title: 87-CD8 RNA seq

city: Daejeon

first: Su-Hyung

last: Park

address: 291 Daehak-ro

institute: Korea Advanced Institute of Science and Technology

data_processing:
Reads were trimmed based on sequencing quality using Sickle.
Poly-A tails and adaptor contents were removed using Cutadapt.
Trimmed reads were aligned on a human reference sequence (hg19) using Tophat2.
The number of mapped reads on the 3’ end of each gene was calculated using Bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read count

source_name: hepatocellular carcinoma tissue

extract_protocol:
Cells were cryopreserved in Trizol reagent and RNA extracted according to the manufacturer’s instructions.
Total RNA quality was assessed with the Agilent 2100 Bioanalyzer System. Extracted RNA samples were processed using the QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Vienna) and sequenced on an Illumina NextSeq 500. A median 2.0x107 (range 1.7x107 to 2.4x107) single-end reads with 75 bp were generated.

value: CD8 T cells


title: 92-CD8 RNA seq

status: Public on Aug 14 2019

type: SRA

country: South Korea

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type


title: 70-CD8 RNA seq


title: SC277

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

country: USA

institute: University of Pittsburgh

description:
poly-adenylated RNA, surface protein expression with TotalSeq-A antibodies
CONTROL 6
This sample was sequenced twice-- once on the NextSeq 500 and once on the NovaSeq 6000. The output .h5 file contains the combined data from both of these instruments following alignment to the GRCh38 reference genome.

data_processing:
10X Genomics' Cell Ranger 3.0.2 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 transcriptome using 10X Genomics' Cell Ranger 3.0.2 software's cellranger count function
Cell Ranger output of raw_feature_bc_matrix.h5 files were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis.  Cell Ranger 3.0.2's Feature Barcoding
Genome_build: GRCh38
Supplementary_files_format_and_content: The .h5 files contain gene expression and antibody capture counts for each donor or patient

source_name: upper lobe lung_healthy donor

extract_protocol:
Explanted lungs were finely diced and digested for 45 minutes in a mix of Liberase DL/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 2%FBS.  Cells were labeled with TotalSeq-A Cell Hashing HTO and CITE-Seq ADT antibodies according to the New York Genome Center's CITE-Seq and Cell Hashing protocol.  Follwing antibody-hashtag labeling, cells were resuspended in PBS containing 0.04% BSA and loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v3 User Guide; Cell Hashing HTO and CITE-Seq ADT libraries measuring surface protein expression were generated according to the New York Genome Center's CITE-seq & Cell Hashing Protocol

tag: subject status

value: healthy donor

tag: tissue

value: lung

tag: lung section/portion

value: upper lobe lung

tag: 10x genomics chemistry

value: 10X Genomics 3 Prime V3 chemistry + CITE-Seq Feature Barcoding with BioLegend Total-Seq A antibodies


title: SC281

description:
poly-adenylated RNA, surface protein expression with TotalSeq-A antibodies
SSC 9/10
This sample was sequenced twice-- once on the NextSeq 500 and once on the NovaSeq 6000. The output .h5 file contains the combined data from both of these instruments following alignment to the GRCh38 reference genome.

source_name: mix of hashtagged upper  lobe + hashtagged lower lobe lung_scleroderma patient

value: scleroderma patient

value: 10X Genomics 3 Prime V3 chemistry + Cell Hashing HTO + CITE-Seq Feature Barcoding with BioLegend Total-Seq A antibodies


title: 69-CD8 RNA seq


title: 68-CD8 RNA seq


title: 66-CD8 RNA seq


title: BAR-KT41_t12months

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Genome-wide DNA methylation dynamic in obese persons

hyb_protocol: Illumina protocol

scan_protocol: iscan

data_processing: Champ package

label: Cy3 and Cy5

molecule: genomic DNA

source_name: vastus lateralis

label_protocol: Illumina protocol

extract_protocol: using Invisorb® Genomic DNA Kit II according to the manufacturer’s protocol. An amount of 500 ng of genomic DNA from each participant was bisulfite-converted using Zymo EZ DNA Methylation-Gold kit (Zymo Research Corporation, Irvine, CA, USA)

treatment_protocol: genomic DNA was extracted from frozen muscle biopsies.

tag: tissu

value: Skeletal muscle

tag: group

value: Obese

tag: time point

value: 52 weeks after metabolic surgery


title: BAR-TK22_t12months


title: 38-CD8 RNA seq


title: 34-CD8 RNA seq


title: 32-CD8 RNA seq


title: BAR-RR44_T12months


title: BAR-IG47_T12months


title: SS52_T0

description: Genome-wide DNA methylation  in obese persons before metabolic surgery

value: before metabolic surgery


title: BAR-DN39_T12months


title: BAR-RR44_T0


title: BAR-TK22_t0


title: 25-CD8 RNA seq


title: NA51_T0


title: nw59_t0


title: MM21_t0


title: TR38_T0


title: ES18_t0


title: GDF11_3

city: S. Giovanni Rotondo (FG)

first: Tommaso

last: Mazza

address: Viale Cappuccini, 1

department: Bioinformatics

country: Italy

institute: IRCCS Casa Sollievo della Sofferenza

description: RIN: 8.92

data_processing:
Reads trimming performed using Trimmomatic
Residual adapter removed using cutadapt
Reads aligned with STAR 2.6
Reads were rlog transformed
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file includes rlog values for each sample

molecule: total RNA

source_name: HepG2 - immortalized cell line

growth_protocol: HepG2 cell line was purchased from ATCC and cultured in DMEM (1X) supplemented with 10% fetal bovine serum (FBS), with 1% penicillin/streptomycin.

extract_protocol:
Total RNA was reverse transcribed using the Quantitect Transcription kit (Qiagen), according to the manufacturer's instructions
Indexed libraries were prepared from purified RNA with the TruSeq Total Stranded RNA Sample Prep Kit (Illumina) according to the manufacturer’s instructions. Libraries were quantified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Index-tagged samples were equimolar and the overall concentration was 2 nM. The pooled samples were subject to cluster generation and sequenced using an Illumina HiSeq 2500 System (Illumina) in a 2x100 paired-end format at a final concentration of 8 pmol.

treatment_protocol: After plating, HepG2 an cells were treated with 200 nM GDF11, for 24 hours

value: Hepatocellular Carcinoma

value: Liver

tag: age

value: 15-year-old Caucasian American male


title: 92-4-1BB-posRNA seq

tag: 4-1bb level / pd1 level


title: CTL_3

description: RIN: 9.60


title: BAR-NS20_t12months


title: 92-PD-1-intRNA seq


title: GDF11_2

description: RIN: 8.91


title: BAR-NS20_t0


title: CTL_2

description: RIN: 9.70


title: BAR-MG48_T0


title: 147-4-1BB-negRNA seq


title: 147-4-1BB-posRNA seq


title: CTL_1

description: RIN: 9.10


title: SH64_T0


title: IK36_T0


title: 136-PD-1-intRNA seq


title: 92-4-1BB-negRNA seq


title: GDF11_1

description: RIN: 8.90


title: 147-PD-1-intRNA seq


title: PAB8_CLIP-seq

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

department: State Key Laboratory of Plant Genomics

country: China

institute: Institute of Genetics and Developmental Biology

description: high-throughput profiling of AtPAB8 binding

data_processing:
CLIP-seq reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using NovoAlign. Pyicoclip was used to identify AtPABs binding clusters.
Ribosome profiling reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count.
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig program

organism: Arabidopsis thaliana

source_name: 2-week seedlings

growth_protocol: The wild-type Col, atpabs mutants and AtPABs complementary lines were grown on Murashige and Skoog plates with 3% Suc for 14 days

extract_protocol:
The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).
CLIP-seq libraries generated from Col and AtPABs complementary lines were constructed following the published method in Arabidopsis (Zhang et al., 2015). Ribosome profiling libraries generated from Col and atpabs were constructed following the published method in Arabidopsis (Juntawong et al., 2014). Strand-specific RNA-Seq libraries generated from Col, atpabs were constructed mRNA-Seq library by SMART method (Levin et al., 2010)

treatment_protocol: The seedlings grown at 23°C under 16 h of light followed by 8 h of darkness

tag: genotype

value: PAB8 complementary line

tag: clip antibody

value: anti-HA (sigma, H6908)

tag: developmental stage

value: 2-week seedlings

value: seedling


title: hsPool: wt scS100 -CMC

city: Cambridge

first: Thomas

middle: M

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

department: Biology

institute: MIT

data_processing:
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed using fastx_collapser
PCR duplicates collapsed using fastx_collapser
Sequences were trimmed of 3′ adapter (both pools) and 10 random Ns (yeast pools only) using cutadapt
Reads were mapped to bowtie indices of the pools with tophat2
Pseudouridylation was assessed using cutom python scripts (see text)
Genome_build: Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)

source_name: Human Pool

extract_protocol:
Oligo pools (yeast, Twist Biosciences; human Custom Array) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
RNA was phenol:chloroform extracted from pseuoduridylation reactions, treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.
OTHER: Pseduo-seq

tag: pus activity source

value: S100 extract from Wild Type Yeast

tag: cmc use

tag: bowite fasta


title: MV42_T0


title: ESC_100ng

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

description: LM-PCR is the library strategy used for all the samples. But it is our own modified protocol that enables methylation detection in all samples concurrently with copy number aberrations and we call it DARE- DNA Analysis by Restriction Enzymes.

library_source: genomic

data_processing:
UMI processed using umi-tools version 0.5.4
Unmethylation and methylation reads were separated and the tags were removed using Cutadapt version 1.5
Reads were aligned to the human genome using bowtie2 version 2.3.4.1
PCR duplicates were removed using umi-tools version 0.5.4
Genome_build: hg38
Supplementary_files_format_and_content: bed files containing chromosome, start, end, methylation ratio and coverage for each CCGG site

source_name: Embryonic stem cell line

extract_protocol:
For bulk samples, DNA was extracted using Qiagen Dneasy Blood and Tissue kit. Single cells were stained with Calcein-AM dye and isolated into tubes.
Cells were lysed and protease treated prior to HpaII digestion. Digested unmethylated sites were ligated with unmethylation-tag (U-tag) adapters. Excess adapters were then removed using NEB Thermolabile USER II enzyme. This was followed by the second round of digestion with MspI and NlaIII enzymes. Methylation-tag (M-tag) and Nla-tag (N-tag) adapters were ligated with the digested fragments. Excess adapters and oligonucleotides were removed with Thermolabile USER and Exonuclease enzymes. The Read1 and Read2 Illumina sequencing adapters were added through PCR. The amplified library was size selected using BluePippin and quantified using Kapa Library Quantification kit.

