title: set33.WT.4.Input.rep1

description: sample 91 to 94 are in one group


title: RNAseq_invitro_Rptorflfl_org1_rep2

status: Public on Jun 08 2022

type: SRA

city: Amsterdam

first: William

last: Faller

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute

library_source: transcriptomic

data_processing:
For Riboseq samples, adapters were removed with cutadapt version 1.18.
Transcript quantifications were done with salmon version 1.1.0 using Gencode vM21 annotation.
For invitro Ribo-seq transcript quantifications, UTRs were discarded from transcripts.
Differential Translation Efficiency analysis was performed with RiboDiff version 0.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: "quant.sf" files are tab-seperated salmon outputs (includes transcript id, transcript length, effective length, TPM and raw_reads as columns).
Supplementary_files_format_and_content: *TE.RiboDiff.tsv: Differential Translation Efficiency measurements

molecule: polyA RNA

organism: Mus musculus

source_name: intestinal organoid

extract_protocol:
Briefly, for in vitro analyses, organoids were generated from VillinCre.ERT2.RPL22.HA and VillinCre.ERT2Rptor.fl/fl.RPL22.HA animals. Around 120-150 plugs of 30 μl BME were used for each replicate. Cells were treated with 100 μg/ml cycloheximide for 3-5 min at 37°C and immediately incubated on ice for the remainder of the experiment. After collecting the cells, pellets were washed twice with cold PBS supplemented with 100µg/mL cycloheximide, resuspended in ice-cold lysis buffer (20mM Tris HCl pH 7.4, 10mM MgCl2, 150mM KCl, 1% NP-40, 100µg/mL cycloheximide and 1x EDTA-free proteinase inhibitor cocktail (Roche)) and incubated for 20 min on ice. Lysates were then centrifuged at max speed for 20 min at 4°C and the supernatants were collected. For in vivo analyses, Lgr5CreERT2RPL22.HA and Lgr5CreERT2Rptor fl/flRPL22.HA animals were euthanized by CO2 and small intestines were immediately dissected, flushed with cold PBS supplemented with 100 µg/mL of cycloheximide and snap frozen using liquid nitrogen. Frozen samples were then homogenized by pestle and mortar while submerged in liquid nitrogen and the resulting powder was resuspended in ice-cold lysis buffer and incubated on ice for 30 min. Finally, lysates were centrifuged at max speed for 20 min at 4°C and the supernatants were collected. For Riboseq, HA pulldown was performed followingly. All lysates were incubated with Pierce™ Control Agarose Matrix (ThermoFisher) for 20min at 4’C in order to remove any non-specific binding, following by an incubation with pre-washed 425 AntiHA.11 Epitope Tag Affinity Matrix (BioLegend) for 4 hours (in vitro samples) or overnight (in vivo samples) at 4’C. Tagged ribosomes were then eluted from the beads by incubating with 200µg/mL HA peptide (ThermoFisher Scientifc) for 15 min at 30’C with constant agitation. Non-protected RNA was digested with 10 ul of RNase I (ThermoFisher Scientific) for 40min at 25’C and the reaction was stopped by adding 13ul of SUPERASE (ThermoFisher Scientific). Ribosome protected fragments (RPFs) were finally purified using miRNeasy minikit (Qiagen) accoridng to manufacturer’s instructions.
Riboseq library preparation was performed as previously described (Loayza-Puch et al., 2013) with some modifications. To discard undigested RNA fragments, RPFs were run in a 10% TBE-Urea polyacrylamide gel and size selected between 19 nt and 32 nt using marker RNAs. 3’ ends were dephosphorylated using T4 polynucleotide kinase (PNK) (NEB) and 1.5xMES buffer (150mM MES-NaOH, 15mM MgCl2, 15mM β-mercaptoethanol and 450mM NaCl, pH 5.5) and incubated at 37’C for 4h. After purifying RNAs with Trizol, 3’adpaters were ligated with T4 RNA ligase I (NEB) and incubated overnight at 24’C. After size-selecting the ligated products, 5’ ends were phosporylated with T4 PNK and incubated at 37’C during 30min. 5’ adapters were then ligated with T4 RNA ligase I and incubated 37’C for 2,5 hours. The RPFs containing both adapters were then size-selected one more time and rRNA depletion was performed by first denaturing the samples at 100’C for 1min followed by incubation with 10uM biotinylated oligos (5’-UGAUCUGAUAAAUGCACGCAUCCCCCC-3’; 5’-CGUGCGAUCGGCCCGAGGUUAUCUAGAGUCACCA-3’; 5’-AUUCCAUUAUUCCUAGCUGCGGUAUCCAGGCGGCUC-3’; 5’-GGGCCUCGAUCAGAAGGACUUGGGCCCCCCACGA-3’; 5’-UGGCUUCCUCGGCCCCGGGAUUCGGCGAAAGC-3’; 5’-ACGGACGCUUGGCGCCAGAAGCGAGAGCCCCUCGGG-3’; 5’-ACCCGGCUAUCCGGGGCCAACCGAGGCUCCUUCGGCG-3’; 5’-ACCGACGCUCAGACAGGCGUAGCCCCGGGAGGA-3’; 5’-GGCGGACGGGGGGAGAGGGAGAGCGC-3’; 5’-GGCGAGACGGGCCGGUGGUGCGCCCUCGGC-3’; 5’-CCAGAAGCAGGUCGUCUACGAAUGGUUUAG-3’; 5’-AUCCCCGAUCCCCAUCACGAAUGGGGUUCA-3’; for the in vivo samples also added the following: 5’-GCUCUGCUACGUACGAAACCCCGACC-3’; 5’-GUGUCGAGGGCUGACUUUCAAUAGAUCG-3’; 5’-AGAUCCAACUACGAGCUUUUUAACUG-3’; 5’-AACGCCACUUGUCCCUCUAAGAAGU-3’; 5’-CAAGUGCGUUCGAAGUGUCGAUGAUC-3’) in 2xSSC buffer (ThermoFisher Scientific) for 15min at 37’C. Pre-washed MyOne Streptavidin C1 DynaBeads (ThermoFisher Scientific) were then incubated with samples in wash/bind buffer (2M NaCl, 1mM EDTA, 5mM Tris and 0.2% Triton X-100) for 30min at 37’C with agitation. Supernatants were collected and RPFs were purified and re-suspended in 8µL of RNase-free water. cDNA was synthesized with SuperScript III (ThermoFisher Scientific) according to manufacturer’s instructions and using the RTP primer (seq). After purification with G50 columns (Merck), cDNA was amplified using Phusion High-Fidelity DNA Polymerase (ThermoFisher Scientific) for 18 cycles, with primers containing different indexes to allow for sequencing (see table). PCR products were purified using the QIAquick PCR purification kit (Qiagen) followed by a final size selection with a E-Gel SizeSelect II 2%, (ThermoFisher Scientific). All samples were accessed with the Agilent 2100 Bioanalyzer to assure high quality and quantify the molarity and the libraries were sequenced on the Illumina HiSeq2500.

treatment_protocol: To generate stem cell enriched (SCe) cultures, organoids were grown in ENR media supplemented with 10 μM of CHIR 99021 (Cayman Chemical) and 1.5 mM of valproic acid. To promote differentiation, stem cell depleted (SCd) cultures were achieved by growing the organoids in normal ENR media for the first 2 days, and removing R-spondin from the media for the last 2 days.

