmental stage

value: yellow eel

value: rete mirabile


title: FG1907_04


title: FG1907_03

value: silver eel


title: Sample2.Horse.203203210051_R02C01


title: FG1907_01


title: Lung Nfat5fl/fl hypoxia mouse C

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression of RNA extracted from lung of Nfat5fl/fl mouse in hypoxia conditions

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: Lung of Nfat5fl/fl mouse in hypoxia conditions

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Standard husbandry conditions according to GV solas suggestions

extract_protocol: Immediate ectomy and freezing of lungs after sacrificing the animals. RNA was extracted by RLT buffer (Cat. no. 79216, Qiagen)

treatment_protocol: Exposure to normoxia of hypoxia (10% oxygen) for 7 days

value: 1 lung lobe

tag: condition

value: hypoxia


title: Nfat5(SMC)-/- mouse4

description: Gene expression of lung lobe of Nfat5(SMC)-/- mouse

source_name: lung lobe of Nfat5(SMC)-/- mouse

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

treatment_protocol: Exposure to hypoxia (10% oxygen) for 7 days


title: Lung Nfat5fl/fl hypoxia mouse D


title: Nfat5fl/fl mouse4

description: Gene expression of lung lobe of Nfat5fl/fl mouse

source_name: lung lobe of Nfat5fl/fl mouse

value: Exposure to hypoxia (10% oxygen) for 7 days


title: Nfat5(SMC)-/- mouse2


title: Nfat5fl/fl mouse1


title: FG1907_02


title: Lung Nfat5fl/fl normoxia mouse H

description: Gene expression of RNA extracted from lung of Nfat5fl/fl mouse in normoxia conditions

source_name: Lung of Nfat5fl/fl mouse in normoxia conditions

value: normoxia


title: Nfat5(EC)-/- mouse 1

description: Gene expression of lung from Nfat5(EC)-/- mouse exposed to 10% oxygen for 7 days

treatment_protocol: Hypoxia, 10% oxygen, 7 days

value: 10% oxygen for 7 days


title: Nfat5fl/fl mouse2


title: Lung Nfat5fl/fl normoxia mouse F


title: Nfat5(SMC)-/- mouse1


title: Nfat5(EC)-/- mouse 4

source_name: lung from Nfat5(EC)-/- mouse exposed to 10% oxygen for 7 days


title: Lung Nfat5fl/fl normoxia mouse I


title: Nfat5fl/fl mouse 4

description: Gene expression of lung from Nfat5fl/fl mouse exposed to 10% oxygen for 7 days


title: Lung Nfat5fl/fl hypoxia mouse A


title: Nfat5(EC)-/- mouse 3


title: Nfat5fl/fl mouse 3

source_name: lung from Nfat5fl/fl mouse exposed to 10% oxygen for 7 days


title: Nfat5fl/fl mouse 1


title: Lung Nfat5fl/fl hypoxia mouse B


title: Lung Nfat5fl/fl normoxia mouse G


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 66), biological rep2

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

hyb_protocol: standard Affymetrix protocol

scan_protocol: The GeneChip Scanner 3000

data_processing: Transcriptome Analysis Console Software; Normalization: SST-RMA; The significant genes were ranked by fold-change with a cutoff of 2 and the ANOVA p-value less than 0.05 according to Affymetrix.

source_name: Mouse colonic mucosal tissues before administration of AOM/DSS (Day 0)

label_protocol: Microarray was performed at the Genomics Core Facility at National Health Research Institute (Miao-Li, Taiwan).

growth_protocol: Specific pathogen free BALB/c mice (6 to 8 weeks of age) purchased from the National Applied Research Laboratories (NARL) were kept in temperature-controlled rooms (23 ± 2°C) with 12 h light-dark cycles. Mice were fed standard chow and water ad libitum.

extract_protocol: Total RNA was isolated by Trizol, according to the manufacturer’s instructions.

treatment_protocol: Mice were subjected to azoxymethane (AOM)/dextran sodium sulfate (DSS) for induction of colorectal cancers.

value: BALB/c

tag: age

value: 6 to 8 weeks

tag: treatment/timepoint

value: colonic mucosal tissues


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 66), biological rep1


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 66), biological rep3


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 56), biological rep3


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 56), biological rep2


title: A549_shctrl

city: Dalian

first: Wang

last: Yang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

data_processing:
Library strategy: Ribo-seq
Ribo-seq data were analyzed according to Calviello et al
reads aligning to rRNA sequences were removed using Bowtie
Unaligned Ribo-seq reads and RNA-seq reads were aligned to GENCODE comprehensive gene annotation  using STAR (version 2.4.2)
Gene expression was estimated from RSEM  (version 1.3.1, default parameters) using transcriptome alignments and is reported in transcripts per kilobase million (TPM)
Differential expression analysis was performed by DESeq2
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: The gene expressiong matrix from Ribo-seq

source_name: lung cancer cells

growth_protocol: A549 cells were cultured in F12K medium containing 10% FBS.

extract_protocol:
After treated with cycloheximide (CHX, 100 μg/mL) for 15min, cells were washed with CHX/PBS and lysed in polysome lysis buffer (100 mmol/L KCl, 5 mmol/L MgCl2, 10 mmol/L HEPES, 1 mmol/L DTT, 100μg/mL CHX, supplemented with protease inhibitor, RNase inhibitor, and DNase I, pH=7.4), followed by shearing 20 times with 26-gauge needles gently. Lysates were cleared by centrifugation. 10% of cleared lysate was retained as input for total RNA extraction. The remained lysates from the polysome profiling procedure were treated with RNase I (Thermo Fisher Scientific, Waltham, USA) at room temperature for 5 min to obtain ribosome-protected mRNA fragments (RPF). The reaction was stopped by adding SUPERaseIn RNase Inhibitor (Invitrogen, Carlsbad, USA). Subsequently, lysates were loaded onto the 12mL 10-50% sucrose gradients, and ultracentrifuged for 3 h at 35,000rpm, 4˚C on an SW41Ti rotor (Beckman Coulter). 0.75mL fractions were collected using a Brandel Density Gradient Fractionation System with a 254 nm filter lens. Fractions containing 80S ribosome particles were combined and underwent RNA clean-up by TriZol reagent.
The RNA sequencing library was prepared according to Ingolia et al.with some modifications. In brief, rRNAs were depleted in both total RNA and RPF RNA samples with the Ribo-Zero Gold kit (Illumina, San Diego, USA). Total RNA was fragmented as input control. Subsequently, the ends of both the RPF RNA and fragmented total RNA samples were repaired prior to 3’ and 5’ adapter ligation, as described in Illumina Small RNA Library Prep Reference Guide. RNA samples were reverse transcribed by Superscript III reverse transcriptase (Invitrogen, Carlsbad, USA). cDNA libraries then were gel purified and amplified by limited-cycle PCR with index primers. Libraries were cleaned up and subjected to next-generation sequencing on Illumina Hiseq X10 under the PE150 sequencing model.

treatment_protocol: We generated RBMS1 stably depleted and expressed A549 lung cancer cells

tag: cell line

value: human lung cancer cells

value: RBMS1 knockdown ctrl


title: A549_sh1196

value: RBMS1 knockdown


title: PBt_5

city: Hangzhou

first: Xingyuan

last: Xu

address: No.79 qingchun road

institute: the First Affiliated Hospital, Zhejiang University school of medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: naïve T cells

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq X-ten at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PBMC

value: untreated

tag: disease

value: HCC


title: A549_pcdh

value: RBMS1 overexpress ctrl


title: A549_sh1088


title: 3651_hpNPC_d5

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 or panTro5 as appropriate using BWA-mem
RNA-seq data were analyzed with kallisto using hg19 or panTro5 as appropriate
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: hg19 for Homo sapiens samples and panTro5 for Pan troglodytes samples.
Supplementary_files_format_and_content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq

organism: Pan troglodytes

source_name: PT Rep 1 (3651 line)

growth_protocol: The iPSC lines were expanded in feeder-free, serum-free mTeSR™1 medium (STEMCELL Technologies). Cells were passaged ~1:10 at 80% confluency using ReLeSR (STEMCELL Technologies) and small cell clusters (50–200 cells) were subsequently plated on tissue culture dishes coated overnight with Geltrex™ LDEV-Free hESC-qualified Reduced Growth Factor Basement Membrane Matrix (Fisher-Scientific).

extract_protocol: 50000 cells per condition were processed as described in the original ATAC-seq protocol paper (Buenrostro et al 2013)

treatment_protocol: The stem cells were treated with a previously published media for differentiation into hippocampal intermediate progenitors (Yu et al 2014). This consists of 1:1 DMEM/F12 supplemented with N2, B27, Noggin, Cyclopamine, DKK-1 and SB43154 and PennStrep antibiotic. The cells were exposed to this media for five days prior to collection.


title: 8861_hpNPCd5_RNA

source_name: PT Rep 3 (8861 line)

extract_protocol:
Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library


title: 8861_hpNPC_d5


title: 3651_hpNPCd5_RNA_REP


title: 40280_hpNPCd5_RNA_REP

source_name: PT Rep 2 (40280 line)


title: A549_R1A

value: RBMS1 overexpress


title: 40280_hpNPC_d5


title: ILC2_T3

source_name: ILC2 cells

value: liver


title: 3651_hpNPCd5_RNA


title: 40280_hpNPCd5_RNA


title: ILC2_T2


title: ILC2_T1


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 46), biological rep3


title: Mouse colonic mucosal tissues before administration of AOM/DSS (Day 0), biological rep2


title: Mouse colonic mucosal tissues before administration of AOM/DSS (Day 0), biological rep3