tag: cell line

tag: sample type

value: bulk


title: BAR-MD35_T12months


title: PAB4_CLIP-seq

description: high-throughput profiling of AtPAB4 binding

value: PAB4 complementary line


title: hsPool: Truncated Pus1 -CMC

value: Recombinant Truncated hPus1


title: PAB2_CLIP-seq

description: high-throughput profiling of AtPAB2 binding

value: PAB2 complementary line


title: hsPool: Full Length Pus1 +CMC

value: Recombinant Full Length hPus1

value: 0.4M CMC


title: BAR-YF_K2

value: Skeletal muscle

value: Control

value: No metabolic surgery


title: BAR-KT41_t0

value: Obese

value: before metabolic surgery


title: hsPool: wt scS100 +CMC


title: 106-PD-1-intRNA seq

tag: cell type

value: CD8 T cells


title: Output 4BX [332-OU-4BX]

city: barcelona

first: benedetta

last: bolognesi

state: Barcelona

address: c comte borrell 232 5a-1a

country: Spain

institute: IBEC

description: from plasmid library

data_processing:
library strategy: DNA-seq of PCR amplicon
Read trimming (with cutadapt)
Paired end read merging (PEAR)
Base-calling (custom python scripts)
Toxicity score calculation :Sample-wise counts for variants identical at the AA level were aggregated. For each replicate selection, relative toxicity of variants was calculated from variant counts in input (Fx input) and output (Fx output) samples as Relative toxicityx= ESwt-ESx, where ESx= log(Fx output/Fx input) and ESwt  represents the wild-type enrichment score.
Error calculation:Uncertainty of toxicity values was estimated as  a combination of expected error based on read counts and error between replicate selections as ������I= sqrt (1/Fx input + 1/Fx output + 1/FWT input + 1/FWT output + ������r2 ). Here, ������r, the error between replicate selections, is estimated from the variance of toxicity estimates across replicates for variants whose expected count-based error approaches zero. Toxicity estimates and associated errors per replicate selection were also normalized by the replicate-specific number of cell doublings during selection to yield relative growth rates per generation.
Supplementary_files_format_and_content: BB_AJF_BL_processed_data.xlsx - Tabular format. Headers: Pos= AA position of single mutation WT_AA = WT residue, Mut = mutated residue Nmut,_nt = number of nt mutations involved, N_mut_codon = number of codon changes involved, STOP = mutations causing introduction of stop codons, mean_count = mean read counts ofthe input replicates, sigma= error over toxicity(see Methods), toxicity= Relative toxicity of single mutation, Pos1=AA position of mutation 1 in double mutant  Pos2=AA position of mutation 2 in double mutant, WT_AA1 = WT residue 1,WT_AA2=WT residue 2, Mut1= mutated residue 1, Mut2 =mutated residue 2, sigma1= error over toxicity 1, sigma2= error over toxicity 2,  sigma_uncorr = uncorrected error over toxicity of double mutation, sigma_cond= corrected error over toxicity of double mutation (see Methods), toxicity1= Relative toxicity of mutation 1 in double mutant, toxicity2=Relative toxicity of mutation 2 in double mutant, toxicity_uncorr = uncorrected relative toxicity of double mutant, toxicity_cond = corrected relative toxicity fo double mutant, region= Library to which mutation(s) belong, Pos_abs = absolute residue position of single mutant in the TDP-43 sequence , Pos_abs1= absolute residue position of mutation 1 of double mutant in the TDP-43 sequence, Pos_abs2= absolute residue position of mutation 2 of double mutant in the TDP-43 sequence, mut_code = ID of mutation for single mutants, mut_code1 = ID of mutation 1 of double mutant ,mut_code2= ID of mutation 2 of double mutant.
Supplementary_files_format_and_content: BB_AJF_BL_processed_data_replicates.xlsx: Same as BB_AJF_BL_processed_data.xlsx, but with information about individual replicates.

organism: Saccharomyces cerevisiae

source_name: yeast culture_output

growth_protocol: Yeast cells were transformed with the TDP-43 doped plasmid and  grown overnight in 30 ml YPDA medium at 30ºC for each replica. After ~50 h of growth, cells were diluted in SC-URA 2% raffinose medium and grown for 4.5 generations. At this stage, each replica was harvested, washed, split into two tubes and frozen at -20ºC for later extraction of input DNA. To induce plasmid expression, for each replicate two cultures were diluted in in SC-URA 2% galactose medium. After 5-6 generations, 2 aliquots for each replicate were harvested to obtain output pellets for DNA extraction

extract_protocol:
Cell pellets  were resupended in 1.5 mL extraction buffer (2% Triton-X, 1% SDS, 100mM NaCl, 10mM Tris-HCl pH8, 1mM EDTA pH8), frozen by dry ice-ethanol bath and incubated at 62ºC water bath twice. Subsequently, 1.5mL of Phenol/Chloro/Isoamyl 25:24:1 (equilibrated in 10mM Tris-HCl, 1mM EDTA, pH8) was added, together with 1.5 g of glass beads and the samples were vortexed for 10 min. Samples were centrifuged at RT for 30 min at 4,000 rpm to phase separate and the aqueous phase was transferred into new tubes. The same step was repeated twice. 1:10V of NaOAc 3M and 2.2V of cold ethanol 100% were added to the aqueous phase. The mix was incubated at -20ºC for 30 min and after that, centrifuged for 30 min at full speed at 4ºC to precipitate the DNA. The ethanol was removed and the DNA pellet allowed to dry overnight at RT. DNA pellets were resuspended in 900 µL TE 1X and treated with RNAseA (10 mg/mL, Thermo Scientific) for 30 min at 37ºC. To desalt and concentrate the DNA solution, QIAEX II Gel Extraction Kit was used (75 µL of QIagen beads). Finally the sample was washed 3 times with PE and eluted twice in 375 10 mM Tris·Cl, pH 8.5
PCR amplification in two steps using Q5 High-Fidelity DNA Polymerase (NEB). In step 1, 300 million plasmids were amplified for 15 cycles using frame-shifted adaptor primers with a partial homology to standard Ilumina sequencing primers. PCR products from the first step were used as templates in the second PCR step, where indexed Illumina primers were used for a 10 cycles amplification. DNA concentration was then quantified by means of a Quant-iT™ PicoGreen® dsDNA Assay Kit (Promega). All replicates were pooled together in an equimolar ratio. Finally, the pooled sequencing library was run on a 2% agarose gel, purified and sent for 125 bp paired-end Illumina sequencing.

tag: strain

value: Strain BY4741

value: library  TDP aa 332-373 output

tag: molecule subtype

value: PCR amplicon


title: 106-4-1BB-posRNA seq


title: Output 4AX [332-OU-4AX]

description: from plasmid library


title: 106-4-1BB-negRNA seq


title: control_CLIP-seq

description: high-throughput profiling of anti-HA binding in Col (wild type)

value: wild type

value: anti-HA (sigma, H6908)

value: 2-week seedlings

tag: tissue

value: seedling


title: 136-4-1BB-negRNA seq


title: Output 3AX [332-OU-3AX]

description: from plasmid library


title: BAR-IG47_T0

tag: tissu


title: Output 2BX [332-OU-2BX]

description: from plasmid library


title: 101-PD-1-intRNA seq


title: BAR-MD35_T0

tag: group


title: Output 2AX [332-OU-2AX]

description: from plasmid library


title: AxLN_HE_3

city: Würzburg

first: Gustavo

middle: Campos

last: Ramos

address: AM Schwarzenberg, 15

department: DZHI

institute: Universitätsklinikum Würzburg

description:
TCR-beta
5e5 cells

data_processing:
The sequenced data was put through iRepertoire's software pipeline. Raw data was analyzed using the previously described iRmap program (Wang,C., PNAS and Yang Yang, eLife). Briefly, sequence reads were de-multiplexed according to barcode sequences at the 5’ end of reads from the TCR beta constant regions. Reads were then trimmed according to their base qualities with a 2-base sliding window. If either quality value in this window is lower than 20, this sequence stretches from the window to 3’ end were trimmed out from the original read. Trimmed pair-end reads were joined together through overlapping alignment with a modified Needleman-Wunsch algorithm. If paired forward and reverse reads in the overlapping region were not perfectly matched, both forward and reverse reads were thrown out without further consideration. The merged reads were mapped using a Smith-Waterman algorithm to germline V, D, J and C reference sequences downloaded from the IMGT web site (Lefranc, 2003). To define the CDR3 region, the position of CDR3 boundaries of reference sequences from the IMGT database were migrated onto reads through mapping results, and the resulting CDR3 regions were extracted and translated into amino acids.
Genome_build: IMGT
Supplementary_files_format_and_content: csv showing TCRb CDR3 sequence, J-gene segment, V-gene segment, and relative frequency

organism: Mus musculus

source_name: CD4+ T-cells, Ax_LN

growth_protocol: Mice were kept in individually ventilated cages under specific pathogen-free (SPF) conditions with a 12-hour light-dark cycle, at standard diet ad libitum.

extract_protocol:
mice were sacrificed by cervical dislocation, whole-body perfusion with PBS was conducted, and organs were extracted for ex vivo analyses. Lymph nodes cells were obtained after grinding the tissue against a 30um filter mesh in Hank's balanced salt solution. A cardiac cell suspension was obtained after enzimatic digestion with Collagenase-II. CD4+ TCRbeta+ single cells were FACSed (FACS Aria-II, purity > 98%) into RLT lysis buffer (Qiagen,  Hilden, Germany) and stored at -80oC. RNA purification was performed using the Qiagen microKit plus. RNA quality was checked using the Agilent 2100 Bioanalyzer. TCRb-sequencing was outsourced to the specialized company iRepertoire.
For the construction of mouse TCR beta chain libraries, iRepertoire used amplicon rescued multiplex PCR (arm-PCR) to amplify each of the 19 submitted RNA samples. The cDNA synthesis protocol involved initial first-round RT-PCR using high concentrations of gene-specific primers (iRepertoire's MTBIvc primers), followed by Beckman Coulter's SPRIselect bead-cleanup procedure, and PCR2 using universal primers to amplify the cDNA exponentially. Each constructed library was measured for concentration and quality using Thermoscientific's Nanodrop 1000, then pooled using 200 ng per constructed library. This pool was QC'ed using a bioanalyzer, KAPA qPCR analysis, and Qubit quantitation. The QC'ed pool was then sequenced according to Illumina's HiSeq sequencing guidelines using a 300-cycle reagent kit.
Libraries were pooled and sequenced with the Illumina HiSeq. The output of the mouse TRB sequence covers within the third framework region through the CDR3 and the beginning of the constant region.

treatment_protocol: Myocardial infarction group: ligation of left-anterior descending coronary artery. Sham-operatoin group: thoracotomy without artery ligation. Pain management for 72 h post-surgery (buprenorphine s.c. 0.1 mg/kg body weight). Immunized animals received s.c. immunization with porcine cardiac myosin (100 µg, s.c. Sigma-Aldrich, Schnelldorf, Germany) or with a mouse heart protein extract (1 mg s.c., ax-LNs and si-LNs), both emulsified in 200 or 600 µl of Titermax Gold® (Sigma-Aldrich, Schnelldorf, Germany) as adjuvant. The heart extract was obtained after mechanical homogenization (TissueRuptor, Qiagen) of whole hearts in PBS, ratio 1:15 (wt/vol), as previously described (17), and the total protein concentration was determined by the BCA method (Pierce). As a control, we purified CD4+ T cells from the ax-LNs of mice receiving the 200 µl adjuvant injection only. FACS purification (day 7 post-MI or postimmunization)

value: Balb/c

value: Axilary lymph node

value: CD4+ T-cells

tag: treatment

value: Heart extract-immunization

tag: time (days post-operation/immunization)

value: 7 d


title: BAR-NS_K11

description: Genome-wide DNA methylation in controls

value: Skeletal muscle

value: Control

tag: time point


title: Output 1AX [332-OU-1AX]

description: from plasmid library


title: AxLN_HE_1

description:
TCR-beta
5e5 cells


title: BAR-DK_K15

description: Genome-wide DNA methylation in controls

value: No metabolic surgery


title: 101-4-1BB-posRNA seq

tag: 4-1bb level / pd1 level


title: Input 4 [332-IN-4A]

description: from plasmid library

source_name: yeast culture_input

value: library  TDP aa 332-373 input


title: Input 3 [332-IN-3A]

description: from plasmid library


title: 101-4-1BB-negRNA seq

value: CD8 T cells


title: AxLN_Myosin_2

description:
TCR-beta
5e5 cells

value: Myosin-immunization


title: BAR-SS_K7

description: Genome-wide DNA methylation in controls


title: AxLN_Myosin_1

description:
TCR-beta
5e5 cells


title: Input 2 [332-IN-2A]