tag: strain

tag: tissue

value: intestinal organoid

tag: genotype

tag: treatment

value: untreated


title: 4957

city: Asheville

first: Melissa

middle: Marie

last: Heintz

state: NC

address: 31 College Place, Suite B118

country: USA

institute: ToxStrategies

data_processing:
no adapter trimming for TempO-Seq fastqs, default settings for clusters passing filters
bcl2fastq v2.17.1.14 or v2.18.0.12 for demultiplexing
fastqs were aligned to a pseudo transcriptome using Bowtie allowing up to 2 mismatches
Assembly: probe-based targeted sequencing
Supplementary files format and content: comma-separated text files include raw count values for each gene_probe

molecule: total RNA

source_name: liver

extract_protocol:
Mounted, unstained FFPE liver sections from HFPO-DA-exposed male and female mice (n = 5 per dose group per sex, total of 40 samples) were scraped from the slides and processed according to the TempO-Seq® protocol by BioSypder Technologies
TempO-Seq® protocol by BioSypder Technologies

treatment_protocol: Mice were administered 0, 0.1, 0.5 or 5 mg/kg HFPO-DA by oral gavage once daily for a total of 84 – 85 or 53 – 65 doses in male or female mice, respectively. Male mice (F0) were dosed 70 days prior to mating through completion of mating period (14 days). Female mice (F0) were dosed 14 days prior to mating through lactation day 20 or 21. Following the last treatment, mice were euthanized by CO2 anesthesia and exsanguination. Livers were fixed in 10% neutral-buffered formalin, embedded in paraffin (FFPE), and sections approximately 4 – 6 µm in thickness were mounted to glass slides.

value: liver

tag: Sex

value: female

value: WT

value: 0.1 mg/kg HFPO-DA


title: set33.WT.TOP3B_eCLIP-seq.rep1

city: Baltimore

first: Weidong

last: Wang

state: MD

address: 251 Bayview Blvd

department: National Institute on Aging

institute: Shuaikun Su

description: sample 91 to 94 are in one group

data_processing:
For Ribo-seq, low-quality reads and the linker sequence (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were removed by FASTX-Toolkit from FastQ files. Then reads less than 25 nt were also removed by FASTX-Toolkit. Align the remaining reads to an rRNA reference using the Bowtie short-read alignment program, discard the rRNA alignments and collect unaligned reads. For PRO-seq, adaptor sequences (ADAPT1=GATCGTCGGACTGTAGAACTCTGAA, ADAPT2=TGGAATTCTCGGGTGCCAAGG) were removed by cutadpt. For eCLIP-seq, adaptor sequences were also removed before mapping to the genome.
RNA-seq, Ribo-seq and eCLIP-seq reads were mapped to the hg38 human genome with HISAT2 or TopHat. PRO-seq reads were mapped to the genome using Bowtie2 allowing maximum of 2 mismatches.
For RNA-seq and Ribo-seq, the raw counts were generated using HTSeq-Counts. Then DESeq2 was used to identify the differentially expressed genes (DEGs) and generate the normalized counts. The genes with total counts (untreated and treated groups) less than 10 were filtered. The genes (Fold change > 1.5 and adjust P-value < 0.1) were identified as DEGs. The bedGraph files were generated by deepTools and normalized using RPKM. The bedGraph files were visualized using the Integrative Genomics Viewer (IGV). For PRO-seq, normalized reads at specific sub-regions were used to calculate the DEGs (fold change > 1.2-fold). eCLIP-seq reads were mapped to the genome using TopHat. Other steps were similar to the RNA-seq analysis pipeline. Genes with criterion (WT-IP_fpkm/WT-Input_fpkm > 1.5 and WT-IP_fpkm/TOP3B-KO-IP_fpkm > 1.5) in both biological replicates were selected as TOP3B eCLIP targets. RSeQC was used to analyze the read distribution of Ribo-seq, RNA-seq and eCLIP-seq on CDS, 5’UTR and 3’UTR.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph file

organism: Homo sapiens

source_name: human colorectal carcinoma cell line

growth_protocol: HCT116 cells were cultured in  DMEM with 10% fetal bovine serum (HyClone) and 1% antibiotics (Penicillin-Streptomycin, Sigma).

extract_protocol:
Different sequencing types have different protocols, please follow the protocols in the "Materials and Methods" part in the article. Briefly, for RNA-seq, total RNAs were extracted with TRizol. For Ribo-seq, ribosome protected fragments were collected through sucrose cushion and extracted with TRizol, then the 24 to 34 nt RNA fragments were collected through 15% TBE-Urea gel. For eCLIP-seq, protein-RNA complexes were isolated with antibody. For PRO-seq, nascent RNA fragments were extractd and made library.
For RNA-seq, library construction protocol can be found here (Y. Joo et al., Topoisomerase 3beta knockout mice show transcriptional and behavioural impairments associated with neurogenesis and synaptic plasticity. Nat Commun 11, 3143 (2020).). For Ribo-seq, library was constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs). For eCLIP-seq, library construction protocol can be found here (E. L. Van Nostrand et al., Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol 1648, 177-200 (2017).). For PRO-seq, library construction protocol can be found here (D. B. Mahat et al., Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq). Nature Protocols 11, 1455-1476 (2016).).
RNA-seq; Ribo-seq; eCLIP-seq; PRO-seq

treatment_protocol: For the Ribo-seq samples and the RNA-seq samples, cells were treated with 100µg/mL cycloheximide for 10min

tag: cell line

value: Wild type

tag: molecule

value: RNA fragments


title: set24.TOP3B-KO1.Ribo-seq.rep2

description: sample 2, 5, 8,10,13,16 are in one group

value: Cells were treated with 100µg/mL cycloheximide for 10min and then were used for Ribo-seq.

value: Ribosome protected RNA fragments


title: set20.TOP3B-KO1.RNA-seq.rep3

description: sample 3,6,11,14 are in one group

value: Cells were treated with 100µg/mL cycloheximide for 10min and then lysed in polysome lysis buffer. After centrifugation, 100 µL cell lysates were used to extract RNA with TRIzol. Then 5~10 µg RNA was used to purify mRNAs with oligo dT beads. The purified mRNAs were used for RNA-seq library preparation.

value: polyA RNA


title: set24.TOP3B-KO2.Ribo-seq.rep1

description: sample 1,4,7,9,12,15 are in one group


title: set24.TOP3B-KO1.Ribo-seq.rep1

description: sample 1,4,7,9,12,15 are in one group


title: set24.TOP3B-KO1.RNA-seq.rep1

description: sample 1,4,7,9,12,15 are in one group


title: set20.WT.1.RNA-seq.rep3

description: sample 3,6,11,14 are in one group


title: PRAD64_Prostate Adenocarcinoma - AR

city: Boston

first: Elio

last: Adib

address: 20 Shattuck Street

institute: Brigham and Women's Hospital

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Burrows-Wheeler Aligner (bwa) version 0.7.15
Non-uniquely mapped/redundant reads were discarded.
Narrow peaks were called using MACS version 2.1.2 on deduplicated bam files using the following command: macs2 callpeak --SPMR -B -q 0.01 --keep-dup 1 -g hs -f BAMPE --extsize 146 --nomodel -t {treat.bam} -c {input.bam}.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig and peak text files (BED) were generated

molecule: genomic DNA

source_name: Prostate Adenocarcinoma

extract_protocol:
Using a 2 mm2 core needle, one core was extracted from frozen RP tissue blocks in the areas marked on the corresponding slide. Frozen cores were pulverized using the Covaris CryoPrep system.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics). Libraries were sequenced on an Illumina HiSeq 4000 to generate 150-bp paired-end reads (Novogene).