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 46), biological rep1


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 56), biological rep1


title: Mouse colonic mucosal tissues after administration of AOM/DSS (Day 46), biological rep2


title: ILC2_N3


title: Mouse colonic mucosal tissues before administration of AOM/DSS (Day 0), biological rep1


title: 8861_hpNPCd5_RNA_REP


title: PBt_4


title: ILC2_N1


title: n2_control_3

city: Saint Louis

first: Ciro

last: Cubillas Ramirez

state: Missouri

address: 4577 McKinley, Campus Box 8103, 3607 Cancer Research Building

department: Developmental Biology

institute: Washington University in St Louis, School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultipler written in python
Fastq files were aligned with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and annotated with Ensembl Biomart
Genome_build: Ensembl WBcel235.76
Supplementary_files_format_and_content: Gene counts in tab-delimitted text MS Excel format

organism: Caenorhabditis elegans

source_name: wild type 0mM Cd 2

growth_protocol: Mixed-stage populations of the wild type and hizr-1 strains were collected by washing and then cultured 16-18h at 20oC on NAMM dishes seeded with 10X concentrated E. coli OP50 and supplemented with 0mM and 100 mM Cadmium chloride (CdCl2). For this purpose, 80 NGM plates seeded with 1X E. coli OP were used. A half of the plates containing 3 C. elegans wild type L4 stage hermaphrodites were grown for 4 days at 20oC, the other 40 plates contained 3 C. elegans hizr-1 L4 stage hermaphrodites and were grown in parallel. After these 4 days, the mixed-stage populations were collected by washing them with M9 buffer and then cultured on the same number of NAMM plates seeded with 10X E. coli OP50 supplemented with either 0mM CdCl2 (40 plates) or with 100mM CdCl2 (40 plates) as follows: one group of 20 wild type NGM plates were transferred into NAMM supplemented with 100mM CdCl2 while the other 20 wild type NGM plates were transferred into NAMM without supplemented CdCl2. This same procedure was followed with the hizr-1 loss-of-function mutant allele, am286. The animals were grown for 16-18h at 20oC and then collected by washing with M9; animals from 10 plates were pooled into one biological sample, so duplicated samples for wild type and hizr-1 mutant coming from the NAMM 0mM and NAMM 100mM supplemented CdCl2 were used to extract RNA.

extract_protocol:
Trizol extraction, in-column DNAase treatment followed by Rneasy column purification
Ribo-Zero v1

treatment_protocol: Noble Agar Minimal Medium plates supplemented with or without 100mM Cadmium chloride (CdCl2)

value: whole animal

value: wild type


title: n2_control_2

source_name: wild type 0mM Cd 1


title: n2_100_cd_9

source_name: wild type 100mM Cd 2


title: n2_100cd_8

source_name: wild type 100mM Cd 1


title: am286_100cd_19

source_name: hizr-1 100mM Cd 1

value: N2 derivative


title: am286_control_14

source_name: hizr-1 0mM Cd 2


title: am286_control_13

source_name: hizr-1 0mM Cd 1


title: am286_100cd_20

source_name: hizr-1 100mM Cd 2


title: SMF3

city: Aachen

first: Lin

last: Gan

address: Pauwelsstr. 30

department: IZKF

institute: University Hospital Aachen

hyb_protocol: Overnight hybridization of end-labelled cDNA was applied on the HTA 2.0 Human (Affymetrix) arrays for 16 hours, at 60 rpm, at 45ºC in a Hybridization Oven 645 (Affymetrix). Washing and staining of the arrays were done on an Affymetrix 450 Fluidics Station using the protocol FS450_0001.

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the manufacture manual

data_processing: Batch correction was applied using sva and Combat. Downstream analysis was performed in R. Data were normalized with signal space transformation (SST) in conjunction with robust multiple-array (RMA) average normalization method (SST-RMA) with Affymetrix Expression console.

source_name: CD34+ cells

label_protocol: Total RNA was process with Affymetrix GeneChip WT Plus Reagent Kit.

extract_protocol: Blood and bone marrow mononuclear cells from MPN patients were isolated using Ficoll density gradient centrifugation. Enrichment of the CD34+ cell population was performed by magnetic cell separation (MACS) with the CD34 MicroBead Kit, human (Miltenyi). RNA was isolated using the RNeasy Micro Kit (QIAGEN).

value: bone marrow

tag: Sex

value: F

tag: diagnosis

value: pET-MF


title: HC8

value: peripheral blood

value: healthy control


title: PMF5

value: M

value: PMF


title: PMF4


title: SMF1

value: pPV-MF


title: PMF8


title: HC9


title: PMF1


title: HC5


title: PMF3


title: HC7


title: PMF10


title: HC6


title: PV10

value: PV


title: PMF2


title: PMF9


title: PV3


title: HC4


title: PV8


title: PV9


title: PV7


title: SMF5


title: SMF2


title: PV11


title: PV5


title: PMF7


title: PV4


title: HOM7_LSK

city: Rotterdam

first: Roger

last: Mulet-Lazaro

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were aligned against mm10 using TopHat 2.0.4 with parameters --max-insertion-length 5 --max-deletion-length 5 --output-dir Sample_HOM1_CMP/tophat_HOM1_CMP --bowtie1 --num-threads 1 --transcriptome-index /hematology/ucsc/mm10/bowtie/refGene --mate-inner-dist 147 --mate-std-dev 114 --segment-length 25 --fusion-search --fusion-min-dist 100000
Raw counts were computed with HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: One table for each sample containing raw gene counts for every gene

source_name: Hematopoietic stem cells

extract_protocol:
Total sample RNA was extracted using Trizol with Genelute LPA (Sigma) as a carrier and SMARTer Ultra Low RNA kit for Illumina Sequencing (Clontech) was used for cDNA synthesis according to the manufacturer’s protocol
cDNA was sheared with the Covaris device and processed according to the TruSeq RNA Sample Preparation v2 Guide (Illumina). Amplified sample libraries were subjected to paired-end sequencing (2 x 75 bp).

tag: strain

value: Bone marrow

value: Cebpa +42kb enhancer -/-

value: Hematopoietic stem cells


title: HOM1_LSK

tag: genotype


title: WT8_CMP

source_name: Common myeloid progenitors

value: Cebpa +42kb enhancer WT

tag: cell type

value: Common myeloid progenitors


title: HOM2_LSK


title: WT6_LSK


title: PV2


title: ET7

value: ET


title: MEF_cells_Ribo-seq_PateamineA_8h

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

data_processing:
The adaptor and low quality bases of all sequencing data were removed by Cutadapt.
For Ribo-seq, the adaptor CTGTAGGCACCATCAAT was used. The first SIX nucleotides (3 randome nucleotides + 3-word barcode sequence) and the last FOUR nucleotides were removed (3 random nucleotides). PCR duplicates were removed. PCR duplicates were defined as the reads with exact same random sequences at both sides. More details can be found in PMID: 27450428. For 80S-seq, 40S-seq and eIF3-seq, the adaptor was set as AAAAAAAAAA. The trimmed reads were aligned to mouse (human) transcriptome, using STAR with default parameters.
Genome_build: GRCm38/GRCh38
Supplementary_files_format_and_content: For Ribo-seq, the processed data files are tab separated read count. The first column is gene name, and the second column is footprint count on mRNAs. For 80S-seq, 40S-seq and eIF3-seq,  the processed data files are read count at individual sites of gene, which were seperated by comma. The first column is chromosome name, the second column is strand of the gene, the third column is gene name. The others are read count at individual sites of the gene. The read count section was seperated by colon. The first value is the genomic coordinate, the second value is the length of footprint, the third value is the count of footprint.

source_name: MEF Ribo-seq PateamineA treatment 8h

growth_protocol: MEF and HEK293 cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with 10% fetal bovine serum (FBS).

extract_protocol:
For cell lysates, at least four 10 cm dishes of cells were harvested in 400 µl ice-cold polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2). Cells were then disrupted by vortexing six times for 20s using lysing matrix D (Fisher), followed by a 40 s interval each time on ice, then centrifuged at 12,000g, 4 °C for 10 min. Samples were then subjected to sucrose gradient sedimentation. Sucrose solutions were prepared in polysome buffer (10 mM HEPES, pH 7.4, 100 mM KCl, 5 mM MgCl2 and 2% Triton X-100). A 15%-45% (w/v) sucrose density gradients were freshly prepared in SW41 ultracentrifuge tubes (Backman) using a Gradient Master (BioComp Instruments). 500 µl of supernatant from cell lysates prepared as described above was loaded onto sucrose gradients followed by centrifugation for 2.5 hr at 32,000 rpm, 4 °C in a SW41 rotor. Separated samples were fractionated at 1.5 ml min-1 through an automated fractionation system (Isco) that continually monitors OD254 values. Ribosome fractions separated by sucrose gradient sedimentation were pooled and digested with E. coli RNase I (Ambion, 750 U per 100 A260 units) by incubation at 4 °C for 1 hr. SUPERase•In (50 U per 100 U RNase I) was then added into the reaction mixture to stop the digestion. Total RNA was extracted using TRIzol LS reagent.
Fragmented RNAs were separated on a 15% polyacrylamide TBE-urea gel (Invitrogen) and visualized using SYBR Gold (Invitrogen). Selected regions of the gel corresponding to 20-70 nt (for 40S-seq and eIF3-seq) or 25-35 nt (for Ribo-seq) were excised. The gel slices were disrupted by using centrifugation through the holes at the bottom of the tube. RNA fragments were dissolved by soaking overnight in 400 µl RNA gel elution buffer (300 mM NaOAc pH 5.5, 1 mM EDTA, 0.1 U/µl SUPERase•In). The gel debris was removed using a Spin-X column (Corning), followed by ethanol precipitation.
Purified RNA fragments were re-suspended in Nuclease-free water, then dephosphorylated for 1 hr at 37 °C in a 15 µl reaction (1× T4 polynucleotide kinase buffer, 10 U SUPERase•In and 20 U T4 polynucleotide kinase). Dephosphorylated RNA fragments were precipitated using ethanol and re-suspended in Nuclease-free water. 0.15 μg linker (rApp/NNNNCTGTAGGCACCATCAAT/3ddC) then was added to the RNA fragments, heated at 70 °C for 90 s and then cooled to room temperature, followed by ligation for 3 hr at at 22 °C in a 20 µl reaction (1× T4 Rnl2 reaction buffer, 10 U SUPERase•In, 15% PEG8000 and 20 U T4 RNA ligase 2 truncated). The reaction was heat inactivated at 80 °C for 10 min and the products were separated on a 10% polyacrylamide TBE-urea gel and selected regions in the gel corresponding to 45-95 nt (for 40S-seq and eIF3-seq) or 60-70 nt (for Ribo-seq) were excised. RNA fragments were dissolved by soaking overnight in 400 μl RNA gel elution buffer. RNA fragments were purified from RNA gel elution buffer as described earlier and re-suspended in Nuclease-free water. For reverse transcription, the following oligos containing barcodes were used:
(Phos)CTANNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)AGCNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)ATTNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
(Phos)CCGNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC
(SpC18)CACTCA(SpC18)TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG
where Phos represents phosphorylation, NNN represents random sequence, SpC18 represents Hexa-ethyleneglycol spacer.
The linker ligated RNA sample was mixed with 0.5 mM dNTP and 2.5 mM synthesized primer and incubated at 75 ° C for 3 min, followed by incubation on ice for at least 1 min. The reaction master mix was then added with 20 mM Tris (pH 8.4), 50 mM KCl, 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT and 200 U SuperScript III. Reverse transcription reaction was performed according to the manufacturer’s instruction. Reverse transcription products were separated on a 10% polyacrylamide TBE-urea gel. Corresponding region was excised, which was expected to be approximately 200 nt. The first-strand cDNA products were recovered in DNA gel elution buffer (300 mM NaCl, 1 mM EDTA), then purified and re-suspended in Nuclease-free water as described earlier.
cDNA products were circularized in 20 μl of reaction containing 1×CircLigase buffer, 2.5 mM MnCl2, 1M Betaine and 100 U CircLigase II (Epicentre). Circularization was performed at 60 °C for 1 hr and the reaction was heat inactivated at 80 °C for 10 min.