description: from plasmid library

value: Strain BY4741


title: hsPool: Truncated Pus1 +CMC

value: Recombinant Truncated hPus1

value: 0.4M CMC


title: Input 1 [332-IN-1A]

description: from plasmid library

value: PCR amplicon


title: Output 8B [bTDP1-OU-8B]

description: from plasmid library

value: library TDP aa 290-331 output


title: SC136SSCUP

description: SSC 7

data_processing:
10X Genomics' Cell Ranger 2.0 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 2.0 software's cellranger count function
Cell Ranger output of raw_gene_bc_matrices were utilized for further downstream analysis in R with the package Seurat 2.3.4, only cells expressing at least 200 genes were kept for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: tsv files contain lists of genes and barcodes for each sample, mtx files count gene UMI couns for each sample

source_name: upper lobe lung_scleroderma patient

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide

tag: subject status

value: systemic sclerosis-  associated interstitial lung disease (SSc-ILD) patient

value: lung

tag: lung section/portion

value: upper lobe lung

tag: 10x genomics chemistry

value: 10X Genomics 3 Prime V2 chemistry


title: AxLN_Adj_4

description:
TCR-beta
5e5 cells

value: Balb/c

value: Axilary lymph node

value: CD4+ T-cells

value: Adjuvant-immunization


title: Output 8A [bTDP1-OU-8A]

description: from plasmid library


title: Output 7B [bTDP1-OU-7B]

description: from plasmid library


title: BAR-DN39_T0

value: Skeletal muscle

value: Obese

value: before metabolic surgery


title: Output 7A [bTDP1-OU-7A]

description: from plasmid library


title: hsPool: Full Length Pus1 -CMC

tag: pus activity source

value: Recombinant Full Length hPus1

tag: cmc use


title: SC135SSCLOW

description: SSC 8

source_name: lower lobe lung_scleroderma patient

value: lower lobe lung


title: Output 6B [bTDP1-OU-6B]

description: from plasmid library

value: Strain BY4741


title: AxLN_Adj_2

description:
TCR-beta
5e5 cells

value: 7 d


title: SC108SSCLOW

description: SSC 6


title: AxLN_Adj_3

description:
TCR-beta
5e5 cells


title: BAR-SP_K9

description: Genome-wide DNA methylation in controls

value: Control

value: No metabolic surgery


title: SC109SSCUP

description: SSC 5

value: systemic sclerosis-  associated interstitial lung disease (SSc-ILD) patient


title: AxLN_HE_2

description:
TCR-beta
5e5 cells

value: Heart extract-immunization


title: SC64SSCUP

description: SSC 3

value: lung

value: upper lobe lung


title: BAR-HP_K6

description: Genome-wide DNA methylation in controls


title: Input 8 [bTDP1-IN-8A]

description: from plasmid library

value: library TDP aa 290-331 input

value: PCR amplicon


title: SC63SSCLOW

description: SSC 4

value: 10X Genomics 3 Prime V2 chemistry


title: Heart_MI_3

description:
TCR-beta
5e3 cells

source_name: CD4+ T-cells, cardiac

value: Balb/c

value: Heart

value: CD4+ T-cells

value: Myocardial infarction


title: Input 6 [bTDP1-IN-6A]

description: from plasmid library


title: Input 5 [bTDP1-IN-5A]

description: from plasmid library


title: Input 7 [bTDP1-IN-7A]

description: from plasmid library


title: Output 5B [bTDP1-OU-5B]

description: from plasmid library

value: library TDP aa 290-331 output


title: SC52SSCUP

description: SSC 1


title: BAR_KS_K3

description: Genome-wide DNA methylation in controls

value: Skeletal muscle


title: Heart_MI_1

description:
TCR-beta
5e3 cells


title: 136-4-1BB-posRNA seq

value: CD8 T cells


title: AxLN_Adj_1

description:
TCR-beta
5e5 cells

value: Axilary lymph node

value: Adjuvant-immunization

value: 7 d


title: Output 5A [bTDP1-OU-5A]

description: from plasmid library

value: Strain BY4741


title: SC51SSCLOW

description: SSC 2

value: systemic sclerosis-  associated interstitial lung disease (SSc-ILD) patient

value: lower lobe lung


title: MedLN_MI_3

description:
TCR-beta
5e5 cells

source_name: CD4+ T-cells, Med-LN

value: Mediastinal lymph node


title: CK rep3

city: 咸阳

first: Jian

last: Luo

address: 西北农林科技大学

institute: 西北农林科技大学

description: Wheat inferior grain grain filling

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: Triticum_aestivum.IWGSC1_popseq.31
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Triticum aestivum

source_name: wheat grain

growth_protocol: Under field conditions

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Exogenous spermidine

value: inferior grain

tag: development stage

value: At 8 and at 16 days post anthesis

tag: cultivar

value: Xinong 538


title: SC156NORUP  [re-used]

description: CONTROL 4

value: healthy control

value: lung

value: upper lobe lung

value: 10X Genomics 3 Prime V2 chemistry


title: SPD rep3

description: Wheat inferior grain grain filling


title: SPD rep2

description: Wheat inferior grain grain filling


title: Heart_MI_2

description:
TCR-beta
5e3 cells

value: Balb/c

value: Heart

tag: cell type

value: CD4+ T-cells

value: Myocardial infarction


title: SC155NORLOW  [re-used]

description: CONTROL 5

source_name: lower lobe lung_healthy donor


title: MedLN_MI_2

description:
TCR-beta
5e5 cells

tag: strain


title: MedLN_MI_1

description:
TCR-beta
5e5 cells


title: SPD rep1

description: Wheat inferior grain grain filling


title: SC59NOR  [re-used]

description: CONTROL 3

source_name: mix of upper + lower lobe lung_healthy donor

value: mix of upper + lower lobe lung


title: CK rep2

description: Wheat inferior grain grain filling


title: SC56NOR  [re-used]

description: CONTROL 2


title: MedLN_SHAM_4

description:
TCR-beta
5e5 cells

value: Sham-operation

value: 7 d


title: MedLN_SHAM_3

description:
TCR-beta
5e5 cells


title: Raji_30min

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 or hg38 genome using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to reads per kilobase per million (RPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 3 reads per million (Raji B cells) or 10 reads per million (mouse ASC) in all samples.
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: RPKM normalized read counts for all detected genes from the mouse ASC samples mapped to mm10 or from the Raji B cell samples mapped to hg38.

source_name: Raji B cells

growth_protocol: Raji B cells were cultured in RPMI supplemented with 10% FCS and 100 U/ml Penecillin/Streptomycin

extract_protocol:
RNA lysates were incubated at 65 degrees C for the indicated time and total RNA extracted using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMARTer Stranded Total RNA-seq kit v2 (Takara).

treatment_protocol: Splenocytes were intracellulary stained using the BD Cytofix/Cytoperm kit (Cat# 554714) according to the manufacturers instructions and sorted directly into RLT +1% Bme lysis buffer (Qiagen).

tag: gender

value: male

tag: cell line

value: Raji (ATCC, CCL-86)

value: Raji B cells

tag: decrosslinking time at 65 degrees c

value: 30 min

tag: genome build


title: SC45NOR  [re-used]

description: CONTROL 1

tag: tissue


title: MedLN_SHAM_2

description:
TCR-beta
5e5 cells

value: Mediastinal lymph node

tag: treatment

tag: time (days post-operation/immunization)


title: MedLN_SHAM_1

description:
TCR-beta
5e5 cells


title: Raji_15min

value: 15 min


title: Raji_5min

value: 5 min


title: Output 6A [bTDP1-OU-6A]

description: from plasmid library

value: Strain BY4741

tag: sample type

value: library TDP aa 290-331 output

tag: molecule subtype

value: PCR amplicon


title: Wild-type agr-positive nares strain, replicate B

city: New York

first: Kieran

middle: Ifan

last: Chacko

state: NY

address: One Gustave L. Levy Place

department: Genetic & Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were first trimmed by removing Illumina adapter sequences from 3’ ends using cutadapt with a minimum match of 32 base pairs and allowing for 15% error rate. Trimmed reads were mapped to the reference genome using Bowtie2, and htseq-count was used to produce strand-specific transcript count summaries. Read counts were then combined into a numeric matrix and used as input for differential gene expression analysis with the limma R package in Bioconductor. Normalization factors were computed on the data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voom mean-variance transformation in preparation for Limma linear modeling.
Genome_build: PS00089_1A (genome fasta and annotations included as raw data files)
Supplementary_files_format_and_content: Tab-delimited text files containing the Gene ID and the normalized Log2 count per million reads.

organism: Staphylococcus aureus

source_name: Wild-type agr-positive nares strain

growth_protocol: Overnight cultures were diluted and grown to late-log phase (~0.80 OD) and stabilized in RNALater

extract_protocol:
Total RNA was isolated and purified using the QIAGEN RNeasy Mini Kit. Lysozyme and lysostaphin were used for cell wall degradation, followed by two cycles of two-minute bead beating with 1 ml of 0.1 mm silica beads in a mini bead-beater (BioSpec), and eluted in nuclease-free water. Isolated RNA was treated with 1 uL of Baseline Zero DNase (Epicentre) at 37°C for 30 min and ribosomal RNA depletion was performed using Epicenter Ribo-ZeroTM Magnetic Gold Kit (Illumina), according to the manufacturer’s instructions.
After RNA extraction, barcoded stranded RNA-Sequencing libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina). RNA quality and quantity was assessed using the Agilent Bioanalyzer and Qubit RNA Broad Range Assay kit (Thermo Fisher), respectively. Finally, Libraries were pooled and sequenced on the Illumina HiSeq platform in a 100 bp single-end read run format.

tag: phenotype

value: wild type


title: CK rep1

description: Wheat inferior grain grain filling

value: inferior grain

value: At 8 and at 16 days post anthesis

value: Xinong 538


title: atpabs_RNA-seq_rep2

description: high-throughput profiling of transcriptome in atpabs (mutant)

tag: genotype

value: atpabs mutant

tag: developmental stage

value: 2-week seedlings

value: seedling


title: Agr knock-out nares strain, replicate A

source_name: Agr knock-out nares strain

value: delta-agr


title: Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_4

type: RNA

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description:
Clec4f+ macrophages at day 18 of embryogenesis
Clec4f+ macrophages at day 18 of embryogenesis

hyb_protocol: All Methods listed in Bonnardel et al.  Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Bioconductor. Normalisation was done by RMA.
All samples passed quality control, and the Robust Multi-array Average (RMA) procedure was used to normalize data within arrays (probeset summarization, background correction and log2-transformation) and between arrays (quantile normalization).

label: Biotin

source_name: Liver


title: Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_4

description:
Clec4f+ macrophages at day 17 of embryogenesis
Clec4f+ macrophages at day 17 of embryogenesis

label_protocol: All Methods listed in Bonnardel et al.  Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.


title: Kupffer cells at day of birth KC_D0_4

description:
Kupffer cells at day of birth
Kupffer cells at day of birth

growth_protocol: All Methods listed in Bonnardel et al.  Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.


title: Kupffer cells at day of birth KC_D0_1

extract_protocol: All Methods listed in Bonnardel et al.  Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.


title: atpabs_RNA-seq_rep1

source_name: 2-week seedlings


title: Output 3BX [332-OU-3BX]

description: from plasmid library

value: library  TDP aa 332-373 output


title: Kupffer cells at day of birth KC_D0_3

treatment_protocol: All Methods listed in Bonnardel et al.  Stellate cells, hepatocytes and endothelial cells imprint the Kupffer cell identity on monocytes colonizing the liver macrophage niche . Immunity. 2019.