value: Prostate Adenocarcinoma

tag: gleason score

tag: t-stage

tag: pathology assessment (t

value: tumor, b:benign tissue, s:stroma):6S:85% T,~10% S, <5% B

value: Untreated

tag: antibody

value: AR Antibody - Spring Bioscience #E2724

tag: ancestry

value: European


title: set24.TOP3B-KO2.RNA-seq.rep1

description: sample 1,4,7,9,12,15 are in one group


title: set24.TOP3B-KO2.RNA-seq.rep2


title: set24.TOP3B-KO1.RNA-seq.rep2


title: set24.WT.1.RNA-seq.rep1

description: sample 1,4,7,9,12,15 are in one group


title: PRAD38_Prostate Adenocarcinoma - AR

value: tumor, b:benign tissue, s:stroma):5S:75% T, 25% S, 0 B


title: set24.WT.1.RNA-seq.rep2


title: PRAD52_Prostate Adenocarcinoma - AR

value: tumor, b:benign tissue, s:stroma):1S:85% T, 5% B, 10% S


title: PRAD46_Prostate Adenocarcinoma - AR

value: tumor, b:benign tissue, s:stroma):4S:80% T, 10% S,10% B


title: PRAD32_Prostate Adenocarcinoma - AR

tag: tissue block size

value: 9 x 2 mm

value: tumor, b:benign tissue, s:stroma):75-85% T, 5-10% B, 5-10% S

value: African


title: PRAD29_Normal Prostate - AR

source_name: Normal Prostate

value: Normal Prostate

value: 5 x 4 mm

value: tumor, b:benign tissue, s:stroma):all B:~70% B, 30% S


title: PRAD23_Prostate Adenocarcinoma - AR

value: 2 x 2 mm plus pieces

value: tumor, b:benign tissue, s:stroma):small piece T:1 x 1 mm; rest is B:~65% b, 35% S


title: PRAD25_Normal Prostate - AR

value: 4 x 4 mm

value: tumor, b:benign tissue, s:stroma):all B:~40% B, 60% S


title: PRAD19_Prostate Adenocarcinoma - AR

value: Prostate Adenocarcinoma

value: tumor, b:benign tissue, s:stroma):all tumor:75% T, 25% S


title: PRAD31_Normal Prostate - AR

value: 7 x 3 mm

value: tumor, b:benign tissue, s:stroma):all B:~50% B, 50% S

value: Untreated

value: AR Antibody - Spring Bioscience #E2724


title: PRAD35_Normal Prostate - AR

value: 6 x 2 mm

value: tumor, b:benign tissue, s:stroma):all B:2 circles:~60% B, 40% S (non-circled tissue is FMT and lymphs


title: PRAD18_Normal Prostate - AR

value: tumor, b:benign tissue, s:stroma):all benign:~45-50% benign glands, 50-55% stroma


title: PRAD33_Normal Prostate - AR

value: 4 x 3 mm

value: tumor, b:benign tissue, s:stroma):all B:~30% B, 70% S

value: African


title: PRAD21_Prostate Adenocarcinoma - AR

value: 5 x 4 mm

value: tumor, b:benign tissue, s:stroma):~90% T, <5% B, 5% S


title: PRAD30_Prostate Adenocarcinoma - AR

value: 5 x 5 mm

value: tumor, b:benign tissue, s:stroma):T circle:~80% T, 20% B; non circled tissue is B&S (with rare T glands at edge)


title: PRAD22_Normal Prostate - AR

value: Normal Prostate

value: tumor, b:benign tissue, s:stroma):all benign:~50% B, 50% S


title: PRAD34_Prostate Adenocarcinoma - AR

value: Prostate Adenocarcinoma

value: 4 x 4 mm

value: tumor, b:benign tissue, s:stroma):T circle:~90% T, <5% B, 5% S


title: PRAD16_Normal Prostate - AR

value: 5 x 3 mm

value: tumor, b:benign tissue, s:stroma):40-50% B, 50-60% S; no T

value: Untreated


title: SNU1_MMC_DAY14

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to GeCKO V2 Human library A sgRNA sequences using MAGeCK with parameters mageck count --fastq -l -n
Normalization measurements were generated using MAGeCK with parameters mageck count -k --norm-method median -n
Differential analysis between two groups was proceeded by MAGeCK with parameters mageck mle
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include the normalized counts of sgRNAs.

growth_protocol: Cells were maintained in RPMI 1640 with 10% FBS and 1% penicillin & streptomycin. Cell were passaged every 3 days. After spininfection with the lentivirus containing human GeCKOv2 library, cells were selected with puromycin for 7 days.

extract_protocol:
Genome DNA in per group was extracted using Wizard ® Genomic DNA Purification Kit (Promega).
Genome DNA in per group was amplified using two-step PCR.
GeCKO library  screen

treatment_protocol: After puromycin selection, cells were divided into three groups, 2*10^7 cells without further treatment wre harvesteg as SNU1_DMSO_DAY0 group, 2*10^7 cells receiving 0.1% DMSO for 14 days as SNU1_DMSO_DAY14 group, 2*10^8 cells treated with 0.3 µM MMC for14 days as SNU1_MMC_DAY14 group.

tag: cell type

value: gastric cancer cell line

value: treated with mitomycin C (MMC) for 14 days after puromycin selection


title: SNU1_DMSO_DAY0

value: no furhter treatment after puromycin selection


title: PRAD28_Prostate Adenocarcinoma - AR

value: 6 x 4 mm

value: tumor, b:benign tissue, s:stroma):all T:~ 90% T, 10% S

value: AR Antibody - Spring Bioscience #E2724


title: PRAD17_Prostate Adenocarcinoma - AR

value: tumor, b:benign tissue, s:stroma):omit long edges, or core centrally:T 40-45%, S 50-50% B 5-10%

value: African


title: PRAD15_Prostate Adenocarcinoma - AR

value: 9 x 3 mm


title: PRAD58_Prostate Adenocarcinoma - AR

value: tumor, b:benign tissue, s:stroma):1S:95% T, 5% S

value: European


title: PRAD27_Normal Prostate - AR

value: Normal Prostate

value: tumor, b:benign tissue, s:stroma):all B:~40% B, 60% S


title: SNU1_DMSO_DAY14

value: treated with vehicle for 14 days after puromycin selection


title: tumor_res

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ
Cellranger count to generate count matrix
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Tumor derived cells from sensitive MFP 4T1 tumors following doxorubicin administration

extract_protocol:
Single-cell suspensions of tumor cells were prepared by passing the tumor through a syringe without a needle followed by a 1 h digestwith shaking at 37◦C in 100μg/mL DNase I (Roche, Basel, Switzerland; catalog no. 11284932001),300 U/mL collagenase/100 U/mL hyaluronidase (Stemcell Technologies, Vancouver, Canada; catalogno. 07912), 0.6 U/mL Dispase II (Roche, Basel, Switzerland; catalog no. 4942078001) in DMEM/D12with 10% FBS (Gibco, Waltham, MA, USA). Digests were filtered through a 100μm cell strainer prior to library construction. For T cell sequencing, Immune and cancer cell depletions were performed for T cell specific reactions using Pan T Cell Isolation Kit II, mouse (Miltenyi Biotec, Bergisch Gladbach, Germany; Cat# 130-095-130) in combination with CD90.1 MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany; Cat# 130-121-273) per manufacturers protocols prior to were cell depletion using LS columns (Miltenyi Biotec, Bergisch Gladbach, Germany; Cat# 130-042-401).
Cells were resuspended in PBS with 0.04% non-acetylated BSA prior to the single-cell sequencing step using Chromium Single-cell 3ʹ GEM, Library & Gel Bead Kit v3 (10× Genomics) on a 10x Genomics Chromium Controller following manufacturers protocol. Single-cell library preparation was performed using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics, Pleasanton, CA, USA; Catalog no. 1000075) following the manufacturer’s protocol.