tag: cell line/type

value: Mouse embryonic fibroblasts

tag: genotype/treatment

value: PateamineA treatment 8h

tag: molecule subtype

value: Ribosome associated RNA


title: MEF_cells_Ribo-seq_Hippuristanol_2h

source_name: MEF Ribo-seq Hippuristanol treatment 2h

value: Hippuristanol treatment 2h


title: MEF_cells_Ribo-seq_Hippuristanol_8h

source_name: MEF Ribo-seq Hippuristanol treatment 8h

value: Hippuristanol treatment 8h


title: WT6_CMP

tag: tissue


title: HOM7_CMP


title: HOM1_CMP


title: HOM2_CMP


title: WT8_LSK


title: WT1_LSK


title: MEF_cells_Ribo-seq_Control_rep2

source_name: MEF Ribo-seq control

value: control


title: ET9

value: bone marrow

value: triple-negative

value: F


title: PV1

value: peripheral blood

value: M


title: ET4


title: ET8


title: ET1


title: MEF_cells_Ribo-seq_Control_rep1

source_name: MEF Ribo-seq Control

value: Control


title: ET2


title: PV12

value: PV


title: MEF_cells_Ribo-seq_eIF4A1_KD_rep2

source_name: MEF Ribo-seq eIF4A1 knockdown

value: eIF4A1 knockdown


title: WT1_CMP

value: Bone marrow

value: Cebpa +42kb enhancer WT


title: MEF_cells_Ribo-seq_eIF4A1_KD_rep1


title: MEF_cells_Ribo-seq_PateamineA_2h

source_name: MEF Ribo-seq PateamineA treatment 2h

value: PateamineA treatment 2h


title: WT

city: Baltimore

first: Peter

last: Espenshade

state: Maryland

address: 725 N Wolfe St., Physiology 107

department: Cell Biology

institute: Johns Hopkins University School of Medicine

data_processing:
Illumina's CASAVA 1.8.2 was used to convert BCL files to FASTQ files. Default parameters were used.
rsem-1.2.09 was used for running the alignments as well as generating gene and transcript expression levels. The "rsem-calculate-expression" module was used with the following options: bowtie-chunkmbs 200, calc-ci, output-genome-bam, paired-end, forward-prob.
The data was aligned to the "mm10" reference genome.
rsem-1.2.09's EBSeq was used for Differential Expression analysis. "rsem-run-ebseq" and "rsem-control-fdr" scripts probided by RSEM were used to run EBSeq. Apart from "FDR_rate" of 0.05, default parameters were used.
Genome_build: mm10
Supplementary_files_format_and_content: matrix table with TPM values for every gene and every sample

source_name: Liver

extract_protocol:
Livers were harvested, snap frozen with liquid nitrogen, and RNA was harvested using RNA STAT-60 reagent (Amsbio). DNase digestion was performed on column with an RNAeasy Kit (Qiagen) according to manufacturer's instructions. RNA concentration was estimated with a NanoDrop (Thermo Fisher). Equal masses of RNA (2.5 ug) from mice of the same genotype were pooled to create one sample per genotype. Library preparation was completed with an Illumina TruSeq Stranded Total RNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: 8-12 weeks

value: WT


title: KO

value: Pgrmc1 KO (Pgrmc1 -/Y)


title: LogPhase-B

city: New York

first: Kohta

last: Saito

state: NY

address: 413 E 69th St

institute: Weill Cornell Medicine

description: Logarithmically growing cells in nutrient rich media

data_processing:
10-20 x 106 paired-end reads were obtained for each sample replicate on an Illumina HiSeq 2500.
Post-run de-multiplexing and adapter removal were performed and fastq files were inspected using fastqc
Trimmed fastq files were then aligned to the reference genome
Bam files were sorted and merged using SAMtools
Gene counts were obtained using featureCounts from the Bioconductor Rsubread package; differentially expressed genes were identified using the DESeq2 R package
Genome_build: ASM107861v1
Supplementary_files_format_and_content: text files for differentially expressed genes among conditions, with FPKM data. Note that the counts were aligned to Mbovis as above, but the annotations here are to H37Rv to aid in the needed data analysis for the manuscript.

organism: Mycobacterium tuberculosis variant bovis

source_name: cell culture

growth_protocol: see samples section

extract_protocol:
After incubation in RNAprotect, samples were lysed in TRIzol (Invitrogen) with bead beating, and RNA was extracted using RNeasy mini kit (Qiagen) as per manufacturer protocol.
Sample libraries were prepared for RNA-seq using the Ribo-Zero Magnetic Bacterial kit (Epicentre) in conjunction with TruSeq Stranded Total RNA kit (Illumina).

treatment_protocol: see samples section

tag: culture media

value: 7h9 with glycerol, OADC, and tyloxapol

tag: treatment


title: LogPhase-A


title: 3RC259Lb

city: Lausanne

first: Ana

last: Rodriguez Sanchez-Archidona

state: Vaud

address: Genopode building - Quartier Sorge

department: CIG

country: Switzerland

institute: University of Lausanne

data_processing:
Reads were mapped and quantified with STAR-2.5.3a software (18) usingM.musculus-mm15 as reference genome and GRCm38.83 from ENSEMBL as the reference annotation index.
Counts were filtered, excluding those genes with less than one count per million in nine libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.
Genome_build: M.musculus-mm15 reference genome.
Supplementary_files_format_and_content: Normalized matrix in log2 were raw counts were filtered, excluding those genes with less than one count per million in nine libraries, and normalized using trimmed mean normalization method (TMM) with 'edgeR'.

extract_protocol:
Total RNA from liver, soleus muscle and visceral adipose tissue was extracted using the RNeasy Plus micro kit (Qiagen, Hombrechtikon, Switzerland).
Integrity of RNA was verified on a Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, CA 95051, USA) and all preparations had a RNA quality number (RQN) between 8.2 and 9.3. RNA-seq libraries were prepared using 250ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents
Sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. A sequencing depth of 27 to 46 million reads using 100bp single reads was used.

value: BALB/cJ

tag: diet

value: RC

tag: time


title: 3RC255V

source_name: Visceral adipose tissue

value: Visceral adipose tissue


title: 3RC259L


title: 3RC252L


title: Starved-B

description: Nutrient starved for 2 weeks

value: Phosphate buffered saline with 0.02% tyloxapol


title: 3RC259La


title: 3RC252V


title: 3RC255S

source_name: Soleus muscle

value: Soleus muscle


title: 3RC251V


title: 3RC255L


title: 3RC251S


title: 3RC251L


title: Starved-A

description: Nutrient starved for 2 weeks


title: 3RC230V


title: 3RC230Lb


title: ILC2_N2

source_name: ILC2 cells

value: liver

value: untreated

value: HCC


title: 3RC230La


title: RIF10-C

description: Nutrient starved for 2 weeks, followed by 5 days of indicated treatment

value: Rifampin 10 microM


title: 3RC259S


title: LogPhase-C


title: 3RC252S


title: 3RC230L


title: 3RC228V


title: Starved-C

description: Nutrient starved for 2 weeks


title: 3RC259V


title: 3RC228S


title: RIF10-A


title: CoIP_pProQR80A_rep1

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

description:
The bacteria were grown in LB to OD600= 2.0 before collecting 50ODs. The bacterial pellets were resuspended in lysis buffer ((20 mM Tris pH8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1unit/ul DNase I) and lysed using the Retsch MM200 (0.1 mm glass beads; 30Hz for 10min). The cleared lysate was then incubated with 25 µl (1 µl/2 OD600 nm of cells) of monoclonal anti-FLAG M2 (Sigma #F1804) at 4°C with rotation for 30 min. The sample was then added to 75 µl of pre-washed Protein A sepharose beads (Sigma-Aldrich) and further incubated with rotation at 4 °C for an additional 30 min. The beads were washed with 500 µl of lysis buffer for five times and finally resuspended in 532 µl of lysis buffer for elution of ProQ 3xFLAG variants and co-immunoprecipitated RNA. For RNA elution, co-immunoprecipitated RNA was extracted by phenol:chloroform:isoamyl alcohol (P:C:I) (25:24:1, pH 4.5, Roth) extraction. The purified RNA samples were treated by DNase I and subsequently purified by P:C:I extraction. Samples were resuspended in H2O to a final concentration of 1 OD/µl for elution samples and 0.1 OD/µl for lysate, flowthrough and wash.
CoIP_pProQR80A_1_forward.wig
CoIP_pProQR80A_1_reverse.wig

data_processing:
The raw reads were processed with FastQC and adapters removed. Mapping and read counting was done with READemption pipeline 0.4.3. Normalization and enrichment analysis was done with edgeR version 3.28.1. To calculate normalization factors the trimmed means of M values (TMM) method was used between pulse expression and empty vector libraries.    All features that had more than 50 read counts in at one group were included in the analysis.
Genome_build: NC_016810.1
Supplementary_files_format_and_content: Mutational Scanning: counts of individual mutant (.xlsx); CoIP: coverage files (.wig)