title: Wild-type agr-positive nares strain, replicate A


title: Agr knock-out nares strain, replicate B


title: col_RNA-seq_rep2

description: high-throughput profiling of transcriptome in Col (wild type)


title: Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_1


title: Kupffer cells at day of birth KC_D0_2


title: Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_3


title: Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_4

description:
Clec4f- macrophages at day 17 of embryogenesis
Clec4f- macrophages at day 17 of embryogenesis


title: Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_3


title: Clec4f+ macrophages at day 17 of embryogenesis C4pos_mac_E17_2


title: Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_1


title: Clec4f+ macrophages at day 18 of embryogenesis C4pos_mac_E18_2


title: Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_3


title: Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_2


title: Agr complemented blood strain, replicate B

source_name: Agr complemented blood strain


title: col_RNA-seq_rep1


title: Wild-type agr-deficient blood strain, replicate B

source_name: Wild-type agr-deficient blood strain


title: Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_3

description:
Clec4f- macrophages at day 15 of embryogenesis
Clec4f- macrophages at day 15 of embryogenesis


title: Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_4


title: Agr complemented blood strain, replicate A


title: Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_2


title: atpabs_RF_rep1

description: high-throughput profiling of ribosome protected fragments in atpabs (mutant)

data_processing:
Library strategy: Ribosome profiling
CLIP-seq reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using NovoAlign. Pyicoclip was used to identify AtPABs binding clusters.
Ribosome profiling reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count.
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig program


title: Clec4f- macrophages at day 17 of embryogenesis C4neg_mac_E17_1


title: Clec4f- macrophages at day 15 of embryogenesis C4neg_mac_E15_1


title: Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_3

description:
Clec4f- macrophages at day 12 of embryogenesis
Clec4f- macrophages at day 12 of embryogenesis


title: Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_4


title: Wild-type agr-deficient blood strain, replicate A


title: col_RF_rep2

description: high-throughput profiling of ribosome protected fragments in Col (wild type)


title: col_RF_rep1


title: K562_SC10

source_name: Chronic myelogenous leukemia

value: Single cell


title: K562_SC9


title: miR-124 25 let-7AR-transfected Muller glia

city: Seattle

last: Reh

state: WA

address: 1959 NE Pacific St

department: Biological Structure

institute: University of Washington

data_processing:
Data preprocessing and alignment to the mm10 genome was done using cell ranger V2
Cells were filtered by the percentage of mitochondrial gene expression, and number of features per cell
Data were processed, aggregated and analyzed using Seurat v2
Genome_build: mm10
Supplementary_files_format_and_content: counts matrix tables, barcodes and cells are provided for each treatment

source_name: Retina

growth_protocol: Muller glial cultures were generated by dissociating retinas in papain and culturing in neurobasal media supplemented with 10% FBS, N2, L-glutamine, and EGF

extract_protocol:
10x genomics single cell system (V2)
RNA libraries were prepared for sequencing using standard 10x genomics and illumina protocols

treatment_protocol: MG cultures mice were transfected using Lipofectamine 3000 in Optimem medium, in accordance with manufacturer’s instructions. For individual mimics or antagomiR, the final concentration in the medium was 500 nM; in the case where multiple mimics were added, or combined with an antagomiR, each RNA was present in the medium at a final concentration of 500 nM

value: Retina

value: Muller glia

value: Let-7 antagomiR, miR-25 mimic and miR-124 mimic


title: let-7AR_miR-25-transfected Muller glia

value: Let-7 antagomiR and miR-25 mimic


title: atpabs_RF_rep2


title: Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_2


title: MiR-124-transfected Muller glia

value: Mir-124 mimic


title: K562_SC7


title: Yolk sac macrophages at day 11 of embryogenesis yolkSac_mac_E11_2

description:
Yolk sac macrophages at day 11 of embryogenesis
Yolk sac macrophages at day 11 of embryogenesis


title: K562_SC6


title: K562_SC5


title: Clec4f+ macrophages 7 days after Kupffer cell depletion C4pos_mac_D7_1

description:
Clec4f+ macrophages 7 days after Kupffer cell depletion
Clec4f+ macrophages 7 days after Kupffer cell depletion


title: Clec4f- macrophages at day 12 of embryogenesis C4neg_mac_E12_1


title: MiR-25-transfected Muller glia

value: MiR-25 mimic


title: F4/80+ macrophages 3 days after Kupffer cell depletion F4-80pos_mac_D3_1.1

description:
F4/80+ macrophages 3 days after Kupffer cell depletion
F4/80+ macrophages 3 days after Kupffer cell depletion


title: K562_SC4


title: F4/80+ macrophages 3 days after Kupffer cell depletion F4-80pos_mac_D3_1


title: F4/80+ macrophages 3 days after Kupffer cell depletion F4-80pos_mac_D3_1.2


title: K562_SC8


title: Control-transfected Muller glia

value: control miRNA mimic and antagomiR


title: Clec4f+ macrophages 7 days after Kupffer cell depletion C4pos_mac_D7_2


title: Yolk sac macrophages at day 11 of embryogenesis yolkSac_mac_E11_1


title: Yolk sac macrophages at day 11 of embryogenesis yolkSac_mac_E11_3


title: Clec4f+ macrophages 7 days after Kupffer cell depletion C4pos_mac_D7_3


title: Monocytes 1 day after Kupffer cell depletion mono_D1_3

description:
Monocytes 1 day after Kupffer cell depletion
Monocytes 1 day after Kupffer cell depletion


title: let-7AR-transfected Muller glia

value: Let-7 antagomiR


title: K562_SC3


title: Sample:D4

city: Oxford

first: Sarah

last: Gooding

state: Oxon

address: John Radcliffe Site, Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: Oxford University

description: processed data file: healthy_v_myeloma-bearing_rpkm_table.txt

data_processing:
Reads were aligned with STAR version 2.4.0, to the GRCm38 (mm10) genome build.
Reads were quantified as read counts using the featureCounts function from the Subread package version 1.4.5-p1.
Reads were quantified by edgeR as rpkm (reads per kilobase per million).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: All processed data for all expressed genes in all cell types is combined into rpkm table healthy_v_myeloma-bearing_rpkm_table.txt, such that normalised transcript abundance can be compared across tissues and between conditions.

source_name: 5TGM1-GFP Myeloma cells, bone lining

growth_protocol: 8-10 week-old C57Bl/KaLwRij mice were inoculated IV with PBS vehicle or 1 x10e6 5TGM1-GFP cells, and prospectively culled on day +23 from tumour inoculation.

extract_protocol:
Bones were flushed, washed, crushed, collagenase digested and bone lining niche cells were FACS sorted. 100 cells per sample were sorted into 4µl lysis buffer (Gooding et al., Nature Communications 2019).
RNA was extracted and libraries constructed according to SmartSeq2 protocol (Picelli et al., Nature Protocols 2014).

treatment_protocol: No treatments given.

tag: healthy vs. myeloma-bearing

value: myeloma-bearing

value: 5TGM1-GFP Myeloma cells, bone lining


title: Sample:E4


title: Sample:J6

source_name: 5TGM1-GFP Myeloma cells, central marrow

value: 5TGM1-GFP Myeloma cells, central marrow


title: Sample:I4


title: Monocytes 1 day after Kupffer cell depletion mono_D1_1


title: Sample:G4


title: K562_SC2


title: Sample:J4


title: Sample:G4A


title: Sample:I6


title: Monocytes 1 day after Kupffer cell depletion mono_D1_2


title: K562_SC1


title: Sample:D4a


title: Sample:J3

source_name: stromal progenitors

value: stromal progenitors


title: Sample:I3


title: Liver Hepatocyte 36h after Kupffer cell depletion Hepatocyte-36h-3

description:
Liver Hepatocyte 36h after Kupffer cell depletion
Liver Hepatocyte 36h after Kupffer cell depletion

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample


title: Liver Hepatocyte 36h after Kupffer cell depletion Hepatocyte-36h-2


title: Liver Hepatocyte 36h after Kupffer cell depletion Hepatocyte-36h-1


title: Sample:G3


title: HepG2_SC9

source_name: Hepatocellular carcinoma


title: Liver Hepatocyte 36h after Kupffer cell depletion Hepatocyte-36h-4


title: HepG2_SC10


title: Sample:D3


title: Sample:E3


title: Sample:O3

value: healthy


title: HepG2_SC8


title: HepG2_SC7


title: Sample:L3


title: Liver Hepatocyte 12h after Kupffer cell depletion Hepatocyte-12h-1

description:
Liver Hepatocyte 12h after Kupffer cell depletion
Liver Hepatocyte 12h after Kupffer cell depletion


title: Liver Hepatocyte 12h after Kupffer cell depletion Hepatocyte-12h-2


title: Liver Hepatocyte 12h after Kupffer cell depletion Hepatocyte-12h-3


title: HepG2_SC6


title: Sample:M3


title: Sample:N3


title: Sample:I2

source_name: osteoprogenitors

value: osteoprogenitors


title: Sample:E4a


title: HepG2_SC5


title: Sample:G2


title: Liver Hepatocyte in WT condition Hepatocyte-WT-4

description:
Liver Hepatocyte in WT condition
Liver Hepatocyte in WT condition


title: HepG2_SC4


title: Liver Hepatocyte 12h after Kupffer cell depletion Hepatocyte-12h-4


title: Sample:D2


title: Sample:N2


title: Liver Hepatocyte in WT condition Hepatocyte-WT-3


title: Liver Hepatocyte in WT condition Hepatocyte-WT-2


title: HepG2_SC2


title: Sample:M2


title: Sample:L2


title: HepG2_SC1


title: Liver Hepatocyte in WT condition Hepatocyte-WT-1


title: Sample:G1

source_name: endothelial cells

value: endothelial cells


title: Liver Sinusoidal Endothelial Cells 36h after Kupffer cell depletion LSEC-36h-4

description:
Liver Sinusoidal Endothelial Cells 36h after Kupffer cell depletion
Liver Sinusoidal Endothelial Cells 36h after Kupffer cell depletion


title: Sample:E1


title: Sample:O1


title: Sample:D1


title: Liver Sinusoidal Endothelial Cells 36h after Kupffer cell depletion LSEC-36h-3


title: K562_1ng_2

value: bulk


title: Liver Sinusoidal Endothelial Cells 36h after Kupffer cell depletion LSEC-36h-2


title: K562_1ng_1


title: Sample:J2


title: Sample:C3


title: Sample:N1


title: K562_100ng_2


title: Sample:O2


title: Sample:L1


title: HepG2_SC3

value: Single cell


title: K562_100ng_1


title: HepG2_1ng_2


title: Sample:I1


title: Sample:C1


title: Sample:J1


title: Liver Sinusoidal Endothelial Cells 36h after Kupffer cell depletion LSEC-36h-1


title: Liver Sinusoidal Endothelial Cells 12h after Kupffer cell depletion LSEC-12h-3

description:
Liver Sinusoidal Endothelial Cells 12h after Kupffer cell depletion
Liver Sinusoidal Endothelial Cells 12h after Kupffer cell depletion


title: C12KO_3RplusMSU4

city: Los Angeles

first: Kai

last: Li

address: 8700 Beverly Boulevard

institute: Cedar-Sinai Medical Center

data_processing:
The RNA-seq data were analyzed by using the Tuxedo pipeline accroding to Trapnell C, et al. (2012) Nat Protoc 7(3):562–578
The resulting reads were mapped to the mm9 mouse genome assembly by using Tophat2 (v2.1.1)
FPKM values of all samples from different experimental conditions were quantified and normalized by sequentially using Cuffquant and Cuffnorm (v2.2.0)
Genome_build: mm9
Supplementary_files_format_and_content: Nomalized FPKM values, Cuffnorm output

source_name: Bone marrow-derived dendritic cell

growth_protocol: 22-gauge needle was inserted into mouse femur and tibiae bones to flush out the bone marrow into R5 medium (RPMI supplemented with 5% FBS). Erythrocytes were lysed with G-DEX II RBC lysis buffer (Intron Biotechnology) and 5 million bone marrow cells were seeded into 10 cm non-treated petri dish (Sarstedt) in 10 ml complete RPMI supplemented with 10% FBS (PAN), 50 mM beta-mercaptoethanol, 100 U/ml penicillin, 100 mg/ml streptomycin and 20 ng/ml recombinant GM-CSF (immunotools). 10 ml of additional medium was given on day three. 10 ml of old medium was replaced with fresh medium on day six. On day nine, non-adherent and loosely adherent cells were collected by pipetting. Cells were washed once with R5 before stimulation.