treatment_protocol: Route of infection: Female mice (8-10 weeks old) NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG) or BALB/c mice (Jackson Laboratories, Bar Harbor, ME, USA) were injected with 1×10^5 4T1 cells into the mammary fat pad, as previously described (24).  Tumors were established to 70–140mm3 size range prior to Doxorubicin (Sigma Aldrich, St. Louis, MO, USA) (DOX) administration. DOX was introduced intravenously (IV) by tail vein injection at 5 mg/kg for 3 treatments, 3-days apart.

value: BALB/c

tag: dox sensitivity

value: Resistant

value: tumor

tag: age


title: 4T1_thy1.1_IL17A_rep2

data_processing:
Sequencing data quality was checked using FastQC software and low quality bases were trimmed using Trimmomatic. Then reads were mapped to mouse genome mm10 using STAR.  After read mapping, ‘featureCounts’ from Rsubread package was used to generate gene-wise read counts.  Data was then normalized using TMM normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: 4T1 murine breast cancer cells with Thy1.1 transgene expression

extract_protocol:
Cultures were lysed in culture well using Qiagen Buffer RLT with β-mercaptoethanol added followed by total RNA isolation using RNeasy mini spin columns (Qiagen).
Library preparation was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen; Cat# 015.96) according to manufacturer’s protocols.

treatment_protocol: Route of infection: 4T1-thy1.1 cells were cultured to 25% confluency in a 12 well culture plate then exposed to a doxorubicin (200ng/ml, Sigma Aldrich, St. Louis, MO, USA) and/or recombinant mouse IL-17A protein (25ng/mL, R&D Systems, Minneapolis, MN, USA) were administered for 48 hours prior to RNA isolation.

tag: culturing condition


title: tumor_sen

tag: strain

value: Sensitive


title: 4T1_thy1.1_dox_IL17A_rep5


title: 4T1_thy1.1_dox_rep4


title: tumor_control

source_name: Tumor derived cells from sensitive MFP 4T1 tumors following a sham (saline) administration


title: 4T1_thy1.1_IL17A_rep5


title: 4T1_thy1.1_IL17A_rep3


title: 4T1_thy1.1_dox_rep2


title: 4T1_thy1.1_control_rep5


title: 4T1_thy1.1_dox_IL17A_rep2


title: t_cell_res

source_name: Tumor derived T cells from resistant MFP 4T1 tumors following doxorubicin administration

value: tumor residing T-cell


title: t_cell_sen

source_name: Tumor derived T cells from sensitve MFP 4T1 tumors following doxorubicin administration


title: 4T1_thy1.1_dox_rep3


title: 4T1_thy1.1_control_rep1


title: 4T1_thy1.1_dox_rep1


title: Null10_3

city: New York

first: Agata

last: Smogorzewska

state: NY

address: 1230 York Ave

department: Genome Maintenance

institute: The Rockefeller University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 genome assembly using Rsubread
Reads falling on each gene are counted by HT-Seq
Genome_build: mm10
Supplementary_files_format_and_content: countsRaw_EntrezID.csv

source_name: Mouse embryonic fibroblast

extract_protocol:
Total RNA using RNAeasy extraction (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cre


title: Null40_2


title: Null40_3


title: 4T1_thy1.1_control_rep3


title: 4T1_thy1.1_dox_IL17A_rep3


title: Null10_2


title: Null10_1


title: WT40_2

value: Rtf2+/+ MEFline2


title: WT10_3

value: Rtf2+/+ MEFline1


title: WT10_2


title: scRNA-seq: H11-EA07-1

city: Stanford

first: Seung

last: Kim

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

data_processing:
Raw reads passed quality control using FastQC
Reads were aligned to a custom reference genome consisting of Fasta files for mm10, ERCC knock in, and three transgenes: eGFP, tdTomato, and cre. STAR was used to create the custom genome and read alignment
BAM/SAM files created a counts table using ht-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes a matrix of normalized tag counts for each sample

source_name: Pancreas

extract_protocol: Smart-Seq2 (Picelli et al 2014) was used to extract total RNA from single cells.