source_name: German Collection of Microorganisms and Cell Cultures GmbH

extract_protocol: Library preparation from co-immunoprecipitated RNA samples were carried out with NEBNext Multiplex Small RNA Library Prep Set (New England Biolabs) that allow sequencing in Illumina platforms. The library preparation was carried out in a thermocycler and manufacturer’s guidelines were followed with minor modifications. Briefly, 3.5 l of RNA was mixed with 1 l of 3’ SR Adaptor (1:10 diluted) and incubated at 70°C for 2 min. The tubes were transferred to ice and then, 6.5 l of 3’ ligation mix (5 l of 3’ ligation buffer, 1.5 l of 3’ enzyme mix) were added to each tube and incubated at 25°C for 1 hour (without lid heated). 2.75 l of SR mix (2.5 l of water, 0.25 l of SR RT primer, 1:10 diluted) was added to the samples and incubated as follows: 75°C for 5 min (lid 85°C), 37°C for 15 min (no lid heated), 25°C for 15 minutes (no lid heated). For ligation of the 5’ adaptor the 5’ ligation mix was added to each sample (0.5 l of 5’ ligation reaction buffer, 1.25 l 5’ ligation enzyme mix and 0.5 l of denatured 5’adaptor (1:5 diluted)) and incubated at 25°C for 1 hour (no lid heated).   To generate the first strand of cDNA 5 l of the cDNA mix (4 l first strand buffer, 0.5 l Murine RNase inhibitor, 0.5 l SuperScript II RT) was added to each reaction and incubated at 50°C for 1 hour followed by 15 min at 70°C to inactivate the RT enzyme. 10 l of cDNA was PCR amplified with barcoded NEB Index primer (1:10 diluted) and SR primer (1 :10 diluted) in a 50 l volume reaction (25 l LongAmp Taq 2x mix, 12.5 l nuclease-free water, 1.25 l SR primer, 1.25 l index primer). The following PCR program was carried out: 30s at 94°C for initial denaturation, 15s at 94°C, 30s at 62°C and 70°C for 16 or 20 cycles, and a final elongation of 5 min at 70°C. PCR products were purified via AMPure XL beads. The distribution of the library and concentration of library DNA was determined by DNA bioanalyzer and a DNA Qubit measurement respectively. Amplified cDNAs from different libraries were pooled and sequenced on an Illumina NextSeq 500 platform at the Core Unit SysMed at the University of Würzburg.

value: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 delta Lon

tag: sample type

value: CoIP sample - ProQ R80A - replicate 1


title: RIF100-A

value: Rifampin 100 microM


title: 3RC209V


title: DMSO-A

value: 1% DMSO


title: CoIP_pProQ_rep2

description:
The bacteria were grown in LB to OD600= 2.0 before collecting 50ODs. The bacterial pellets were resuspended in lysis buffer ((20 mM Tris pH8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1unit/ul DNase I) and lysed using the Retsch MM200 (0.1 mm glass beads; 30Hz for 10min). The cleared lysate was then incubated with 25 µl (1 µl/2 OD600 nm of cells) of monoclonal anti-FLAG M2 (Sigma #F1804) at 4°C with rotation for 30 min. The sample was then added to 75 µl of pre-washed Protein A sepharose beads (Sigma-Aldrich) and further incubated with rotation at 4 °C for an additional 30 min. The beads were washed with 500 µl of lysis buffer for five times and finally resuspended in 532 µl of lysis buffer for elution of ProQ 3xFLAG variants and co-immunoprecipitated RNA. For RNA elution, co-immunoprecipitated RNA was extracted by phenol:chloroform:isoamyl alcohol (P:C:I) (25:24:1, pH 4.5, Roth) extraction. The purified RNA samples were treated by DNase I and subsequently purified by P:C:I extraction. Samples were resuspended in H2O to a final concentration of 1 OD/µl for elution samples and 0.1 OD/µl for lysate, flowthrough and wash.
CoIP_pProQ_2_forward.wig
CoIP_pProQ_2_reverse.wig

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

value: CoIP sample - ProQ WT - replicate 2


title: RIF100-B


title: RIF10-B


title: 3RC208V


title: 3RC211S


title: CoIP_WT_VC_rep1

description:
The bacteria were grown in LB to OD600= 2.0 before collecting 50ODs. The bacterial pellets were resuspended in lysis buffer ((20 mM Tris pH8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1unit/ul DNase I) and lysed using the Retsch MM200 (0.1 mm glass beads; 30Hz for 10min). The cleared lysate was then incubated with 25 µl (1 µl/2 OD600 nm of cells) of monoclonal anti-FLAG M2 (Sigma #F1804) at 4°C with rotation for 30 min. The sample was then added to 75 µl of pre-washed Protein A sepharose beads (Sigma-Aldrich) and further incubated with rotation at 4 °C for an additional 30 min. The beads were washed with 500 µl of lysis buffer for five times and finally resuspended in 532 µl of lysis buffer for elution of ProQ 3xFLAG variants and co-immunoprecipitated RNA. For RNA elution, co-immunoprecipitated RNA was extracted by phenol:chloroform:isoamyl alcohol (P:C:I) (25:24:1, pH 4.5, Roth) extraction. The purified RNA samples were treated by DNase I and subsequently purified by P:C:I extraction. Samples were resuspended in H2O to a final concentration of 1 OD/µl for elution samples and 0.1 OD/µl for lysate, flowthrough and wash.
CoIP_WT_VC_1_forward.wig
CoIP_WT_VC_1_reverse.wig

value: CoIP sample - vector control - replicate 1


title: 3RC208L

value: Liver


title: 3RC211V


title: 3RC211L


title: 3RC202V


title: CoIP_pProQR80A_rep2

description:
The bacteria were grown in LB to OD600= 2.0 before collecting 50ODs. The bacterial pellets were resuspended in lysis buffer ((20 mM Tris pH8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1unit/ul DNase I) and lysed using the Retsch MM200 (0.1 mm glass beads; 30Hz for 10min). The cleared lysate was then incubated with 25 µl (1 µl/2 OD600 nm of cells) of monoclonal anti-FLAG M2 (Sigma #F1804) at 4°C with rotation for 30 min. The sample was then added to 75 µl of pre-washed Protein A sepharose beads (Sigma-Aldrich) and further incubated with rotation at 4 °C for an additional 30 min. The beads were washed with 500 µl of lysis buffer for five times and finally resuspended in 532 µl of lysis buffer for elution of ProQ 3xFLAG variants and co-immunoprecipitated RNA. For RNA elution, co-immunoprecipitated RNA was extracted by phenol:chloroform:isoamyl alcohol (P:C:I) (25:24:1, pH 4.5, Roth) extraction. The purified RNA samples were treated by DNase I and subsequently purified by P:C:I extraction. Samples were resuspended in H2O to a final concentration of 1 OD/µl for elution samples and 0.1 OD/µl for lysate, flowthrough and wash.
CoIP_pProQR80A_2_forward.wig
CoIP_pProQR80A_2_reverse.wig

value: CoIP sample - ProQ R80A - replicate 2


title: Input DNA

city: Cambridge

first: Matthew

middle: R

last: Brown

state: MA

address: 75 Ames St

institute: Broad Institute

data_processing:
Illumina's RTA version 2.7.7. for basecalling
ChIP-sequencing reads were mapped to the rn6 build of the rat reference genome using HISAT v2.1.0 with default settings. DBP peaks were called using the MACS2 v2.2.7 algorithm using a false discovery rate of 1%. Peak classification, motif enrichment, and gene ontology were performed by HOMER v4.11.1 using default settings.
Genome_build: rn6
Supplementary_files_format_and_content: bigwig, bed

organism: Rattus norvegicus

extract_protocol: 40 million INS1 832/13 cells were cross-linked with 4% formaldehyde for 10 min, followed by quenching with 125 mM glycine for 5 min at room temperature. Fixed cells were washed with 1X TBS and kept at -80oC. Briefly, about 40 million cells were resuspended in 2 ml of cell lysis buffer (10 mM Tris-HCl, pH7.5, 10 mM NaCl, 0.5% NP-40) and incubated on ice for 10 min. The lysates were washed with MNase digestion buffer (20 mM Tris-HCl, pH7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2) and incubated with 3,000 or 5,000 gel units of MNase (M0247S, New England Biolabs, Ipswich, MA) for 20 minutes at 37 °C. After adding the same volume of sonication buffer (100 mM Tris-HCl, pH8.1, 20 mM EDTA, 200 mM NaCl, 2% Triton X-100, 0.2% Sodium deoxycholate), the lysate was sonicated for 3.5 min (30 sec-on / 30 sec-off) in Diagenode bioruptor and centrifuged at 15,000 rpm for 10 min. The cleared supernatant equivalent to about 40 million cells was incubated with 2.5 µg of anti-DBP antibody (PM079, MBL Life Science, Woburn, MA) previously validated for ChIP-seq. Subsequent immunoprecipitation and library preparation were performed as described (Zhong, J. et al, BMC Genomics, 2017).  The libraries were sequenced to 51 base pairs from both ends on an Illumina NextSeq instrument (Illumina) according to manufacturer’s instructions.