extract_protocol:
Total RNA was extracted by using the RNeasy plus mini kit (Qiagen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing with Illumina TrueSeq using standard Illumina protocols

treatment_protocol: BMDCs left untreated or stimulated with 3pRNA (0.4ug/ml) alone or costimulated with 3pRNA+MSU crystal (500ug/ml) for 3 hours

value: Bone marrow-derived dendritic cell

tag: stimuli

value: 3pRNA transfected and MSU crystal stimulated


title: HepG2_1ng_1


title: C12KO_3RplusMSU1


title: Liver Sinusoidal Endothelial Cells 12h after Kupffer cell depletion LSEC-12h-2


title: Liver Sinusoidal Endothelial Cells 12h after Kupffer cell depletion LSEC-12h-1


title: WT_3RplusMSU4

value: wild type


title: Sample:M1


title: WT_3RplusMSU2


title: C12KO_3R4

value: 3pRNA transfected


title: C12KO_3RplusMSU3


title: WT_3RplusMSU1


title: Liver Sinusoidal Endothelial Cells in WT condition LSEC-WT-4

description:
Liver Sinusoidal Endothelial Cells in WT condition
Liver Sinusoidal Endothelial Cells in WT condition


title: Liver Sinusoidal Endothelial Cells in WT condition LSEC-WT-3


title: hsPool: PUS10_+CMC

data_processing:
Library strategy: Pseduo-seq
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed using fastx_collapser
PCR duplicates collapsed using fastx_collapser
Sequences were trimmed of 3′ adapter (both pools) and 10 random Ns (yeast pools only) using cutadapt
Reads were mapped to bowtie indices of the pools with tophat2
Pseudouridylation was assessed using cutom python scripts (see text)
Genome_build: Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)

source_name: Human Pool

extract_protocol:
Oligo pools (human, Twist Biosciences) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
RNA was phenol:chloroform extracted from pseuoduridylation reactions, treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.

tag: pus activity source

value: Recombinant Full Length hPUS10

tag: cmc use

value: 0.4M CMC

tag: bowtie fasta


title: Liver Sinusoidal Endothelial Cells 12h after Kupffer cell depletion LSEC-12h-4

tag: strain


title: hsPool: PUS10_-CMC


title: C12KO_3R2

tag: cell type


title: WT_3R4


title: Liver Sinusoidal Endothelial Cells in WT condition LSEC-WT-2


title: Liver Sinusoidal Endothelial Cells in WT condition LSEC-WT-1


title: C12KO_3R1


title: hsPool: RPUSD2_+CMC

value: Recombinant Full Length hRPUSD2


title: HepG2_100ng_2


title: C12KO_3R3


title: C12KO_Mock4

value: Mock stimulated


title: hsPool: noPUS_B_+CMC


title: C12KO_3RplusMSU2


title: Hepatic Stellate Cells 36h after Kupffer cell depletion HSC-36h-3

description:
Hepatic Stellate Cells 36h after Kupffer cell depletion
Hepatic Stellate Cells 36h after Kupffer cell depletion


title: C12KO_Mock2


title: WT_3R2


title: WT_3R3


title: C12KO_Mock3


title: Hepatic Stellate Cells 36h after Kupffer cell depletion HSC-36h-2


title: hsPool: noPUS_B_-CMC


title: WT_Mock4


title: hsPool: TRUB2_+CMC

value: Recombinant Full Length hTRUB2


title: C12KO_Mock1


title: HepG2_100ng_1


title: hsPool: TRUB2_-CMC


title: WT_Mock3


title: Hepatic Stellate Cells 36h after Kupffer cell depletion HSC-36h-1


title: WT_Mock2


title: Hepatic Stellate Cells 12h after Kupffer cell depletion HSC-12h-4

description:
Hepatic Stellate Cells 12h after Kupffer cell depletion
Hepatic Stellate Cells 12h after Kupffer cell depletion


title: hsPool: RPUSD2_-CMC


title: Hepatic Stellate Cells 12h after Kupffer cell depletion HSC-12h-3


title: WT_Mock1


title: hsPool: noPUS_A_-CMC


title: hsPool: noPUS_A_+CMC


title: Hepatic Stellate Cells 36h after Kupffer cell depletion HSC-36h-4


title: E2

city: Hershey

first: Yuka

last: Imamura Kawasawa

address: 500 University Dr.

department: College of Medicine, Pharmacology

institute: Penn State University

data_processing:
Bcl converion and demultiplexing using CASAVA 1.8.2. Adapter trimmed fastq files were generated.
Quality filter by FASTX Toolkit 0.0.13 (fastq_quality_filter: -Q33 -q 20 -p 80 was used as a parameter, fastq_quality_trimmer: -Q33 -t 20 -l 10 was used as a parameter). Fastq files were generated.
Read alignment using Tophat 2.0.9 using GRCh37 reference genome. BAM files were generated.
Log2-transformed RPKM (Reads Per Kilobase per Million mapped reads) values was calculated using HTSeq-count, followed by GC-correction provided with the Ensemble gene annotation using cqn R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: xlsx file including log2-RPKM gene expression data with WAD statistics from differential gene expression analysis

source_name: cultured in medium containing 50mM ethanol

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen). Optical density values of extracted RNA were measured using NanoDrop (Thermo Scientific) to confirm an A260:A280 ratio above 1.9. RNA integrity number (RIN) was measured using BioAnalyzer RNA 6000 Pico Kit (Agilent Technologies) to confirm RIN above 8.
The cDNA libraries were prepared using  KAPA Stranded RNA-Seq Kit with RiboErase (Kapa Biosystems) as per the manufacturer's instructions. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent) and Kapa Library Quantification Kit (Kapa Biosystems). The libraries were pooled and diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto TruSeq SR v3 flow cells on an Illumina HiSeq 2000 (Illumina) and run for 51 cycles using a single-read recipe (TruSeq SBS Kit v3, Illumina) according to the manufacturer's instructions.

value: cerebral cortex

tag: age (gestational weeks)

value: 18 gestational weeks


title: Hepatic Stellate Cells 12h after Kupffer cell depletion HSC-12h-1


title: E1

value: 15 gestational weeks


title: C2

source_name: cultured in control medium


title: Hepatic Stellate Cells in WT condition HSC-WT-4

description:
Hepatic Stellate Cells in WT condition
Hepatic Stellate Cells in WT condition


title: Hepatic Stellate Cells in WT condition HSC-WT-3


title: Hepatic Stellate Cells in WT condition HSC-WT-2


title: Hepatic Stellate Cells 12h after Kupffer cell depletion HSC-12h-2


title: 13E

description: processed data file: LDN-treated_v_vehicle-treated_rpkm_table.txt

data_processing:
Reads were aligned with STAR version 2.4.0, to the GRCm38 (mm10) genome build.
Reads that were identified as PCR duplicates using Samtools version 0.1.19 were discarded.
Reads were quantified as read counts using the featureCounts function from the Subread package version 1.4.5-p1.
Reads were quantified by edgeR as rpkm (reads per kilobase per million).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: All processed data for all expressed genes in all cell types is combined into rpkm table LDN-treated_v_vehicle-treated_rpkm_table.txt, such that normalised transcript abundance can be compared across tissues and between conditions.

source_name: Stromal Progenitors

treatment_protocol: From day +5 LDN193189 (3mg/kg, Sigma) or vehicle (20% (2-hydroxypropyl) betacyclodextrin) was injected IP daily, until day of cull.

tag: disease status

value: myeloma-bearing

tag: ldn vs. vehicle-treated

value: LDN

value: Stromal Progenitors


title: Hepatic Stellate Cells in WT condition HSC-WT-1

source_name: Liver


title: 12E


title: RAd4_cluster2_5

city: Stanford

first: Zhana

last: Duren

state: CA

address: 318 Campus Drive

institute: Stanford university

description: Retinoic-acid induction

data_processing:
Library strategy: HiChIP
Reads are mapped to mm9 using HiC-Pro
Call loop by HiChIPPer
Genome_build: mm9
Supplementary_files_format_and_content: bedpe file contain all valid pairs

source_name: mouse embryonic stem cell

growth_protocol: mESC were routingly grown in medium consisting of knockout DMEM supplemented with 15% knockout serum replacement with LIF growth factor. The cells were trypsinized when the cell density reached 80% confluent and replate on gelatin-coated plates.

extract_protocol:
Cells were crosslinked with freshly prepared 1% formaldehyde and lysed with Hi-C lysis buffer.
For bulk HiChIP data, we followed the HiChIP protocol developed by Mumbach et al., using antibody to H3K27ac.

treatment_protocol: mESC were diffferentiated using "hanging drop" method. The formation of embryonic bodies were then grown in the well of a 6-well ultra-low attachment plate with differentiation medium containg 0.5 uM retinoic acid for up to 4 days, with the medium being changed daily.

value: mouse embryonic stem cell

tag: treatment

value: retinoic acid for 4 days


title: scrib_14d rep4

city: Hong Kong

first: Yan

last: Yan

address: Clear Water Bay

department: LIFS

institute: HKUST

data_processing:
Cleaned raw reads were mapped to the reference genome using STAR with settings:        --outFilterMultimapNmax 20 --outFilterMultimapScoreRange 1 --outFilterScoreMinOverLread 0.33 \          --outFilterMatchNminOverLread 0.33 --outFilterMismatchNmax 10 --alignIntronMax 100000 --alignMatesGapMax 1000000 \          --alignSJDBoverhangMin 1 --sjdbOverhang 149 --sjdbScore 2 \ (Dobin et al., 2013).
Counts are generated by featureCounts available in Subread package (Liao et al., 2013).
Count normalization was performed using edgeR (Robinson et al., 2010).
Genome_build: GCF_000001215.4
Supplementary_files_format_and_content: txt files include Computes counts per million (CPM) values for each Sample

organism: Drosophila melanogaster

source_name: Imaginal wing disc

growth_protocol: Around 50 embryos collected within 3 hours were put in an individual vial of fly food to avoid crowding and the larvae were raised at 25-degree incubator for appropriate lengths of time before dissection.

extract_protocol:
Total RNA was extracted from control and scrib¹ wing imaginal discs with RNeasy Mini Kit (Qiagen).
Construction of cDNA libraries and 150bp paired-end sequencing on Illumina HiSeq platform were performed by Novogene.