tag: embryonic stage

tag: plate code

value: Neurog3-Cre, Rosa-mTmG

tag: tissue

value: Pancreas


title: scRNA-seq: H9-EA07-1

tag: genotype


title: WT40_1

tag: treatment


title: scRNA-seq: G9-EA07-1


title: scRNA-seq: H4-EA07-1


title: scRNA-seq: G5-EA07-1


title: WT10_1


title: scRNA-seq: G6-EA07-1


title: Null40_1


title: scRNA-seq: H3-EA07-1


title: scRNA-seq: H1-EA07-1


title: scRNA-seq: G8-EA07-1


title: scRNA-seq: H10-EA07-1


title: WT40_3


title: scRNA-seq: H8-EA07-1


title: scRNA-seq: G3-EA07-1


title: scRNA-seq: H6-EA07-1


title: scRNA-seq: F7-EA07-1


title: scRNA-seq: F8-EA07-1


title: scRNA-seq: F5-EA07-1


title: scRNA-seq: G2-EA07-1


title: scRNA-seq: G11-EA07-1


title: scRNA-seq: F6-EA07-1


title: scRNA-seq: G7-EA07-1


title: scRNA-seq: F9-EA07-1


title: scRNA-seq: F4-EA07-1


title: scRNA-seq: G10-EA07-1


title: scRNA-seq: G4-EA07-1


title: scRNA-seq: F3-EA07-1


title: scRNA-seq: F2-EA07-1


title: scRNA-seq: F12-EA07-1


title: scRNA-seq: E2-EA07-1


title: scRNA-seq: E3-EA07-1


title: scRNA-seq: E9-EA07-1


title: scRNA-seq: E5-EA07-1


title: scRNA-seq: F10-EA07-1


title: scRNA-seq: F11-EA07-1


title: scRNA-seq: E4-EA07-1


title: scRNA-seq: E7-EA07-1


title: scRNA-seq: F1-EA07-1


title: scRNA-seq: E1-EA07-1


title: scRNA-seq: D8-EA07-1


title: scRNA-seq: D9-EA07-1


title: scRNA-seq: D7-EA07-1


title: scRNA-seq: D3-EA07-1


title: scRNA-seq: D12-EA07-1


title: scRNA-seq: D5-EA07-1


title: scRNA-seq: C8-EA07-1


title: scRNA-seq: C6-EA07-1


title: scRNA-seq: C5-EA07-1


title: scRNA-seq: C7-EA07-1


title: scRNA-seq: C9-EA07-1


title: scRNA-seq: C12-EA07-1


title: scRNA-seq: C2-EA07-1


title: scRNA-seq: C11-EA07-1


title: scRNA-seq: D6-EA07-1


title: scRNA-seq: C10-EA07-1


title: scRNA-seq: B6-EA07-1


title: scRNA-seq: B9-EA07-1


title: scRNA-seq: B12-EA07-1


title: scRNA-seq: A6-EA07-1


title: scRNA-seq: A3-EA07-1


title: scRNA-seq: D4-EA07-1


title: scRNA-seq: B8-EA07-1


title: scRNA-seq: B7-EA07-1


title: scRNA-seq: D2-EA07-1


title: scRNA-seq: B2-EA07-1


title: scRNA-seq: B10-EA07-1


title: scRNA-seq: A7-EA07-1


title: NT1late

city: Wuerzburg

first: Chase

last: Beisel

address: Josef Schneider Strasse , D15

country: Germany

institute: HIRI

data_processing:
Reads were aligned to reference genome using STAR (version 2.7.4a) with parameters “--alignIntronMax 1 --genomeSAindexNbases 10 --outSAMtype BAM SortedByCoordinate”
Gene counts were calculated from BAM file using HTSeq (version 0.9.1) with parameters “-i locus_tag -r pos --stranded reverse --nonunique none -t gene”
Genome_build: NC_000913.3
Supplementary_files_format_and_content: CSV, TPM counts for each gene

organism: Escherichia coli str. K-12 substr. MG1655

source_name: RNA

extract_protocol:
Cells were grown overnight, then normalized to OD 0.06 and let grow to OD 0.5 and 0.8. Cells were pelleted and snap frozen for RNA extraction with the Directzol RNA mini-prep plus kit (Zymo Research, R2071). The samples were also DNase treated with TURBO DNase (Thermo Fisher Scientific, AM2239), rRNA was removed with Rybo-off rRNA depletion kit (Vazyme Biotech, N407-01) and then sequenced with NovaSeq 6000 (Illumina: flow cell S1, 100 cycles) using a 50 bp paired-end read.
NEBNext Ultra II Directional RNA

value: exponential culture

tag: timepoint

tag: biological replicate


title: NT2early


title: NT2late


title: scRNA-seq: A2-EA07-1


title: NT1early


title: scRNA-seq: A11-EA07-1


title: scRNA-seq: A10-EA07-1


title: scRNA-seq: H8-EA06-1


title: scRNA-seq: H7-EA06-1


title: scRNA-seq: A1-EA07-1


title: scRNA-seq: B11-EA07-1


title: scRNA-seq: A4-EA07-1


title: scRNA-seq: H6-EA06-1


title: Leaves, wounded for 24 hr, and then treated with cycloheximide for 4.5 hr (V24)

type: RNA

city: Minamiminowa

first: Shinpei

last: Katou

state: Kamiina, Nagano

department: Faculty of Agriculture

country: Japan

institute: Shinshu University

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Tobacco Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Fluorescence signals of the hybridized Agilent Oligo Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files.

organism: Nicotiana tabacum

source_name: Tobacco plants transformed with empty vector

label_protocol: 100 ng of total RNA were labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol.

growth_protocol: Plants were grown in pots containing vermiculite in a chamber maintained at 25°C with 16 h of light.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Leaves were wounded by excising discs using a cork borer (diameter 10 mm).  Wounded leaf discs were floated on water for 9 hr (V9 and WS9) or 24 hr (V24 and WS24), and then treated with cycloheximide for 4.5 hr. After treatment, the center of the leaf discs were collected using a cork borer (diameter 5.5 mm).

value: control

value: 6- to 7-week-old

value: Leaves

value: wounded for 24 hr


title: Leaves, wounded for 9 hr, and then treated with cycloheximide for 4.5 hr (V9)

value: wounded for 9 hr


title: Leaves, wounded for 9 hr, and then treated with cycloheximide for 4.5 hr (WS9)

source_name: Tobacco plants in which expression of WIPK and SIPK is suppressed by RNAi

value: WIPK/SIPK-suppressed


title: scRNA-seq: G8-EA06-1


title: scRNA-seq: G9-EA06-1


title: scRNA-seq: H11-EA06-1


title: scRNA-seq: H3-EA06-1


title: scRNA-seq: G4-EA06-1


title: scRNA-seq: G5-EA06-1


title: RPM2

city: Lyon

first: Antoine

last: Larrieu

address: 46, allée d'Italie,

country: France

institute: ENS Lyon

data_processing:
Fastq files were analysed with FastqQC (v 0.11.3, no particular options)
reads mapped to the Arabidopsis genome (TAIR10) using Tophat2 (v2.0.14 (Kim et al., 2013), options: -p8  --read-realign-edit-dist 0 --min-anchor-length 5 --min-intron-length 9 --max-intron-length 15000 --max-multihits 50 --no-coverage-search --microexon-search --min-segment-intron 8 --max-segment-intron 50000 --b2-very-sensitive --prefilter-multihits)
reads that mapped to exons counted using htseq-count (v0.9.1, option: htseq-count -f bam -r pos -m intersection-nonempty -s reverse).
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include read counts for each Sample

organism: Arabidopsis thaliana

source_name: Dissected inflorescence meristems

growth_protocol: All genotypes (except mpS319) were germinated on soil for RNA-seq (mutants and dex-inducible line), phenotyping, confocal microscopy and in situ hybridisation experiments. The plants were initially grown in short days (8hr light, 20°C; 16hr darkness, 20°C) for 3 weeks before being transferred to long days for an additional 3 weeks (16hr light, 20°C; 8hr darkness, 20°C) to synchronise flowering. Whenever meristems were dissected (for RNA-seq, phenotyping, confocal microscopy and in situs), plants had bolted few days before and stems were 2-5 cm high.

extract_protocol:
All RNA extractions were performed using the Arcturus Pico Pure (Thermo Fischer) RNA extraction kit following manufacturer’s recommendations. RNA quality was assessed with a Bioanalyser and only samples with a RIN > 6 were used. Before sequencing, an aliquot of RNA (500 ng) from selected samples was used for cDNA synthesis using Superscript Reverse Transcriptase II and the expression of few targets genes (AHP6, PIN1, MP, PID) as well as a control gene (AT1G04850) tested using qPCR. Four biological replicates were initially generated for all samples and three were sequenced (those with highest RINs).
All the sequencing reactions were performed at the “Plateforme Transcriptome” located in Unité de Recherche en Génomique Végétale (URGV) at the Université d’Evry Val d’Essonne (now Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Sud, Université d'Evry, Université Paris-Saclay). Libraries were prepared using the Agilent RNA6000 Nano kit and sequenced on a HiSeq2000 (Paired End 2x100b). Fastq files of the reads (with adaptors, reads with quality below 20 and reads mapping to the ribosomes removed) were downloaded from the sequencing lab server.