value: Pancreatic beta cell

tag: chip antibody


title: 3RC209L

value: BALB/cJ

value: RC


title: CoIP_pProQ_rep1

description:
The bacteria were grown in LB to OD600= 2.0 before collecting 50ODs. The bacterial pellets were resuspended in lysis buffer ((20 mM Tris pH8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1unit/ul DNase I) and lysed using the Retsch MM200 (0.1 mm glass beads; 30Hz for 10min). The cleared lysate was then incubated with 25 µl (1 µl/2 OD600 nm of cells) of monoclonal anti-FLAG M2 (Sigma #F1804) at 4°C with rotation for 30 min. The sample was then added to 75 µl of pre-washed Protein A sepharose beads (Sigma-Aldrich) and further incubated with rotation at 4 °C for an additional 30 min. The beads were washed with 500 µl of lysis buffer for five times and finally resuspended in 532 µl of lysis buffer for elution of ProQ 3xFLAG variants and co-immunoprecipitated RNA. For RNA elution, co-immunoprecipitated RNA was extracted by phenol:chloroform:isoamyl alcohol (P:C:I) (25:24:1, pH 4.5, Roth) extraction. The purified RNA samples were treated by DNase I and subsequently purified by P:C:I extraction. Samples were resuspended in H2O to a final concentration of 1 OD/µl for elution samples and 0.1 OD/µl for lysate, flowthrough and wash.
CoIP_pProQ_1_forward.wig
CoIP_pProQ_1_reverse.wig

value: CoIP sample - ProQ WT - replicate 1


title: FG1835_06

source_name: rete mirabile tissue

tag: developmental stage

value: silver eel

value: rete mirabile


title: 3RC228L


title: 3RC209S

value: Soleus muscle


title: FG1835_05


title: 3RC203L


title: DMSO-B

value: Phosphate buffered saline with 0.02% tyloxapol


title: DBP ChIP-seq

tag: cell line

value: DBP (MBL Life Science, PM079)


title: FG1835_04


title: 3RC208S


title: 3RC201S


title: 3RC202S


title: CoIP_WT_VC_rep2

description:
The bacteria were grown in LB to OD600= 2.0 before collecting 50ODs. The bacterial pellets were resuspended in lysis buffer ((20 mM Tris pH8.0, 150 mM KCl, 1 mM MgCl2, 1 mM DTT, 1unit/ul DNase I) and lysed using the Retsch MM200 (0.1 mm glass beads; 30Hz for 10min). The cleared lysate was then incubated with 25 µl (1 µl/2 OD600 nm of cells) of monoclonal anti-FLAG M2 (Sigma #F1804) at 4°C with rotation for 30 min. The sample was then added to 75 µl of pre-washed Protein A sepharose beads (Sigma-Aldrich) and further incubated with rotation at 4 °C for an additional 30 min. The beads were washed with 500 µl of lysis buffer for five times and finally resuspended in 532 µl of lysis buffer for elution of ProQ 3xFLAG variants and co-immunoprecipitated RNA. For RNA elution, co-immunoprecipitated RNA was extracted by phenol:chloroform:isoamyl alcohol (P:C:I) (25:24:1, pH 4.5, Roth) extraction. The purified RNA samples were treated by DNase I and subsequently purified by P:C:I extraction. Samples were resuspended in H2O to a final concentration of 1 OD/µl for elution samples and 0.1 OD/µl for lysate, flowthrough and wash.
CoIP_WT_VC_2_forward.wig
CoIP_WT_VC_2_reverse.wig

value: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 delta Lon

value: CoIP sample - vector control - replicate 2


title: 3RC203S


title: 3HF259S

value: HFD


title: 3HF259L


title: 3RC202L


title: HCT-116 cells with DDX3X degron, lentiDDX3Y, auxin treated, rRNA depleted RNA seq, replicate 2

city: San Francisco

first: Srivats

last: Venkataramanan

state: California

address: 513 Parnassus Ave, HSW 740

department: Cell and Tissue Biology

institute: University of California, San Francisco

data_processing:
Ribo-seq fastq files were stripped of the adapter sequences using cutadapt. UMI sequences were removed and reads were collapsed to fasta format. Reads shorter than 20 nt were removed. Reads were first aligned against rRNA (accession number U13369.1), and to a collection of snoRNAs, tRNAs and miRNA (retrieved using the UCSC table browser) using bowtie2 in the ‘local’ alignment mode.
Reads were mapped to the hg38 version of the genome (without scaffolds) using STAR 2.6.0a supplied with the GENCODE 32 .gtf file. The following parameter were used:--alignEndsType EndToEnd (Ribo-seq and PAR-CLIP) --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 0.04 (Ribo-seq) --outFilterMismatchNmax 3 (PAR-CLIP and RNA-seq) --outFilterMultimapNmax 20 --outSAMmultNmax 1 --outMultimapperOrder Random (All)
De-novo splice junction discovery was disabled for all datasets.
Count matrices for Ribo-seq and RNA-seq were built using reads mapping uniquely to CDS regions of protein-coding genes, using the Bioconductor packages GenomicFeatures,  GenomicFiles and GenomicAlignments
Only reads mapping for more than 25nt were used. Genomic and transcript regions for TPM calculation were extracted using Ribo-seQC
Genome_build: hg38
Supplementary_files_format_and_content: comma-separated text or BigWig tracks

source_name: HCT-116 with DDX3X degron, lentiDDX3Y, auxin treated, stranded rRNA depleted RNA seq

growth_protocol: HCT116 cells expressing Oryza sativa TIR1 protein, miniAID-tagged DDX3X, and either FLAG-tagged DDX3X or DDX3Y  were grown in McCoy's 5A medium with 10% FBS.

extract_protocol:
Cells were resuspended in TRI reagent (Zymo), and total RNA was extracted using the DIRECTZol RNA Prep kit (Zymo)
NEBNext Ultra II Library Prep Kit

treatment_protocol: Cells were treated with either DMSO or 500 micromolar Indole-3-acetic-acid for 48 hours

tag: cell line background

tag: genotype/variation

value: HCT-116 pCMV-OsTIR1 DDX3X-mAID lentiDDX3Y

value: 500 micromolar IAA

tag: rna isolation

value: Total RNA

tag: adapter sequence

value: TAGACAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC


title: 3RC230S

tag: strain


title: 3RC201L

value: Liver


title: 3RC203V

value: Visceral adipose tissue


title: 3HF259V

value: BALB/cJ


title: 3RC201V

value: RC


title: HCT-116 cells with DDX3X degron, lentiDDX3Y, auxin treated, ribosome profiling, replicate 2

source_name: HCT-116 with DDX3X degron, lentiDDX3Y, auxin treated, ribosome profiling

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579411

value: ribosome profiling


title: HCT-116 cells with DDX3X degron, lentiDDX3Y, auxin treated, ribosome profiling, replicate 1

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579410


title: FG1835_02

extract_protocol:
Total RNA was isolated from gas gland tissue using the Qiagen miRNeasy kit. Quality and integrity of the RNA waere checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip.
Illumina RNASeq libraries were prepared from 0.5 µg total RNA using the Illumina TruSeq Stranded mRNA Library Prep.

value: yellow eel


title: FG1835_03

value: rete mirabile


title: 3HF256V


title: 3HF258L


title: 3HF258S

value: Soleus muscle


title: 3HF258V


title: FG1835_01


title: 3HF256S


title: 3HF254S


title: HCT-116 cells with DDX3X degron, lentiDDX3Y, auxin treated, rRNA depleted RNA seq, replicate 1


title: HCT-116 cells with DDX3X degron, lentiCTRL, auxin treated, ribosome profiling, replicate 2

source_name: HCT-116 with DDX3X degron, lentiCTRL, auxin treated, ribosome profiling

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579407

value: HCT-116 pCMV-OsTIR1 DDX3X-mAID lentiCTRL


title: 3HF254V


title: HCT-116 cells with DDX3X degron, lentiDDX3X, auxin treated, rRNA depleted RNA seq, replicate 2

source_name: HCT-116 with DDX3X degron, lentiDDX3X, auxin treated, stranded rRNA depleted RNA seq

value: HCT-116 pCMV-OsTIR1 DDX3X-mAID lentiDDX3X


title: HCT-116 cells with DDX3X degron, lentiDDX3X, auxin treated, ribosome profiling, replicate 2

source_name: HCT-116 with DDX3X degron, lentiDDX3X, auxin treated, ribosome profiling

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579409


title: HCT-116 cells with DDX3X degron, lentiDDX3X, auxin treated, rRNA depleted RNA seq, replicate 1


title: HCT-116 cells with DDX3X degron, lentiCTRL, DMSO treated, ribosome profiling, replicate 2

source_name: HCT-116 with DDX3X degron, lentiCTRL, DMSO treated, ribosome profiling

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579405

value: DMSO


title: HCT-116 cells with DDX3X degron, lentiDDX3X, auxin treated, ribosome profiling, replicate 1

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579408


title: 3HF252L


title: HCT-116 cells with DDX3X degron, lentiCTRL, auxin treated, rRNA depleted RNA seq, replicate 1

source_name: HCT-116 with DDX3X degron, lentiCTRL, auxin treated, stranded rRNA depleted RNA seq


title: 3HF254L


title: 3HF224V


title: 3HF230S


title: 3HF224S


title: 3HF230V


title: 3HF252V


title: HCT-116 cells with DDX3X degron, lentiCTRL, DMSO treated, rRNA depleted RNA seq, replicate 1

source_name: HCT-116 with DDX3X degron, lentiCTRL, DMSO treated, stranded rRNA depleted RNA seq


title: 3HF252S


title: 3HF228V


title: HCT-116 cells with DDX3X degron, lentiCTRL, DMSO treated, ribosome profiling, replicate 1