value: scrib^1 FRT82B/TM6B

tag: tissue

value: Imaginal wing disc

tag: age

value: After Egg Laying 14d


title: scrib_14d rep3


title: 15E


title: RR44_12w

city: Nuthetal

last: Vogel

address: Arthur-Scheunert-Allee 114-116

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

description: Gene expression dynamic in response to bariatric surgery

hyb_protocol: For  each cRNA is hybridised on 8x60K microarrays at 65 ◦C for 17 h using Agilent’s recommended hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buﬀer 1 for one minute at ambient temperature followed by a second wash with preheated (37 ◦C) Gene Expression Wash Buﬀer 2 for one minute.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and  5 micron for HD Microarray formats, generating a 20 bit TIFF ﬁle.FSlides were scanned using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11 (Agilent) using default parameters  to obtain background subtracted and spatially detrended Processed Signal intensities. Data was filtered using 0.1 quantile cutoff to eliminate low level signals.

source_name: vastus lateralis

label_protocol: Cy3-labeled cRNA. For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate ﬂuorescent cRNA (complementary RNA). For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed. Please refer the summary ﬁle for details regarding the used primer, yield of cRNA as well as cy3 incorporation rate

extract_protocol: total RNA extracted following the manufacturer's recommendations, miRNA micro kit ( Qiagen, Hilden, Germany), The protocol includes separation of organic and aqueous layers, and an on-column DNase digestion

treatment_protocol: No treatment RNA extracted from frozen tissu

tag: tissu

value: Skeletal muscle

tag: group

value: Obese

tag: time point

value: 12 weeks post metabolic surgery


title: RAd4_cluster2_4

description: Retinoic-acid induction


title: NA51_12w


title: TR38_12w


title: C1


title: 11E


title: NA51_24w

value: 24 weeks post metabolic surgery


title: MV42_24w


title: RR44_24w


title: scrib_14d rep2

tag: genotype


title: SS52_24w


title: SH64_12w


title: NS20_12w


title: SS52_12w


title: NS20_24w


title: RAd4_cluster2_3

description: Retinoic-acid induction


title: TR38_24w


title: SH64_24w


title: TK22_24w


title: scrib_14d rep1


title: scrib_12d rep4

value: After Egg Laying 12d


title: RAd4_cluster2_2

description: Retinoic-acid induction


title: RAd4_cluster2_1

description: Retinoic-acid induction


title: 14E

value: Vehicle


title: 10E


title: RAd4_bulk_12

description: Retinoic-acid induction


title: scrib_12d rep3


title: scrib_12d rep2


title: 7E


title: scrib_12d rep1


title: RAd4_bulk_10

description: Retinoic-acid induction


title: RAd4_bulk_11

description: Retinoic-acid induction


title: 9E


title: 16E


title: 6E


title: RAd4_bulk_9

description: Retinoic-acid induction


title: scrib_10d rep4

value: After Egg Laying 10d


title: scrib_10d rep3


title: RAd4_bulk_8

description: Retinoic-acid induction


title: TK22_12w


title: scrib_10d rep2


title: 4E


title: RAd4_bulk_7

description: Retinoic-acid induction


title: RAd4_bulk_6

description: Retinoic-acid induction


title: 13D

source_name: Osteoprogenitors

value: Osteoprogenitors


title: RAd4_bulk_5

description: Retinoic-acid induction


title: 12D


title: scrib_8d rep4

value: After Egg Laying 8d


title: scrib_10d rep1


title: scrib_8d rep3


title: 5E

value: myeloma-bearing


title: 15D

value: LDN


title: scrib_8d rep2


title: 3E

value: Stromal Progenitors


title: RAd4_bulk_3

description: Retinoic-acid induction

value: mouse embryonic stem cell


title: MV42_12w


title: WT_3RplusMSU3

value: Bone marrow-derived dendritic cell

value: wild type

value: 3pRNA transfected and MSU crystal stimulated


title: MM21_12w


title: 10D


title: scrib_8d rep1

value: scrib^1 FRT82B/TM6B

value: Imaginal wing disc


title: KT41_12w

value: Skeletal muscle

value: Obese


title: MG48_12w

value: 12 weeks post metabolic surgery


title: MD35_12w


title: MD35_24w

value: 24 weeks post metabolic surgery


title: IK36_12w


title: MM21_24w


title: RAd4_bulk_2

description: Retinoic-acid induction

value: retinoic acid for 4 days


title: IG47_24w

description: Gene expression of lean controls


title: RAd4_bulk_1

description: Retinoic-acid induction


title: scrib_6d rep3

value: After Egg Laying 6d


title: ES18_24w

description: Gene expression of lean controls


title: RAd4_bulk_4

description: Retinoic-acid induction


title: 9D

value: Osteoprogenitors


title: IK36_24w


title: IG47_12w

description: Gene expression of lean controls


title: KT41_24w


title: 14D

value: Vehicle


title: scrib_6d rep2


title: MG48_24w


title: m3_IgM

source_name: Antibody Secreting Cell

tag: gender

value: female

tag: infection

value: Influenza A/PR8/34

tag: day post infection

value: Day 14

value: Spleen and Mediastinal Lymph node

value: Antibody Secreting Cell

tag: sorting markers

tag: tetramer staining

value: NP+ HA+

tag: bcr isotype

value: IgM

tag: decrosslinking time at 65 degrees c

value: 15 min

tag: genome build


title: WT_3R1

tag: cell type

value: Bone marrow-derived dendritic cell

tag: strain

value: wild type

tag: stimuli

value: 3pRNA transfected


title: 7D

tag: disease status

value: myeloma-bearing

tag: ldn vs. vehicle-treated


title: scrib_6d rep1

value: scrib^1 FRT82B/TM6B

tag: tissue

value: Imaginal wing disc

tag: age


title: m3_IgG

value: IgG


title: 16D

value: Osteoprogenitors


title: m3_IgA

value: IgA


title: 5D

value: Vehicle


title: m2_IgM

value: female

value: Influenza A/PR8/34


title: scrib_5d rep4

value: After Egg Laying 5d


title: scrib_5d rep3


title: DN39_12w

description: Gene expression of lean controls

tag: tissu

value: Skeletal muscle

tag: group

value: Obese

tag: time point

value: 12 weeks post metabolic surgery


title: m2_IgG

tag: gender

tag: infection

value: Day 14

value: Spleen and Mediastinal Lymph node

value: Antibody Secreting Cell

value: NP+ HA+

value: 15 min


title: m2_IgA

tag: day post infection

tag: sorting markers


title: 13C

source_name: Endothelial cells

value: myeloma-bearing

value: LDN

value: Endothelial cells


title: 4D

value: Osteoprogenitors


title: m1_IgM

tag: tetramer staining

tag: bcr isotype

value: IgM


title: scrib_4d rep4

value: scrib^1 FRT82B/TM6B

value: Imaginal wing disc

value: After Egg Laying 4d

tag: genotype


title: scrib_5d rep1

value: After Egg Laying 5d


title: 12C

tag: cell type


title: SH64_T0

value: Skeletal muscle

value: Before metabolic surgery


title: scrib_5d rep2

tag: strain


title: 3D

value: Vehicle


title: 15C


title: DN39_24w

description: Gene expression of lean controls

value: Obese

value: 24 weeks post metabolic surgery


title: ES18_12w

description: Gene expression of lean controls

value: 12 weeks post metabolic surgery


title: m1_IgG

value: female

value: Influenza A/PR8/34

value: Day 14

value: Spleen and Mediastinal Lymph node

value: Antibody Secreting Cell

value: NP+ HA+

value: IgG

tag: decrosslinking time at 65 degrees c

tag: genome build


title: BAR-NS_K11

value: Control

value: No metabolic surgery


title: m1_IgA

value: IgA

value: 15 min


title: scrib_4d rep2

value: scrib^1 FRT82B/TM6B

value: Imaginal wing disc

value: After Egg Laying 4d


title: BAR-TR38_T2wks

description: Gene expression of lean controls

value: Skeletal muscle

value: Obese

value: 2 weeks after metabolic surgery


title: BAR-TR38_T52wks

description: Gene expression of lean controls

value: 52 weeks after metabolic surgery


title: BAR-TR38_T0

description: Gene expression of lean controls

value: Before metabolic surgery


title: scrib_4d rep1


title: 9C

tag: disease status

value: myeloma-bearing

tag: ldn vs. vehicle-treated

value: LDN

value: Endothelial cells


title: BAR-MV42_T52wks

description: Gene expression of lean controls

tag: tissue


title: 14C

value: Vehicle


title: scrib_4d rep3

tag: age


title: WT_5d rep4

value: After Egg Laying 5d


title: adult Muller glia (MG)

description:
Adult MG
pooled from 40 adult retinas

hyb_protocol: The miRtagged mature miRNA was then hybridized to a probe pair (reporter probe and capture probe) in the standard nCounter gene expression array workflow.

scan_protocol: 200 ng of total RNA per sample (33 ng/μ l, n = 20 mice for adult MG, n = 16 mice for P11 MG, n = 13 mice for cell culture, pooled samples) was submitted for NanoString analysis, performed at the Fred Hutchinson Cancer Center in Seattle, WA, USA.

data_processing: Values from P2 RPCs and P8, P11, and adult MG were normalized against 4 housekeeping genes (β -actin, GAPDH, Rpl19, and B2m), 8 negative controls, and 6 positive controls that were run simultaneously with the samples.

label: barcode

source_name: retina

label_protocol: NanoString nCounter® was used for miRNA expression analysis. DNA sequences called miRtags were ligated to the mature miRNAs through complementary oligonucleotides with sequence-specific binding (bridges). All excess tags and ridges were removed, resulting in sequence-specific tagging of mature miRNAs.

extract_protocol: The sorts of all retinas were pooled for the RNA-purification. RNA was extracted and purified with a miRNeasy Micro Kit in accordance with manufacturer’s instructions (Qiagen).

treatment_protocol: tamoxifen for cre activation: Tamoxifen (Sigma) was administered intraperitoneally at 75 mg/kg in corn oil at P0 and P1 for the P2 RPCs, at P6 and P7 for P8 MG, at P9 + 10 for the P11 MG and for two consecutive days at ages P > 21 for the adult MG assay.

value: retina

value: Muller glia (MG)

tag: labeling

value: Rlbp-Cre:tdTomato mouse

tag: condition

value: FACS-sorted

value: adult


title: WT_5d rep2

value: Imaginal wing disc


title: WT_5d rep3


title: 6C


title: BAR-MV42_T0

description: Gene expression of lean controls

tag: group

tag: time point


title: P11/12  Muller glia (MG)

description:
P11 MG
pooled from 32 P11 retinas


title: WT_5d rep1


title: 5C


title: P8  Muller glia (MG)

description:
P8 MG
pooled from 52 P8 retinas


title: P2 Retinal Progenitor Cells (RPCs)

description:
P2 RPC
pooled from 8 P2 retinas

value: Retinal Progenitor Cells (RPCs)

value: Sox2-Cre:tdTomato mouse


title: WT_4d rep3

value: After Egg Laying 4d


title: SS52_T52wks

tag: tissu

value: Skeletal muscle

value: Obese

value: 52 weeks post metabolic surgery


title: 7C

value: myeloma-bearing


title: 4C


title: WT_4d rep2


title: 16C


title: 13B

source_name: 5TGM1-GFP Myeloma cells, bone lining

value: LDN

value: 5TGM1-GFP Myeloma cells, bone lining


title: SA2-10d-C-Rep2

city: Athens

first: Biyao

last: Zhang

address: CAGT, Rm120, 111 Riverbend RD

department: Horticulture

institute: University of Georgia

data_processing:
Reads were trimed with 5' end 9bp and poly A contaimination using trimmomatic program
Adaptors were cutted with cutadapt
Clean reads mapped to ITAG3.2 Released Tomato Genome using hisat2
Values were normalized into TPM
Genome_build: ITAG3.2 Released Tomato Genome
Supplementary_files_format_and_content: TPM values for each Sample

organism: Solanum pimpinellifolium

source_name: 10dpa fruit columella

growth_protocol: Plants were grown in 10x10x20 cm pots under natural light supplemented with artificial light (16/8 hr light/dark cycle) in the greenhouse in Athens, GA, USA, 2017. The daytime temperature 80-85F and the night time temperature  60-65F, humidity 60%. Approximately 5~8 fruits were collected for each samples from 2 months plants.