treatment_protocol: RNA for dex-inducible: 50µl of a solution containing dexamethasone (dex) (Sigma, 50µM (dissolved in DMSO)) or not (mock control, DMSO only) and Silwet L-77 (Lehle seeds, 0.01% final concentration) was placed on the top of a Col-0 (wild-type control) or pRPS5A::GR-bdl (Weijers et al., 2006) primary inflorescence. Silwet was used to ensure treatments reached the meristem. After 2 hours of treatments, five mock and dex treated primary inflorescences per biological replicate were dissected up to P6 (dissection time +/- 2 minutes), and a section of +/- 500µm from the tip of the meristem cut and directly frozen in liquid N2 per biological replicate. To ensure each sample was treated for 2 hours exactly, inflorescences were treated every four minutes to accommodate for dissection time. To reduce the effects of the circadian clock, biological replicates were harvested alternatively (Col-0 Mock R1, Col-0 Dex R1, GR-bdl Mock R1, GR-bdl Dex R1, Col-0 Mock R2, etc… up to R4) (total harvest time ~ 2 hours 40 minutes).

value: Dissected inflorescence meristems

value: Col-0 RPS5A::GR-bdl

value: Mock


title: ColM3


title: RPD4

value: Dex


title: RPM4


title: RPD2


title: Leaves, wounded for 24 hr, and then treated with cycloheximide for 4.5 hr (WS24)


title: ColM1


title: scRNA-seq: G3-EA06-1


title: ColD3


title: ColM2


title: scRNA-seq: G2-EA06-1


title: RPM3


title: RPD3


title: scRNA-seq: H4-EA06-1


title: ColD2


title: scRNA-seq: G11-EA06-1


title: scRNA-seq: G10-EA06-1


title: ColD1


title: scRNA-seq: G12-EA06-1


title: 120 minutes Auxin rep 3

source_name: Apices (ca. 500µm) of NPA pins (2 cm tall)

growth_protocol: Seeds to generate NPA pins (RNA-seq and confocal microscopy) were surface-sterilised and germinated on solid Arabidopsis medium (modified MS, see (Hamant et al., 2002) for details) complemented with N-1-Naphthylphthalamic Acid (NPA, 10µM) and grown for 2 weeks in long days (16 hours light, 20°C; 8 hours darkness, 20°C). NPA pins used for all experiments did not have any bumps visible on their flank and had a maximum height of 2 cm.  Seeds for in vitro cultures were sterilised in 20% bleach, 0.1% Triton for 20 minutes and rinsed three time with sterile water. Seeds for NPA pins were sown using top-agar to ensure they are evenly spaced, a key parameter to obtain good proportions (~10%) of pins with no visible morphological changes. After the third rinse, water was removed and molten Arabidopsis medium containing 10µM NPA was added to the sterile seeds. Seeds were resuspended in the medium and immediately poured onto round petri dishes already containing 25 mL of solid Arabidopsis medium (with 10µM NPA) to a density of around 100 seeds/plate. All seeds were vernalised on plates for 2 days before growing in growth rooms (see conditions above).

treatment_protocol: RNA for NPA pins: A section of +/- 500µm from the tip of 20 NPA pins per biological replicate with no visible bumps on their flanks were harvested and kept in 2mL Eppendorf tubes containing 500µl of liquid Arabidopsis medium with NPA at 10µM. Once all samples were harvested, an equal volume of liquid Arabidopsis medium containing auxin (Sigma, NAA at 2µM (1µM final)) or not (mock control) and NPA (Sigma, 10µM) was added. Treatments were performed for 30 minutes or 120 minutes after which all liquid medium was removed, and the samples directly frozen in liquid N2. To reduce the effects of the circadian clock, the treatments were started in such a way that all were harvested at the same time. The following samples were generated: Auxin 30 minutes R1, Mock 30 minutes R1, Auxin 120 minutes R1, Mock 120 minutes R1, Auxin 30 minutes R2, etc…, up to R4.

value: Auxin 120 minutes


title: scRNA-seq: F8-EA06-1


title: 120 minutes Auxin rep 2

value: Apices (ca. 500µm) of NPA pins (2 cm tall)


title: 120 minutes Auxin rep 1


title: scRNA-seq: G1-EA06-1


title: scRNA-seq: F4-EA06-1


title: scRNA-seq: F2-EA06-1


title: 120 minutes Mock rep 2

value: Mock 120 minutes


title: scRNA-seq: F5-EA06-1


title: 120 minutes Mock rep 3


title: scRNA-seq: F3-EA06-1


title: scRNA-seq: E9-EA06-1


title: scRNA-seq: E8-EA06-1


title: scRNA-seq: E7-EA06-1


title: scRNA-seq: E3-EA06-1


title: 30 minutes Mock rep 3

value: Mock 30 minutes


title: 30 minutes Auxin rep 1

value: Auxin 30 minutes


title: 30 minutes Auxin rep 2


title: scRNA-seq: E6-EA06-1

value: Neurog3-Cre, Rosa-mTmG

value: Pancreas


title: pin, rep3

growth_protocol: All genotypes (except mpS319) were germinated on soil for RNA-seq (mutants and dex-inducible line), phenotyping, confocal microscopy and in situ hybridisation experiments. The plants were initially grown in short days (8hr light, 20°C; 16hr darkness, 20°C) for 3 weeks before being transferred to long days for an additional 3 weeks (16hr light, 20°C; 8hr darkness, 20°C) to synchronise flowering. Whenever meristems were dissected (for RNA-seq, phenotyping, confocal microscopy and in situs), plants had bolted few days before and stems were 2-5 cm high. Because mpS319 homozygous mutants rarely develop a primary root they often fail to grow beyond the seedling stage. To improve recovery of homozygous mutants, sterilised seeds from a heterozygous parent were germinated on solid ½ Murashige and Skoog (MS, Sigma) salts (2.15g/L, pH 5.7), 1% agar plates containing auxin (1-Naphthaleneacetic acid, NAA at 0.1µM) and grown for 10 days in short days (8hr light, 20°C; 16hr darkness, 20°C). Plants with distinctive mp phenotypes (fused cotyledons) but with a visible and growing primary or adventitious roots were transferred on soil and grown for another 2 weeks before being transferred to long days for 3 weeks.

treatment_protocol: RNA for mutants: Five Col-0 (wild-type control) primary inflorescences per biological replicate were dissected up to P6 (dissection time +/- 2 minutes) and a section of +/- 500µm from the tip of the meristem cut and directly frozen in liquid N2. Five pin inflorescences per biological replicate were mechanically stimulated for 2 minutes to simulate dissection and a section of +/- 500µm from the tip of the meristem cut and directly frozen in liquid N2. Care was made to harvest only healthy Col-0 and pin mutants with no morphological changes at the apex). To reduce any effects due to the circadian clock, biological replicates were harvested alternatively in the following order (Col-0 R1, pin1 R1, pid R1, mp R1, Col-0 R2, etc… up to R4) (total harvesting time ~ 2 hours 30 minutes, 4 biological replicates each genotype).