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579404


title: 3HF256L


title: 3HF224L


title: HCT-116 cells with DDX3X degron, lentiCTRL, auxin treated, ribosome profiling, replicate 1

extract_protocol:
Cells were treated with 100ug/ml cycloheximide, flash frozen, lysed and treated with 2u/ul RNaseI (Ambion). Illustra MicroSpin Columns S-400 HR (GE Healthcare) were used to enrich for ribosome complexes and ribosome protected RNA fragments were extracted using the DIRECTZol RNA prep kit (Zymo)
Library construction for RPFs was performed as described in McGlincy et al. PMID 28579406


title: 3HF203S


title: 3HF228S


title: 3HF230L


title: HCT-116 cells with DDX3X degron, lentiCTRL, auxin treated, rRNA depleted RNA seq, replicate 2


title: 3HF203L


title: 3HF208S


title: 3HF208L


title: 3HF202S


title: 3HF208V


title: HCT-116 cells with DDX3X degron, lentiCTRL, DMSO treated, rRNA depleted RNA seq, replicate 2


title: 3HF202V


title: 3HF202L


title: 3HF203V


title: 3HF228L


title: D2MED8h_rep3

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

data_processing:
Read alignment done by HISAT2 version 2.1.0.
Reads were trimmed using Trimmomatic version 0.36.
Count data were generated by means of the HTSeq method.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: THP1-MD2-CD14 cells

growth_protocol: Pro-monocytic THP1-MD2-CD14 cells which stably express MD2, CD14 and a SEAP NF-κB reporter construct (Invivogen, San Diego, CA ) were cultured in RPMI1640 containing 10% FCS, 100 U/ml penicillin, 2 mM L-glutamine. For stimulations, cells were placed in a 24-well plate (Greiner Bio-One, Frickenhausen, Germany) at 106 cells/well and incubated with medium, Pam3CSK4 (1 µg/mL) or LPS (100 ng/mL) for 4 hours. NF-kB driven SEAP was evaluated using Quanti-Blue™ (Invivogen, San Diego, CA) according to manufacturer’s protocol. To create HIVEP1 deficient THP1-MD2-CD14 cells, plasmid pSpCas9(BB)-2A-GFP (pX458) was used (a kind gift from Dr. F. Zhang; Addgene plasmid # 48138). Target sequences for HIVEP-1 were designed using the web-tool from the Zhang lab (https://zlab.bio/guide-design-resources). Oligonucleotides containing guide RNA sequences for HIVEP-1 exon 3 5’-GAAGCACAAAAAGAACTTAA-3’, HIVEP-1 exon 4 5’-AACCATCTGAACTGCGTAGA-3’ and BbsI adapter sequences were ligated into BbsI digested pX458. The sequence of the constructs was verified by DNA sequencing. Both HIVEP-1 targeting plasmids were co-transfected into THP1-MD2-CD14 cells by transfection using Lipofectamine LTX and Plus reagent (Invitrogen, Waltham, MA). THP1-MD2-CD14 cells were transfected with pX458 containing control guide-1 5’-ACGGAGGCTAAGCGTCGCAA-3’ and control guide-2 5’-ATCGTTTCCGCTTAACGGCG-3 to generate controls. After 24h culture, GFP-expressing cells were sorted and plated at 1 cell per well using a SH800 Cell sorter (Sony, Tokyo, Japan). After cell expansion, chromosomal DNA was screened for gene targeting by PCR analysis and clones were further analyzed. HIVEP1 deficient and two control THP1-MD2-CD14 cell line clones were cultured in the same way as the parent THP1-MD2-CD14 cell line. Cells were seeded at 106 cells/well in a 24-well plate (Greiner Bio-One, Frickenhausen, Germany) and incubated with medium or LPS (100 ng/mL) for 2, 4 and 8 and lysed for RNA isolation.

extract_protocol:
Total RNA was isolated from HIVEP1 deficient THP1-MD2-CD14 cells (n=4) and control cells (n=4), treated with or without 100ng/mL LPS for 2 and 8 hours, using the RNeasy mini kit according to the manufacturer’s instructions (Qiagen, Hilden, Germany). RNA quality was assessed by bioanalysis (Agilent), with all samples having RNA integrity numbers > 7. Total RNA concentrations were determined by Qubit® 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA). RNA-sequencing libraries were prepared from 200ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) library kits and sequenced using the Illumina HiSeq4000 instrument (Illumina) to generate single reads (50bp). Quality was assessed by means of the FastQC method (v0.11.5; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Libraries were prepared from 200ng total RNA using KAPA RNA Hyperprep with RiboErase (Roche) kits.

tag: group

value: HIVEP1 deficient cells

tag: hours post-stimulation

tag: stimulant

value: RPMI medium


title: D2MED8h_rep2


title: 3HF201V

value: HFD

tag: tissue


title: D2MED8h_rep4


title: 3HF201S


title: 3HF201L


title: 2RC231V


title: 2RC231S


title: D2MED2h_rep4


title: D2MED8h_rep1


title: 2RC230S


title: 2RC230L


title: D2MED2h_rep3


title: D2MED2h_rep1


title: 2RC231L


title: 2RC230V


title: D2MED0h_rep3


title: D2MED0h_rep4


title: D2MED2h_rep2


title: D2MED0h_rep1


title: D2MED0h_rep2


title: D2LPS8h_rep4

value: LPS


title: 2RC229V


title: 2RC229S


title: D2LPS8h_rep3


title: 2RC229Lb


title: 2RC229L


title: D2LPS8h_rep2


title: 2RC229La


title: D2LPS8h_rep1


title: 2RC228S


title: 2RC228V


title: D2LPS2h_rep4


title: D2LPS2h_rep3


title: 2RC211V


title: D2LPS2h_rep2


title: D2LPS2h_rep1


title: C2MED8h_rep4

value: control cells


title: C2MED8h_rep1


title: C2MED8h_rep2


title: 2RC210L


title: 2RC211L


title: 2RC209V


title: C2MED2h_rep3


title: 2RC209L


title: 2RC208V


title: C2MED2h_rep1


title: C2MED0h_rep4


title: C2MED2h_rep2


title: C2MED2h_rep4


title: 2RC209S


title: 2RC208S


title: C2MED0h_rep3


title: C2MED0h_rep1


title: 2RC208L


title: 2RC228L


title: C2MED0h_rep2


title: 2RC203S


title: 2RC203V


title: 2RC203L


title: C2LPS8h_rep4


title: 2RC210V


title: 2RC202V


title: C2MED8h_rep3


title: C2LPS8h_rep2


title: 2RC210S


title: 2RC202S


title: 2RC201V


title: 2RC202L


title: C2LPS2h_rep4


title: C2LPS8h_rep1


title: C2LPS2h_rep1


title: 2RC201S


title: C2LPS2h_rep2


title: 2RC200S


title: 2RC200V


title: 2RC201L


title: 2RC211S


title: CD-tRF CT4 (scATAC-seq)

data_processing:
Raw base cell files (BCL; Illumina) were demultiplexed into FASTQ file format by Cell Ranger ATAC v1.2.0 using the cellranger-atac mkfastq function (10X Genomics). ScATAC-seq accessibility counts for each library were obtained using the cellranger-atac count function against the mm10 reference genome. Aligned sequenced fragment files generated by Cell Ranger were then imported into ArchR v1.0.0 for quality control and sample processing (32). Low quality cells were filtered if < 1000 unique fragment counts were detected or given a TSS enrichment score < 10. Predicted doublets were inferred using ArchR’s addDoubletScores algorithm which synthesizes pseudo-doublets by in silico mixing of cellular populations followed by comparison with experimental data. Cells were then filtered using both the default filterDoublets function and given > 4000 unique fragment counts in TSS regions. Dimensionality reduction of the term frequency-inverse document frequency (TF-IDF) normalized scATAC-seq data (16470 cells) was performed using iterative Latent Semantic Indexing (LSI) using genome-wide 500bp tiling of accessible chromatin regions (iterations=2, varFeatures=20000, resolution=0.2, dimsToUse=1:15). The data was then clustered using Seurat’s FindClusters algorithm (resolution=1.2) and visualized using Uniform Manifold Approximation and Projection (UMAP) embedding (nNeighbors=40, minDist=0.5, metric=cosine). Gene activity scores were calculated using ArchR’s gene scoring model which considers both the accessibility within a gene loci and exponentially weighted distal elements based on distance to a gene’s TSS. Gene activity scores for individual cell were visualized on UMAP embeddings following markov affinity-based graph imputation of cells. Marker features of each cluster were quantified using ArchR’s getMarkerFeatures algorithm. Cell-specific clusters were then manually assigned, as previously performed for scATAC-seq protocols  (Corces, M. et al, Nature Genetics, 2020), to endocrine or non-endocrine cell type by enrichment of canonical endocrine markers (NK2 homeobox 2 (Nkx2.2), paired box protein 6 (Pax6), and Neurod1. Endocrine cell types were sub-classified into β-cell (Ins1, Ins2, Nkx6.1, MAF bZip transcription factor A (Mafa), insulin amyloid polypeptide (Iapp)), α-cell (Gcg, aristaless Related Homeobox (Arx), iroquois homeobox factor 1 (Irx1), MAF bZip transcription factor B (Mafb)), δ-cell (Sst, peptide YY (Pyy) and hematopoietically-expressed homeobox protein (Hhex)), and γ-cell clusters (Ppy, tetraspanin 8 (Tspan8), Pyy), while non-endocrine cells were classified into immune (cluster of differentiation 74 (Cd74),C-C motif chemokine ligand 3 (Ccl3),histocompatibility 2, class 2 antigen E beta 2 (H2-Eb2)), endothelial (kinase insert domain receptor (Kdr),SRY-box transcription factor 7 (Sox7),cluster of differentiation 34 (Cd34)), and stellate cell clusters (heart and neural crest derivatives expressed 2 (Hand2), collagen type VI alpha 1 chain (Col6a1),anoctamin 1 (Ano1)). Clusters that had enrichment of endocrine and non-endocrine markers (e.g. Kdr and Ins1) or multiple endocrine cell-specific makers (e.g. Ins1 and Gcg) were considered unclassified as noted in other scATAC-seq protocols and are likely unfiltered doublets (Corces, M. et al, Nature Genetics, 2020). Following cell type identification, peaks were called from pseudo-bulk clustered cell-types using MACS2 v2.2.7 with the default ArchR settings --shift 75 --extsize 150 --nomodel --nolambda.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and arrow files for each sample

source_name: Islet

extract_protocol:
Mouse islets were freshly isolated at CT4 and CT16 (n=2 mice per CT and group), >100 islets were counted, and nuclei isolation was performed as noted above using ice-cold 1X lysis buffer from 10X Genomics (Pleasanton, CA). A portion of isolated nuclei were stained with Trypan Blue for manual counting and to ensure a single-nuclei suspension prior to library preparation. Approximately 5,000 nuclei per sample were subsequently aliquoted for single cell ATAC-seq (scATAC-seq) library preparation using the Chromium Next GEM Single Cell ATAC Kit (10X Genomics). 10μL of 1X Tn5 Transposition enzyme was mixed with 5uL of the diluted nuclei suspension and was incubated 50°C for 1h. The tagmented nuclei were partitioned into Gel Bead-In Emulsions (GEMs) and barcoded by unique molecular identifiers (UMIs) using the Chromium Next GEM  Single Cell ATAC library & Gel Bead kit and the C1 Chromium Instrument (10X Genomics). scATAC-seq libraries were then prepared and indexed using the Chromium i7 Sample Index kit (10X Genomics) with library size determined by Fragment Analysis (Agilent) prior to sequencing. Paired-end, dual-indexed sequencing of the libraries (50bp read #1, 8bp i7 index, 16bp i5 index, 50bp read#2) was performed using an Illumina HiSeq instrument.
scATAC-seq