extract_protocol:
During the collection, all fruits were cut inton halfs and immediately immersed in ice-cold RNAlater (QIAGEN) solution at five times the volume of the sample in order to prevent RNA degradation. After sample collection, vacuum infiltration was applied until tissues sunk to the bottom of RNAlater solution. The tissues were then stored in RNAlater at -80℃.  Dissection were done by forceps under a dissection microscope and immediately put into a 1.5 ml eppendorf tube in 1 ml of fresh RNAlater that was kept on ice. Columella and septa were isolated as columella part; seeds and placenta as seed part; remaining as pericarp part. The samples were stored at -80 ℃ prior to the RNA extraction.RNA extraction was conducted using Trizol® (Invitrogen Inc. USA) following manufacture’s recommendation.
3'Tag mRNA library were constructed by following paper "Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure" of Meyer et al., 2011.

value: columella

tag: ecotype

value: accession LA1589

value: SUN NIL

tag: Stage

value: fruits of 10 days post pollination


title: SA2-10d-S-Rep2

source_name: 10dpa fruit seeds

value: seeds


title: SA2-10d-P-Rep2

source_name: 10dpa fruit pericarp

value: pericarp


title: BAR-MV42_T2wks

first: Heike

description: Gene expression of lean controls

value: 2 weeks after metabolic surgery


title: NA51_T52wks


title: WT_4d rep1

value: Imaginal wing disc


title: ES18_T52wks


title: MM21_T52wks


title: BAR-TK22_T52wks


title: SA1-10d-S-Rep2

value: wildtype


title: 12B


title: BAR-NS20_T52wks


title: 11B


title: 10B


title: SA2-10d-S-Rep1


title: SA1-10d-P-Rep2


title: BAR-MG48_T52wks


title: 9B


title: BAR-RR44_T52wks


title: BAR-MD35_T52wks


title: SA2-10d-C-Rep1


title: adrenal_male_pig24

city: Guelph

first: Niel

last: Karrow

state: Ontario

address: 50 stone road east

department: Animal Biosciences

country: Canada

institute: University of Guelph

description: gene expression of adrenal gland in male pigs from differing maternal diets and maternal LPS treatments

hyb_protocol: 3.5 ug of fragmented and labelled cDNA were hybridized for 16 hr at 65C on Porcine Gene 1.0 ST GeneChip arrays as per manufacturer's protocol

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: Data was analyzed using Applied Biosystems' Transcriptome Analysis Console 4.0

label: biotin

organism: Sus scrofa

source_name: adrenal gland, 2 hours post LPS challenge

label_protocol: Single-stranded cDNA was labeled according to the Affymetrix WT PLUS reagent kit manual

growth_protocol: Sows were fed experimental diets from gestation day 75. On gestation day 112, half the sows in each treatment were challenged with LPS, the other half received saline as a control. Piglets were weaned at 21 days of age. One week after weaning piglets were challenged with LPS, and after two hours the piglets were euhtanized.

extract_protocol: RNA was extracted using Qiagen's RNeasy Mini Kit as per manuacturer's protocol.

treatment_protocol: Two-hours after LPS challenge, piglets were euthanized and whole adrenal tissue was collected. Once the whole adrenal gland was removed from the carcass, it was snap-frozen in liquid nitrogen and stored at -80C until RNA was extracted. Adrenal tissues from 19 male piglets were selected for RNA extraction and microarray analysis.

value: adrenal gland

tag: maternal diet

value: Fish Oil

tag: maternal lps

value: LPS

tag: gender

value: male


title: SA1-10d-C-Rep2

tag: genotype


title: BAR-KH28_T52wks

value: Skeletal muscle

value: Obese

value: 52 weeks post metabolic surgery


title: adrenal_male_pig23

value: Microalgae


title: 7B

tag: strain

value: myeloma-bearing

value: Vehicle

tag: cell type

value: 5TGM1-GFP Myeloma cells, bone lining


title: adrenal_male_pig21

value: Control

value: Saline


title: SA1-10d-S-Rep1

value: seeds

value: accession LA1589

value: fruits of 10 days post pollination


title: SA2-10d-P-Rep1

value: pericarp

value: SUN NIL


title: 16B

tag: disease status


title: 6B

tag: ldn vs. vehicle-treated


title: adrenal_male_pig22

tag: tissue

value: adrenal gland


title: SA1-10d-C-Rep1

value: columella

value: wildtype


title: BAR-IK36_T52wks

value: Skeletal muscle


title: BAR-KT41_T52wks

value: Obese


title: 4B


title: 5B


title: SA2-8d-S-Rep2

source_name: 8dpa fruit seeds

value: fruits of 8 days post pollination


title: adrenal_male_pig19

value: Fish Oil

value: LPS

value: male


title: adrenal_male_pig18


title: 3B

value: myeloma-bearing

value: Vehicle

value: 5TGM1-GFP Myeloma cells, bone lining


title: adrenal_male_pig20


title: SS52_T2wks

value: 2 weeks post metabolic surgery


title: SA2-8d-C-Rep2

source_name: 8dpa fruit columella

value: accession LA1589


title: adrenal_male_pig17

value: Control


title: NA51_T2wks


title: BAR-DN39_T52wks

value: 52 weeks post metabolic surgery


title: BAR-IG47_T52wks


title: adrenal_male_pig16


title: 13A

source_name: 5TGM1-GFP Myeloma cells, central marrow

value: LDN

value: 5TGM1-GFP Myeloma cells, central marrow


title: MM21_T2wks


title: SA1-10d-P-Rep1

value: pericarp

value: fruits of 10 days post pollination


title: 12A


title: SA1-8d-C-Rep2

value: columella

value: wildtype


title: SA1-8d-S-Rep2

value: seeds

value: fruits of 8 days post pollination


title: BAR-TK22_T2wks

value: Skeletal muscle

value: Obese


title: 1A

value: myeloma-bearing


title: adrenal_male_pig13

value: adrenal gland

value: Fish Oil

value: Saline

value: male


title: ES18_T2wks

value: 2 weeks post metabolic surgery


title: adrenal_male_pig14

value: Control


title: SA1-8d-P-Rep2

source_name: 8dpa fruit pericarp

value: accession LA1589


title: adrenal_male_pig11


title: 15A

value: LDN

value: 5TGM1-GFP Myeloma cells, central marrow


title: SA2-8d-S-Rep1

value: SUN NIL


title: SA2-8d-P-Rep2

value: pericarp


title: BAR-RR44_T2wks


title: 2A


title: SA2-8d-C-Rep1

value: columella


title: 11A


title: adrenal_male_pig12

value: Microalgae


title: adrenal_male_pig15


title: 9A


title: adrenal_male_pig10

value: LPS


title: 14A

value: Vehicle


title: SA2-8d-P-Rep1

value: fruits of 8 days post pollination


title: adrenal_male_pig9


title: SA1-8d-S-Rep1

value: seeds

value: wildtype


title: BAR-MD35_T2wks

value: Skeletal muscle

value: Obese


title: 7A

value: myeloma-bearing


title: BAR-MG48_T2wks

value: 2 weeks post metabolic surgery


title: adrenal_male_pig8

value: adrenal gland

value: Control

value: Saline

value: male


title: BAR-KT41_T2wks


title: BAR-NS20_T2wks


title: BAR-KH28_T2wks


title: BAR-IK36_T2wks


title: adrenal_male_pig6


title: 6A

value: 5TGM1-GFP Myeloma cells, central marrow


title: adrenal_male_pig7


title: SA1-8d-P-Rep1

value: pericarp

value: accession LA1589


title: 16A


title: SA2-6d-S-Rep2

source_name: 6dpa fruit seeds

value: SUN NIL

value: fruits of 6 days post pollination


title: BAR-IG47_T2wks


title: 5A

value: Vehicle


title: 12_RA

first: Adam

middle: J

last: Isabella

address: 1100 Fairview Ave N B2-123

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to GRCz11 using STAR 2.5.2a in 2-pass mode.  Counts were generated from STAR alignments at the gene-level using featureCounts from the Subread package v1.5.0.
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include counts generated at the gene-level by featureCounts

organism: Danio rerio

source_name: Vagus motor neurons

extract_protocol:
The posterior hindbrain was manually dissected in calcium-free Ringer’s solution with MESAB, and dissected tissue was dissociated to single-cell suspension by pipetting in 0.25%Trypsin-EDTA for 5 minutes. dissociated cells were transferred into cold DPBS + 1%BSA + 2g/mL DAPI.  Cells were then sorted on an BD FACS ARIA II flow cytometer.  Kaede+, DAPI- cells were collected in lysis buffer from the RNA isolation kit and immediately processed.
RNA was isolated using the RNAqueous-Micro Total RNA Isolation Kit, cDNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.

treatment_protocol: Embryos were treated 0.2mM PTU, as well as with 50nM Retinoic Acid in DMSO, or the equivalent volumen of DMSO as a control, beginning at 24hpf.

value: Vagus motor neurons

tag: developmental stage

value: 38 hpf


title: 9_RA


title: 6_RA


title: 10_DMSO


title: BAR-DN39_T2wks


title: SA2-6d-P-Rep2

source_name: 6dpa fruit pericarp


title: SS52_T0

source_name: vastus lateralis

value: Before metabolic surgery


title: Sorted_cells_pool_4

city: Illkirch-Graffenstaden

first: Gérard

last: Gradwohl

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: Jejunum Enteroids (mini-guts) from Ngn3eYFP mice (adult) were dissociated with TrypLE and mechanically. Single cells were filtered (50 µm) and sorted (FACS ARIA FUSION, noozle 100) directly in 96-well plates (BD, P/N 634100) and processed using BD Precise WTA kit for single cells. 92 cells were collected , 4 wells left empty for controls.