title: 30 minutes Mock rep 1


title: 30 minutes Mock rep 2


title: scRNA-seq: E12-EA06-1


title: scRNA-seq: F9-EA06-1


title: scRNA-seq: F7-EA06-1


title: 120 minutes Mock rep 1


title: scRNA-seq: E10-EA06-1


title: pin, rep1


title: 30 minutes Auxin rep 3


title: pin, rep2


title: scRNA-seq: E1-EA06-1


title: pid, rep2


title: pid, rep1


title: scRNA-seq: D2-EA06-1


title: scRNA-seq: D12-EA06-1


title: pid, rep3


title: mp, rep3


title: mp, rep2


title: scRNA-seq: D11-EA06-1


title: scRNA-seq: C8-EA06-1


title: scRNA-seq: C5-EA06-1


title: mp, rep1


title: scRNA-seq: C3-EA06-1


title: Col-0, rep2


title: scRNA-seq: C12-EA06-1


title: Col-0, rep1


title: scRNA-seq: C11-EA06-1


title: 62g2e215p polysome fraction

city: Taipei

first: Hsing Yi

last: Cho

state: Select One

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: ABRC

country: Taiwan

institute: Academia sinica, Taiwan

description:
polysome fraction
LGL19-VQ62_328bp_S30_L002_R1_001 (paired) (GE)

data_processing:
Reads were mapped by CLC Genomics Workbench 11 (Qiagen).
The raw reads in each batch were analysed to give the expression ratio of genes between indicated time point of submergence and control conditions for the mRNAtotal and mRNAP samples by the Digital Gene Expression (DGE) empirical analysis tool.
For the comparison for Col-0 and three mutant lines, the 75th percentile relative FPKM value for mRNAtotal and mRNAP within the treatment and control was used to normalize.
Genome_build: TAIR10
Supplementary_files_format_and_content: The raw reads in each batch were analysed to give the expression ratio of genes between indicated time point of submergence and control conditions for the mRNAtotal and mRNAP samples by the Digital Gene Expression (DGE) empirical analysis tool (The gene which the P value at all time point show >0.05 was exclued  ).

source_name: 9-day old seedling

growth_protocol: growth protocol Germination and growth of Arabidopsis plants were as described previously. Seeds were sterilized with 0.5% sodium hypochlorite for 10 min and washed at least 3 times with sterilized water and then incubated with sterilized water at 4°C for 3 d to achieve uniform germination. Nine-day-old seedlings into a growth chamber under a 15-h-light (81 mmol m-2 s-1; at 22°C)/9-h-dark (at 18°C) cycle were treated with submergence 2h after the start of photoperiod.

extract_protocol:
extract protocol The nine-day-old seedlings under control conditions and treatment were harvested to extract RNA. The total RNA and the RNA loading on the polysome were isolated and quantified as previously described (New Phytologist (2019) 222: 366–381)
library construction protocol The standard protocol of illumina

treatment_protocol: treatment protocol  The plants were submerged in the ½ MS medium that was prebubbled with 3% oxygen for 1 h (the final oxygen concentration of the medium: 0.006%) in the light (81 mmol m-2 s-1).

tag: ecotype

tag: time point

value: 15min submergence

tag: replicate

value: bioloical rep2


title: scRNA-seq: D8-EA06-1


title: scRNA-seq: C1-EA06-1


title: 60g2e23 total mRNA

description:
total mRNA
LGL19-VQ60_349bp_S28_L002_R1_001 (paired) (GE)

value: 3h submergence


title: 64g2e23p polysome fraction

description:
polysome fraction
LGL19-VQ64_330bp_S32_L002_R1_001 (paired) (GE)


title: scRNA-seq: B6-EA06-1


title: 61g2e20p polysome fraction

description:
polysome fraction
LGL19-VQ61_329bp_S29_L002_R1_001 (paired) (GE)


title: scRNA-seq: B7-EA06-1


title: Col-0, rep3


title: 58g2e215 total mRNA

description:
total mRNA
LGL19-VQ58_352bp_S26_L002_R1_001 (paired) (GE)


title: scRNA-seq: B2-EA06-1


title: 59g2e21 total mRNA

description:
total mRNA
LGL19-VQ59_345bp_S27_L002_R1_001 (paired) (GE)

value: 1h sumbergence


title: 57g2e20 total mRNA

description:
total mRNA
LGL19-VQ57_348bp_S25_L002_R1_001 (paired) (GE)


title: 56e23p polysome fraction

description:
polysome fraction
LGL19-VQ56_340bp_S24_L002_R1_001 (paired) (GE)


title: scRNA-seq: B4-EA06-1


title: scRNA-seq: B10-EA06-1


title: scRNA-seq: B11-EA06-1


title: scRNA-seq: C2-EA06-1


title: 55e21p polysome fraction

description:
polysome fraction
LGL19-VQ55_342bp_S23_L002_R1_001 (paired) (GE)


title: 54e215p polysome fraction

description:
polysome fraction
LGL19-VQ54_325bp_S22_L002_R1_001 (paired) (GE)


title: 63g2e21p polysome fraction

description:
polysome fraction
LGL19-VQ63_331bp_S31_L002_R1_001 (paired) (GE)


title: scRNA-seq: B1-EA06-1


title: scRNA-seq: A8-EA06-1


title: scRNA-seq: A9-EA06-1


title: 52e23_ total mRNA

description:
total mRNA
LGL19-VQ52_348bp_S20_L002_R1_001 (paired) (GE)


title: 51e21_ total mRNA

description:
total mRNA
LGL19-VQ51_361bp_S19_L002_R1_001 (paired) (GE)


title: scRNA-seq: A7-EA06-1


title: scRNA-seq: A5-EA06-1


title: 50e215_ total mRNA

description:
total mRNA
LGL19-VQ50_352bp_S18_L002_R1_001 (paired) (GE)


title: scRNA-seq: A4-EA06-1


title: 49e20_ total mRNA

description:
total mRNA
LGL19-VQ49_356bp_S17_L002_R1_001 (paired) (GE)


title: scRNA-seq: A2-EA06-1


title: 48g23p polysome fraction

description:
polysome fraction
LGL19-VQ48_346bp_S16_L001_R1_001 (paired) (GE)


title: 47g21p polysome fraction

description:
polysome fraction
LGL19-VQ47_335bp_S15_L001_R1_001 (paired) (GE)


title: 46g215p polysome fraction

description:
polysome fraction
LGL19-VQ46_340bp_S14_L001_R1_001 (paired) (GE)


title: scRNA-seq: H8-EA05-1

value: endocrine


title: scRNA-seq: A10-EA06-1


title: scRNA-seq: A1-EA06-1


title: 44g23 total mRNA

description:
total mRNA
LGL19-VQ44_345bp_S12_L001_R1_001 (paired) (GE)


title: 53e20p polysome fraction

description:
polysome fraction
LGL19-VQ53_324bp_S21_L002_R1_001 (paired) (GE)


title: scRNA-seq: H7-EA05-1


title: scRNA-seq: H6-EA05-1


title: 43g21 total mRNA

description:
total mRNA
LGL19-VQ43_334bp_S11_L001_R1_001 (paired) (GE)


title: scRNA-seq: H4-EA05-1


title: 41g20 total mRNA

description:
total mRNA
LGL19-VQ41_338bp_S9_L001_R1_001 (paired) (GE)

value: wildtype


title: scRNA-seq: H5-EA05-1


title: scRNA-seq: H3-EA05-1


title: 40w3p polysome fraction

description:
polysome fraction
LGL19-VQ40_339bp_S8_L001_R1_001 (paired) (GE)


title: scRNA-seq: C4-EA07-1


title: scRNA-seq: H10-EA05-1


title: scRNA-seq: H11-EA05-1


title: scRNA-seq: H9-EA05-1


title: 36w3 total mRNA

description:
total mRNA
LGL19-VQ36_347bp_S4_L001_R1_001 (paired) (GE)


title: 45g20p polysome fraction

description:
polysome fraction
LGL19-VQ45_334bp_S13_L001_R1_001 (paired) (GE)