value: Pancreatic islets

tag: age

value: 20 weeks

value: 8-weeks constant light + 8h time-restricted feeding


title: CD-tRF CT16 (scATAC-seq)

tag: treatment


title: 2HF255V

tag: diet

value: Visceral adipose tissue


title: 2HF255S

tag: time


title: CD CT4 (scATAC-seq)

value: 8-weeks constant light


title: 2HF255L

source_name: Liver

value: Liver


title: CD CT16 (scATAC-seq)


title: 2HF253V


title: 2HF253S


title: CON CT4 (scATAC-seq)

value: Control


title: SAMP8 Control Pooled [RNA-seq]

city: Barcelona

first: Christian

middle: Griñán

last: Ferré

state: Barcelona

address: Joan XIII, s/n

department: Pharmacology, Toxicology and Therapeutic Chemistry

country: Spain

institute: University of Barcelona

data_processing:
Pooled hippocampal tissue samples were aligned with reference genome using Bowtie2.
The gene expression level was estimated using RSEM.
Differentially expressed genes were identified using the edgeR programe.
Genome_build: GRCm38 (39) version of Mus musculus available at https://asia.ensembl.org/Mus_musculus/Info/Index.
Supplementary_files_format_and_content: Adundance measurements

source_name: Hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, anr RNA was obtained using Trizol reagent. Ilumina Truseq was used with 1 ug of toral RNA for the library contruction.
RNA libraries were prepared according to KAPA Stranded RNA-seq Kit with RiboErase (KAPA Biosystems, Wilmington, MA) system.

treatment_protocol: Oral Gavage administration of UNC0642 5 mg/Kg

value: Hippocampus


title: SAMP8 Treated Pooled [RNA-seq]

value: Oral Gavage administration of UNC0642 5 mg/Kg


title: CD-tRF CT16-2 (ATAC-seq)

data_processing:
Illumina's RTA version 2.7.7. for basecalling
Bulk ATAC-sequencing reads were first mapped to the mm9 build of the mouse reference genome using the Burrows-Wheeler Aligner v0.7.16 with default settings. Picard v2.21.6 was used to remove PCR duplicates and which were subsequently removed by Samtools v1.9 along with mitochondrial and multi-mapping reads To call peaks, we used MACS2 v2.2.7.1 on merged replicates with the following settings: -f BEDPE -g mm --keep-dup all --SPMR -q 0.05. Peaks with an FDR <0.05 were retained following removal of peaks overlapping mm9 blacklisted regions.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig and bed files for each sample

extract_protocol: 50 islets (~50,000 cells) per reaction were  counted, washed with ice cold 1X PBS, and lysed for 20-25 min on ice (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630). Nuclei were subsequently obtained following centrifugation for 15min at 500g and 4°C and subjected to the published Omni Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) protocol (Corces, M.R. et al., 2017).


title: 2HF253L

extract_protocol:
Total RNA from liver, soleus muscle and visceral adipose tissue was extracted using the RNeasy Plus micro kit (Qiagen, Hombrechtikon, Switzerland).
Integrity of RNA was verified on a Fragment Analyzer (Agilent Technologies, Inc., Santa Clara, CA 95051, USA) and all preparations had a RNA quality number (RQN) between 8.2 and 9.3. RNA-seq libraries were prepared using 250ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents
Sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. A sequencing depth of 27 to 46 million reads using 100bp single reads was used.


title: 2HF231V

source_name: Visceral adipose tissue


title: C2LPS2h_rep3


title: 2RC200L

value: RC


title: 2HF231S

source_name: Soleus muscle

value: Soleus muscle


title: 2HF231L


title: CD CT16-2 (ATAC-seq)


title: CD-tRF CT4-2 (ATAC-seq)


title: CD CT4-2 (ATAC-seq)


title: 2HF230V


title: CON CT4-2 (ATAC-seq)


title: 2HF230L


title: 2HF211S


title: CON CT16-2 (ATAC-seq)


title: CD-tRF CT4-1 (ATAC-seq)


title: CD-tRF CT16-1 (ATAC-seq)


title: CD CT16-1 (ATAC-seq)


title: 2HF230S


title: 2HF211V


title: 2HF211L


title: CD CT4-1 (ATAC-seq)


title: 2HF210S


title: CON CT16-1 (ATAC-seq)


title: 2HF210V


title: CON CT16 (scATAC-seq)


title: CON CT4-1 (ATAC-seq)


title: 2HF210L


title: C2LPS8h_rep3


title: 2HF209S


title: 2HF209V


title: CD-tRF CT12-2 (RNA-seq)

data_processing:
Illumina's RTA version 2.7.7. for basecalling
RNA-sequencing reads were first mapped to the mm10 or rn6 build of the mouse and rat reference genome, respectively, using HISAT v2.1.0 with default settings. FeatureCounts v2.0.0 from the Subread package was used to count mapped gene-level reads. Gene count matrices were uploaded into the edgeR v3.28.1 package and normalized to counts per million (CPM) reads using the default Trimmed Mean of M-values (TMM) method.
Genome_build: mm10, rn6
Supplementary_files_format_and_content: counts

extract_protocol:
Total RNA was isolated from freshly picked mouse islets or transfected INS-1 832/13 cells using the RNeasy mini kit (Qiagen, Hilden, Germany). RNA size and quality were assessed using the Tape Station Bionalyzer (Agilent, Santa Clara, CA), and concentration was determined by Qubit fluorometry. RNA libraries were prepared using 100 ng of total RNA.
RNA libraries were prepared using polyA selection method (Illumina, San Diego, CA) according to manufacturer's instructions.


title: CD-tRF CT16-2 (RNA-seq)


title: CD-tRF CT20-2 (RNA-seq)


title: 2HF209L


title: CD-tRF CT4-2 (RNA-seq)


title: 2HF208S


title: CD-tRF CT0-2 (RNA-seq)


title: CD-tRF CT8-2 (RNA-seq)


title: 2HF208V


title: CD-tRF CT20-1 (RNA-seq)


title: 2HF203V


title: CD-tRF CT16-1 (RNA-seq)


title: 2HF203S


title: CD-tRF CT12-1 (RNA-seq)


title: CD-tRF CT8-1 (RNA-seq)


title: 2HF203L


title: 2HF202V


title: CD-tRF CT4-1 (RNA-seq)


title: 2HF202S


title: 2HF202L


title: CD CT16-2 (RNA-seq)


title: 2HF201V


title: CD CT20-2 (RNA-seq)


title: CD-tRF CT0-1 (RNA-seq)


title: 2HF201L


title: CD CT12-2 (RNA-seq)


title: 2HF201S


title: 2HF200V


title: 2HF200S


title: CD CT4-2 (RNA-seq)


title: CD CT8-2 (RNA-seq)


title: CD CT0-2 (RNA-seq)


title: 2HF208L


title: CD CT20-1 (RNA-seq)


title: 1RC256V


title: 2HF200L


title: 1RC256S


title: CD CT12-1 (RNA-seq)


title: CD CT8-1 (RNA-seq)


title: CD CT16-1 (RNA-seq)


title: 1RC256L


title: 1RC254S


title: CD CT4-1 (RNA-seq)


title: 1RC254V


title: CON CT20-2 (RNA-seq)


title: 1RC254L


title: CD CT0-1 (RNA-seq)


title: CON CT16-2 (RNA-seq)


title: 1RC252V


title: CON CT12-2 (RNA-seq)


title: 1RC252L


title: 1RC251V


title: CON CT8-2 (RNA-seq)


title: 1RC251S


title: 1RC252S


title: CON CT0-2 (RNA-seq)


title: CON CT4-2 (RNA-seq)


title: 1RC251L


title: CON CT20-1 (RNA-seq)


title: 1RC248V


title: 1RC248S


title: CON CT12-1 (RNA-seq)


title: CON CT8-1 (RNA-seq)


title: 1RC248L


title: 1RC235S


title: 1RC235V


title: CON CT4-1 (RNA-seq)


title: CON CT16-1 (RNA-seq)


title: 1RC229V


title: WT Tumor Treg rep2 (J2)

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1600 6th Ave South

department: Neurosurgery, Microbiology

institute: University of Alabama at Birmingham

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
After extraction of gene hit counts, the gene hit counts table was used for downstream differential expression analysis.
Genome_build: Mus musculus GRCm38 reference genome available on ENSEMBL
Supplementary_files_format_and_content: Matrix table with gene hit counts for every gene and every sample

source_name: Tumor Treg

extract_protocol:
Total RNA was extracted using a QIAshredder kit (QIAGEN) and an RNeasy Plus Micro Kit (QIAGEN) according to the manufacturer’s protocol.
mRNA was specifically enriched from total RNA by removing rRNA and hydrolyzed into small pieces. The fragments were then reverse-transcribed into first-strand cDNA using random hexamer primers, followed by second strand synthesis. The short cDNA strands were ligated with 3′- and 5′-adapters for amplification and sequencing using the Illumina® platforms (HiSeq 2 x 150 bp, single index, per lane).

tag: genotype

value: FoxP3YFP-Cre (WT)

value: Tumor

tag: tumor stage

value: less than or equal to 1.5 cm3


title: 1RC235L


title: WT Tumor Treg rep1 (J1)


title: 1RC229S


title: KO Tumor Treg rep2 (I2)

value: Prdm1fl/flFoxP3YFP-Cre (KO)


title: 1RC228V


title: WT Spleen Treg rep2 (H2)

source_name: Spleen Treg

value: Spleen


title: KO Tumor Treg rep1 (I1)


title: 1RC229L


title: WT_2hr_sample_C

city: Durham

first: Melissa

last: Wells

state: NC

address: 111 TW Alexander Drive

department: LST

institute: NIEHS

data_processing:
Base calling  and generation of FASTQ files was performed with Illumina bcl2fastq2
Read pairs were filtered to remove those where either mate's mean quality score fell below 20
Reads were aligned to D. discoideum reference assembly using STAR 2.5.2b
Counts per gene were determined using featureCounts 1.5.1 based on dictyBase.org gene annotations downloaded in March 2018
Normalized counts were determined using the estimateSizeFactors function
Genome_build: dictyBase.org D. discoideum Chromosomal DNA created 05-13-2009
Supplementary_files_format_and_content: tab-delimited text, raw and normalized read counts per gene

organism: Dictyostelium discoideum

source_name: strain AX3_WT_2hr

growth_protocol: Wild-type and mutant amebae were grown under axenic conditions in growth medium until approximately 80% confluence was reached.  Eight samples were then frozen until RNA extraction was performed.  Other samples of the same type were subjected to nutrient deprivation for 2 and 6 hours, after which the samples were frozen and RNA extracted.