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Fastq files were demultiplexed using the sample index encoded in reads 1.
Reads 2 having a bad quality (--quality-cutoff 20,20) or corresponding to polyA sequences or to adapters were removed using Cutadapt version 1.10.
Reads 2 mapping to rRNA were identified using Bowtie 2 version 2.2.8 and removed.
Reads 2 were aligned to mm10 genome using STAR version 2.5.3a.
Reads corresponding to technical duplicates were removed using UMI-Tools version 0.4.4. (method: "directional-adjacency")
Quantification of gene expression was performed using HTSeq version 0.6.1.post1 (parameter “--mode union”) and gene annotations from Ensembl release 90.
Cells were filtered in function of several quality criteria: % of reads uniquely aligned to genome ≥ 40% ; % of UMIs assigned to genes ≥  50% ; Number of assigned UMIs per cell ≥  200,000 ; % of UMIs assigned to mitochondrial genes < 20%.
Genome_build: mm10
Supplementary_files_format_and_content: The tab-delimited text file include raw UMI-counts for the 290 filtered cells.

source_name: Enteroids

growth_protocol: Mouse enteroids were generated as previously described (Sato et al., 2009) from small intestine (duodenum or jejunum) of CD1 Neurog3eYFP/+ mice (Mellitzer et al., 2004). The Matrigel domes containing enteroids were maintained in culture (37°C, 5% CO2) for 5-8 days in the following medium: basal medium (Advanced DMEM/F-12, HEPES 10mM (Gibco™), GlutaMax 2mM (Gibco™), penicillin/streptomycin 100U/mL (Gibco™)), added with B27 1X (Gibco™), N-acetyl-L-cysteine 1µM (Merck), human recombinant R-spondin-1 500ng/mL (PeproTech®), murine recombinant EGF 50ng/mL (PeproTech®), and human recombinant Noggin 100ng/mL (R&D Systems®).

extract_protocol:
To dissociate the enteroids, the culture medium was removed and the Matrigel was broken. Then, the enteroids were digested to single cells in 500µL of TrypLE™ Express Enzyme (1X) (Gibco™) at 37°C for 20min. The dissociation was improved by passaging into a syringe mounted with a 18G needle. The digestion was stopped by addition of Advanced DMEM/F-12, fetal calf serum 10%, N-acetylcysteine 0,5mM, B27 1X. The cells were pelleted, washed 2 times and resuspended in the same medium. Finally, they are filtered on a 50 µm cell strainer. eYFP+ cells, from dissociated Neurog3eYFP/+ enteroids, were sorted directly into 96 well plates « Precise WTA Single Cell Encoding Plate » (BD™ Precise WTA Single Cell Kit, BD Genomics) (1 cell/well) using a FACS Aria Fusion (BD). DAPI was used to sort only living cells.
Cells were sorted directly into four 96 well plates « Precise WTA Single Cell Encoding Plate » (BDTM Precise WTA Single Cell Kit, BD Genomics) (1 cell/well) using a FACSAria II (BD). The library was prepared by the GenomEast Platform (IGBMC) following the protocol « Library Preparation with the BDTM Precise WTA Single Cell Kit User’s Guide » (910000014 Rev. 02 11/2016, BD Genomics).

value: Jejunum

tag: mouse

value: female

tag: age

value: 12 weeks


title: 4_DMSO


title: SA1-6d-P-Rep2

value: wildtype


title: SA2-6d-S-Rep1

value: seeds


title: 1_DMSO


title: Sorted_cells_pool_2

description: Duodenum Enteroids ( mini-guts) from Ngn3eYFP mice (adult) were dissociated with TrypLE and mechanically. Single cells were filtered (50 µm) and sorted (FACS ARIA FUSION, noozle 100) directly in  96-well plates (BD, P/N 634100) and processed using in BD Precise WTA kit for single cells. 92 cells were collected , 4 wells left empty for controls.

value: Duodenum


title: MM21_T0

value: Skeletal muscle

tag: group

value: Obese


title: NA51_T0

tag: time point


title: ES18_T0

tag: tissu


title: Sorted_cells_pool_1

description: Duodenum Enteroids ( mini-guts) from Ngn3eYFP mice (adult)  were dissociated with TrypLE and mechanically. Single cells were filtered (50 µm) and sorted (FACS ARIA FUSION, noozle 100) directly in  96-well plates (BD, P/N 634100) and processed using in BD Precise WTA kit for single cells. 92 cells were collected, 4 wells left empty for controls.

value: 39 weeks


title: 3A

value: myeloma-bearing

value: 5TGM1-GFP Myeloma cells, central marrow


title: SA2-6d-P-Rep1

value: pericarp

tag: ecotype

value: accession LA1589

value: SUN NIL


title: SA1-6d-S-Rep1

tag: Stage

value: fruits of 6 days post pollination


title: PG

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Reads of low quality were filtered out prior to alignment to GRCz10 using TopHat v2.1.0.  Counts were generated from Tophat alignments at the gene-level employing the "intersection-strict" overlap mode in HTSeq v0.6.1.
Genome_build: GRCz10
Supplementary_files_format_and_content: tab-delimited text files include counts genreated at the gene-level by HTSeq-count.

source_name: Posterior Vagus motor neurons

extract_protocol:
The posterior hindbrain was manually dissected in calcium-free Ringer’s solution with MESAB, and dissected tissue was dissociated to single-cell suspension by pipetting in 0.25%Trypsin-EDTA for 5 minutes. Dissociated cells transferred into cold DPBS + 5% FBS + 1% BSA.  The cell suspension was then transferred onto a glass coverslip, covered with mineral oil, and photoconverted cells were manually picked up using a 10m diameter transplant pipette and transferred into lysis buffer from the RNA isolation kit.
RNA was isolated using the RNAqueous-Micro Total RNA Isolation Kit, cDNA was amplified using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, and libraries were prepared using the Nextera XT DNA library prep kit and sequenced on an Illumina HiSeq 2500 sequencer.

value: Vagus motor neurons


title: 150_I_RFVCT

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Reads mapping to rRNA and ERCC spikes were identified using Bowtie version 1.0.0 and removed from the analysis.
Remaining reads were mapped onto the mm9 assembly of mouse genome using Tophat version 2.0.10 and the Bowtie2 version 2.1.0 aligner.
Quantification of gene expression was performed using HTSeq version 0.6.1 (parameter “--intersection_nonempty”) and gene annotations from Ensembl release 67
Genome_build: mm9
Supplementary_files_format_and_content: The two tab-delimited text file include raw read counts for the two experiments (at 8 days and 3 months)

source_name: RNA in water

growth_protocol: Mutant (Rfx6f/f; Vilin-CreERT2) and control mice  (Rfx6f/+, or Rfx6f/f) were generated starting from Rfx6f/+ (Piccand et al, 2014) and Vilin-CreERT2 mice (El Marjou et al 2004)

extract_protocol:
Ileon was harvested at 8 days and 3 months after tamoxifen gavage. Total RNA was extracred using TRI-reagent or RNeasy® Midi Kit (Qiagen).
Library prep for total RNA-seq Ribozero/standard quantity

treatment_protocol: Adult mice were given tamoxifen (10mg) (Sigma) by gavage twice per day, every second day during 5 days.

value: Rfx6f/f Vilin-CreERT2

tag: time


title: SA2-4d-S-Rep2

source_name: 4dpa fruit seeds

value: fruits of 4 days post pollination


title: BAR-RR44_T0

value: Before metabolic surgery


title: SA1-6d-P-Rep1


title: PB


title: Sorted_cells_pool_3

description: Duodenum Enteroids ( mini-guts)  from Ngn3eYFP mice (adult) were dissociated with TrypLE and mechanically. Single cells were filtered (50 µm) and sorted (FACS ARIA FUSION, noozle 100) directly in 96-well plates (BD, P/N 634100) and processed using BD Precise WTA kit for single cells. 92 cells were collected , 4 wells left empty for controls.

value: female

value: 12 weeks


title: SA2-4d-C-Rep2

source_name: 4dpa fruit columella

value: columella


title: BAR-NS20_T0


title: 152_I_RFVCT


title: PR


title: 130_I_RFVCT


title: 129_I_RFVCT


title: AG

source_name: Anterior Vagus motor neurons


title: SA1-6d-S-Rep2

value: seeds

value: wildtype


title: BAR-MG48_T0

value: Skeletal muscle

value: Obese


title: BAR-MD35_T0


title: BAR-TK22_T0


title: AB


title: BAR-KT41_T0


title: 151_I_RF


title: scPool: 600 nM Pus1 15.0 min +CMC

city: Cambridge

first: Thomas

last: Carlile

address: 77 Massachusetts Ave

institute: MIT

data_processing:
Reverse reads were trimmed of 5′ amplicon sequence using cutadapt (-G)
Trimmed paired end reads collapsed using PEAR (default settings)
PCR duplicates collapsed using fastx_collapser
PCR duplicates collapsed using fastx_collapser
Sequences were trimmed of 3′ adapter (both pools) and 10 random Ns (yeast pools only) using cutadapt
Reads were mapped to bowtie indices of the pools with tophat2
Pseudouridylation was assessed using cutom python scripts (see text)
Genome_build: Bowtie indices made from fasta files of pool sequences
Supplementary_files_format_and_content: Tab delimited text files of peak values for pseudouridylation (see text)

source_name: Yeast Pool

extract_protocol:
Oligo pools (yeast, Twist Biosciences; human Custom Array) were PCR amplified, and in vitro transcribed into RNA, which was then gel purified, folded, and pseudouridylated with a pseudouridine synthase activity source.
RNA was phenol:chloroform extracted from pseuoduridylation reactions, treated with 0.4 M CMC, followed by reversal of CMC modification in bicarbonate buffer. RT was performed, and truncated cDNAs were size selected, followed by circularization & PCR amplification.
OTHER: Pseduo-seq

tag: pus activity source

value: 600 nM Recombinant scPus1

tag: cmc use

value: 0.4M CMC

tag: bowite fasta


title: 142_I_RF

tag: genotype


title: scPool: 600 nM Pus1 2.00 min +CMC


title: scPool: 600 nM Pus1 1.00 min +CMC


title: 131_I_RF


title: scPool: 600 nM Pus1 0.75 min +CMC


title: SA2-4d-S-Rep1


title: SA1-4d-P-Rep2

source_name: 4dpa fruit pericarp

value: pericarp


title: AR

tag: cell type


title: SA1-4d-S-Rep2

value: accession LA1589


title: Poly(A)_Col

city: Beijing

first: xiaofeng

last: cao

address: West Lincui Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

description:
high-throughput profiling of poly(A) tails in Col (wild type)
Col_1

data_processing:
CLIP-seq reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using NovoAlign. Pyicoclip was used to identify AtPABs binding clusters.
Ribosome profiling reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count.
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Poly(A) tail reads were trimmed and aligned to the Arabidopsis genome (TAIR10) using Bowtie2.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig program

extract_protocol:
The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).
CLIP-seq libraries generated from Col and AtPABs complementary lines were constructed following the published method in Arabidopsis (Zhang et al., 2015). Ribosome profiling libraries generated from Col and atpabs were constructed following the published method in Arabidopsis (Juntawong et al., 2014). Strand-specific RNA-Seq libraries generated from Col, atpabs were constructed mRNA-Seq library by SMART method (Levin et al., 2010).PolyA-seq library generated from Col was constructed following treated total RNA with RQ1 DNase and RNase T1, purified poly(A)-containing RNA fragments and ligated with adaptors.

tag: ecotype background

value: Col

value: 2-week seedlings


title: SA2-4d-P-Rep2

value: SUN NIL


title: Degradation_Col_8h_rep3

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 8 hours
C3-8_L5_315X15

tag: treatment

value: cordycepin for 8 hours


title: BAR-IK36_T0


title: SA2-4d-C-Rep1

tag: tissue

value: fruits of 4 days post pollination


title: scPool: 600 nM Pus1 0.50 min +CMC


title: BAR-DN39_T0

value: Before metabolic surgery


title: SA1-4d-C-Rep2


title: BAR-IG47_T0


title: Degradation_Col_8h_rep2

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 8 hours
C2-8_L5_309X09

tag: developmental stage


title: BAR-KH28_T0


title: scPool: 600 nM Pus1 0.25 min +CMC


title: BAR-YF_K2

description: Gene expression of lean controls

value: Control

value: No metabolic surgery


title: BAR-SS_K7

description: Gene expression of lean controls


title: scPool: input Rep2 -CMC


title: SA2-4d-P-Rep1


title: SA1-4d-S-Rep1


title: BAR-SP_K9

description: Gene expression of lean controls


title: SA1-8d-C-Rep1

value: columella

value: fruits of 8 days post pollination


title: Degradation_Col_4h_rep3

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 4 hours
C3-4_L5_314X14

value: cordycepin for 4 hours


title: SA1-4d-C-Rep1

value: wildtype


title: BAR-KS_K3

description: Gene expression of lean controls

value: Skeletal muscle


title: scPool: input Rep2 +CMC


title: scPool: input Rep1 -CMC


title: Degradation_Col_4h_rep2

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 4 hours
C2-4_L5_308X08


title: scPool: input Rep1 +CMC


title: Degradation_Col_4h_rep1

description:
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 4 hours
C1-4_L5_302X02


title: SA1-4d-P-Rep1