extract_protocol:
RNA was purified using the Illustra RNAspin Kit (GE Healthcare Life Sciences) following the manufacturer’s protocol.
Total cellular RNA was quantitated with a Qubit fluorometer, and 250 ng of each sample was transcribed to generate cDNA libraries using the Illumina TruSeq RNA Kit (Illumina Inc, San Diego, CA) following the manufacturer's Low Sample (LS) protocol, with the following modifications:  2 minutes of centrifugation were used during the bead drying steps and 12 cycles were used to enrich DNA fragments.

tag: strain background

value: WT

tag: timepoint


title: 1RC228S


title: WT Spleen Treg rep1 (H1)


title: 1RC228L


title: KO Spleen Treg rep2 (G2)


title: WT_2hr_sample_A


title: CON CT0-1 (RNA-seq)

value: Pancreatic islets


title: KO Spleen Treg rep1 (G1)


title: WT_6hr_sample_B

source_name: strain AX3_WT_6hr


title: 1RC227S


title: WT_0hr_sample_B

source_name: strain AX3_WT_0hr


title: WT_0hr_sample_A


title: 1RC227L


title: Whole kidney E14.5

city: Pittsburgh

first: Dennis

last: Kostka

state: PA

institute: University of Pittsburgh

data_processing:
Cellranger v 2.2.0 (10X Genomics)
Cell filtering, QC and normalization (DropletUtils, scds, scater, scran)
Genome_build: mm10
Supplementary_files_format_and_content: TAR (gzipped, of mtx and csv/txt)

molecule: polyA RNA

source_name: Whole kidney tissue

extract_protocol:
We harvested two kidneys at E14.5 and generated a single cell suspension using 0.05% trypsin at 37°C for 10 minutes. Kidneys were mechanically dissociated with pipetting at 5 and 10 min. 3% fetal calf serum in PBS was added to halt the trypsin. The cell suspension was filtered using a 40 mm filter and pelleted. The cells were resuspended in 90% FCS in DMSO and frozen
Single-cell library preparation and sequencing was performed by GENEWIZ Inc. using the 10X Genomics Inc. Chromium 3’ Single Cell v2 library preparation kit

value: whole kidney

tag: developmental stage

tag: Sex

value: female


title: ttpA-C240ins_6hr_sample_4C

source_name: strain AX3_ttpA-C240ins_6hr


title: ttpA-C240ins_0hr_sample_4C

source_name: strain AX3_ttpA-C240ins_0hr


title: ttpA-C240ins_6hr_sample_4B


title: WT_2hr_sample_B


title: 1RC226S


title: ttpA-C240ins_0hr_sample_4B


title: ttpA-C240ins_0hr_sample_4A


title: WT_0hr_sample_C


title: ttpA-C240ins_6hr_sample_4A


title: WT_6hr_sample_C


title: Roots, Nitrogen 1

city: Udine

first: Fabio

last: Marroni

address: Via delle Scienze 208

country: Italy

institute: Università di Udine

data_processing:
Alignment using Hisat2 with default parameters against
Differential expression analysis using cuffdiff with default parameters
Genome_build: B73 RefGen 4 (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Zea_mays/latest_assembly_versions/GCA_000005005.6_B73_RefGen_v4)
Supplementary_files_format_and_content: GTF file with read counts

organism: Zea mays

source_name: Roots

extract_protocol:
For each sample, roots of four plants were pooled together and total RNA was isolated. One g of maize tissue was homogenized in liquid nitrogen and total RNA was extracted from approximately 60 mg of powder with the Spectrum Plant Total RNA Kit (Sigma-Aldrich, St Louis, MO, USA) according to the manufacturer’s instructions.
Library preparation was performed following the Illumina protocol TrueSeq 2.0 using 2 μg of total RNA for each sample

value: Nitrogen

value: Roots


title: ttpA-C240ins_0hr_sample_2C


title: 1RC227V

value: Visceral adipose tissue


title: ttpA-C240ins_6hr_sample_2C


title: 1RC226L

value: Liver


title: WT_6hr_sample_A


title: Roots, Urea + N 2

value: Urea + Nitrogen


title: 1RC211V


title: Roots, Urea + N 3


title: 1RC211S


title: Roots, Nitrogen 3


title: ttpA-C240ins_0hr_sample_2B


title: Roots, Urea + N 1


title: ttpA-C240ins_6hr_sample_2B


title: ttpA-C240ins_0hr_sample_2A


title: Roots, Nitrogen 2


title: ttpA-C240ins_6hr_sample_1C


title: 1RC226V


title: Roots, Urea 3

value: Urea


title: 1RC210V

value: RC


title: ttpA-C240ins_0hr_sample_1B


title: ttpA-C240ins_6hr_sample_1B


title: Roots, Urea 2


title: 1RC210S

value: Soleus muscle


title: Roots, Urea 1


title: 1RC210L


title: ttpA-C240ins_0hr_sample_1A


title: ttpA-C240ins_6hr_sample_1A


title: Roots, Control 3

value: Control


title: ttpA-C240ins_2hr_sample_4C

source_name: strain AX3_ttpA-C240ins_2hr


title: 1HF259V

value: HFD


title: ttpA-C240ins_6hr_sample_2A


title: ttpA-C240ins_2hr_sample_2C


title: ttpA-C240ins_2hr_sample_2B


title: 1RC211L


title: Roots, Control 2


title: ttpA-C240ins_0hr_sample_1C


title: ttpA-C240ins_2hr_sample_2A


title: Roots, Control 1


title: 1HF259L


title: ttpA-C240ins_2hr_sample_1C


title: 1HF258V


title: ttpA-C240ins_2hr_sample_1A


title: WT_SG_sample_6

data_processing:
Base calling  and generation of FASTQ files was performed with Illumina bcl2fastq2
Read pairs were filtered to remove those where either mate's mean quality score fell below 20
Reads were aligned to D. discoideum reference assembly using STAR 2.6.0c
Counts per gene were determined using featureCounts 1.5.1 based on dictyBase.org gene annotations downloaded in March 2018
Normalized counts were determined using the estimateSizeFactors function
Genome_build: dictyBase.org D. discoideum Chromosomal DNA created 05-13-2009
Supplementary_files_format_and_content: tab-delimited text, raw and normalized read counts per gene

source_name: strain AX3_WT_surface growth

growth_protocol: Amebae were grown under axenic conditions in growth medium until approximately 80% confluence was reached in the case of cells in surface cultures, or approximately 2 million cells/ml in the case of liquid cultures. They were then frozen until RNA extraction was performed.

tag: growth condition

value: surface growth


title: WT_LG_sample_6

source_name: strain AX3_WT_liquid growth

value: liquid growth


title: WT_SG_sample_5


title: 1HF258S


title: WT_LG_sample_5


title: ttpA-C240ins_2hr_sample_4A


title: 1HF258L


title: WT_SG_sample_4


title: 1HF257V


title: WT_LG_sample_4


title: 1HF257S


title: WT_LG_sample_3


title: 1HF259S


title: 1HF257L


title: ttpA-C240ins_2hr_sample_1B


title: WT_LG_sample_2


title: 1HF253V


title: WT_SG_sample_1


title: WT_LG_sample_1


title: ttpA-C240ins_LG_sample_6

source_name: strain AX3_ttpA-C240ins_liquid growth


title: WT_SG_sample_3


title: ttpA-C240ins_SG_sample_5

source_name: strain AX3_ttpA-C240ins_surface growth


title: ttpA-C240ins_LG_sample_5


title: 1HF253L

source_name: Liver


title: ttpA-C240ins_SG_sample_4


title: WT_SG_sample_2


title: nasopharyngeal gene expression of subject M139 at m12 [121150011392]

city: Utrecht

first: Wouter

last: de Steenhuijsen Piters

address: Heidelberglaan 100

institute: UMC Utrecht

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Clariom S Human Pico arrays.

scan_protocol: GeneChips were scanned inhouse by Hologic Ltd. UK.

data_processing: The data were analyzed using R/Rstudio. Outliers were identified using raw intensity data using the arrayQualityMetrics package and removed from the dataset. RMA was performed to reduce the data from 300304 probe-level features to 27189 genes. After removing non-annotated genes/control probes, 18526 genes remained, which were for the conclusions in the paper.

source_name: nasopharyngeal cells

growth_protocol: N/A; study in human infants.

extract_protocol: RNA was extracted by a TRIzol reagent (Invitrogen)/chlorform method, cleaned using the RNAeasy Micro Kit (Qiagen) (OpenWetWare contributors, 2015)

treatment_protocol: Nasopharyngeal cells were collected in RNAprotect Cell Reagent (Qiagen) at -80 °C until extraction.

tag: subject

tag: time point

tag: cell type

value: nasopharyngeal cells


title: ttpA-C240ins_SG_sample_6


title: nasopharyngeal gene expression of subject M136 at m12 [121150011362]


title: nasopharyngeal gene expression of subject M133 at m12 [121150011332]


title: nasopharyngeal gene expression of subject M127 at m12 [121150011272]


title: nasopharyngeal gene expression of subject M131 at m12 [121150011312]


title: ttpA-C240ins_LG_sample_4


title: nasopharyngeal gene expression of subject M135 at m12 [121150011352]


title: 1HF252V

source_name: Visceral adipose tissue

tag: strain


title: nasopharyngeal gene expression of subject M126 at m12 [121150011262]


title: nasopharyngeal gene expression of subject M130 at m12 [121150011302]


title: 1HF252S

source_name: Soleus muscle


title: ttpA-C240ins_LG_sample_3


title: ttpA-C240ins_SG_sample_3


title: ttpA-C240ins_SG_sample_2


title: 1HF252L


title: ttpA-C240ins_SG_sample_1


title: 1HF253S


title: ttpA-C240ins_LG_sample_1