title: 37w0p polysome fraction

description:
polysome fraction
LGL19-VQ37_343bp_S5_L001_R1_001 (paired) (GE)


title: 35w1 total mRNA

description:
total mRNA
LGL19-VQ35_349bp_S3_L001_R1_001 (paired) (GE)


title: scRNA-seq: G8-EA05-1


title: 42g215 total mRNA

description:
total mRNA
LGL19-VQ42_342bp_S10_L001_R1_001 (paired) (GE)


title: 34w15 total mRNA

description:
total mRNA
LGL19-VQ34_346bp_S2_L001_R1_001 (paired) (GE)


title: scRNA-seq: G6-EA05-1


title: scRNA-seq: G9-EA05-1


title: scRNA-seq: G5-EA05-1


title: 32g2e23p polysome fraction

description:
polysome fraction
LGL19-VQ32_337bp_S32_L002_R1_001 (paired) (GE)

value: bioloical rep1


title: 33w0 total mRNA

description:
total mRNA
LGL19-VQ33_348bp_S1_L001_R1_001 (paired) (GE)


title: 30g2e215p polysome fraction

description:
polysome fraction
LGL19-VQ30_338bp_S30_L002_R1_001 (paired) (GE)


title: scRNA-seq: G7-EA05-1


title: scRNA-seq: G3-EA05-1


title: 31g2e21p polysome fraction

description:
polysome fraction
LGL19-VQ31_341bp_S31_L002_R1_001 (paired) (GE)


title: scRNA-seq: G12-EA05-1


title: 38w15p polysome fraction

description:
polysome fraction
LGL19-VQ38_337bp_S6_L001_R1_001 (paired) (GE)


title: scRNA-seq: H2-EA05-1


title: scRNA-seq: H1-EA05-1


title: scRNA-seq: G11-EA05-1


title: 39w1p polysome fraction

description:
polysome fraction
LGL19-VQ39_336bp_S7_L001_R1_001 (paired) (GE)


title: 28g2e23 total mRNA

description:
total mRNA
LGL19-VQ28_346bp_S28_L002_R1_001 (paired) (GE)


title: 29g2e20p polysome fraction

description:
polysome fraction
LGL19-VQ29_335bp_S29_L002_R1_001 (paired) (GE)


title: scRNA-seq: G10-EA05-1


title: scRNA-seq: F9-EA05-1


title: 26g2e215 total mRNA

description:
total mRNA
LGL19-VQ26_349bp_S26_L002_R1_001 (paired) (GE)


title: 23g21p polysome fraction

description:
polysome fraction
LGL19-VQ23_344bp_S23_L002_R1_001 (paired) (GE)


title: scRNA-seq: G1-EA05-1


title: scRNA-seq: F8-EA05-1


title: scRNA-seq: F7-EA05-1


title: scRNA-seq: F6-EA05-1


title: 24g23p polysome fraction

description:
polysome fraction
LGL19-VQ24_336bp_S24_L002_R1_001 (paired) (GE)


title: scRNA-seq: F4-EA05-1


title: scRNA-seq: F3-EA05-1


title: 21g20p polysome fraction

description:
polysome fraction
LGL19-VQ21_332bp_S21_L002_R1_001 (paired) (GE)


title: 22g215p polysome fraction

description:
polysome fraction
LGL19-VQ22_339bp_S22_L002_R1_001 (paired) (GE)


title: scRNA-seq: F5-EA05-1


title: 17g20 total mRNA

description:
total mRNA
LGL19-VQ17_348bp_S17_L002_R1_001 (paired) (GE)


title: scRNA-seq: F12-EA05-1


title: 15e21p polysome fraction

description:
polysome fraction
LGL19-VQ15_348bp_S15_L001_R1_001 (paired) (GE)


title: 20g23 total mRNA

description:
total mRNA
LGL19-VQ20_343bp_S20_L002_R1_001 (paired) (GE)


title: 27g2e21 total mRNA

description:
total mRNA
LGL19-VQ27_354bp_S27_L002_R1_001 (paired) (GE)


title: 19g21 total mRNA

description:
total mRNA
LGL19-VQ19_341bp_S19_L002_R1_001 (paired) (GE)


title: scRNA-seq: F1-EA05-1


title: scRNA-seq: F11-EA05-1


title: 18g215 total mRNA

description:
total mRNA
LGL19-VQ18_349bp_S18_L002_R1_001 (paired) (GE)


title: 14e215p polysome fraction

description:
polysome fraction
LGL19-VQ14_346bp_S14_L001_R1_001 (paired) (GE)-1


title: 25g2e20 total mRNA

description:
total mRNA
LGL19-VQ25_347bp_S25_L002_R1_001 (paired)-1 (GE)


title: scRNA-seq: F10-EA05-1


title: 13e20p polysome fraction

description:
polysome fraction
LGL19-VQ13_336bp_S13_L001_R1_001 (paired) (GE)


title: scRNA-seq: E8-EA05-1


title: scRNA-seq: E9-EA05-1


title: scRNA-seq: E7-EA05-1


title: scRNA-seq: F2-EA05-1


title: 12e23_ total mRNA

description:
total mRNA
LGL19-VQ12_350bp_S12_L001_R1_001 (paired) (GE)


title: 10e215_ total mRNA

description:
total mRNA
LGL19-VQ10_343bp_S10_L001_R1_001 (paired) (GE)


title: 11e21_ total mRNA

description:
total mRNA
LGL19-VQ11_358bp_S11_L001_R1_001 (paired) (GE)


title: 9e20_ total mRNA

description:
total mRNA
LGL19-VQ09_351bp_S9_L001_R1_001 (paired) (GE)


title: scRNA-seq: E5-EA05-1


title: scRNA-seq: E6-EA05-1


title: 8w3p polysome fraction

description:
polysome fraction
LGL19-VQ08_335bp_S8_L001_R1_001 (paired) (GE)


title: scRNA-seq: E4-EA05-1


title: 16e23p polysome fraction

description:
polysome fraction
LGL19-VQ16_341bp_S16_L001_R1_001 (paired) (GE)


title: 7w1p polysome fraction

description:
polysome fraction
LGL19-VQ07_337bp_S7_L001_R1_001 (paired) (GE)


title: 6w15p polysome fraction

description:
polysome fraction
LGL19-VQ06_325bp_S6_L001_R1_001 (paired) (GE)


title: 5w0p polysome fraction

description:
polysome fraction
LGL19-VQ05_317bp_S5_L001_R1_001 (paired) (GE)


title: 3w1 total mRNA

description:
total mRNA
LGL19-VQ03_347bp_S3_L001_R1_001 (paired) (GE)


title: scRNA-seq: E1-EA05-1


title: 2w15 total mRNA

description:
total mRNA
LGL19-VQ02_341bp-S2_L001_R1 (GE)


title: scRNA-seq: E10-EA05-1


title: 1w0 total mRNA

description:
total mRNA
LGL19-VQ01_341bp-S1_L001_R1_001 (paired) (GE)


title: scRNA-seq: E11-EA05-1


title: 4w3 total mRNA

description:
total mRNA
LGL19-VQ04_349bp_S4_L001_R1_001 (paired) (GE)


title: scRNA-seq: D5-EA05-1


title: scRNA-seq: D8-EA05-1


title: scRNA-seq: D9-EA05-1


title: scRNA-seq: D3-EA05-1


title: scRNA-seq: D6-EA05-1


title: scRNA-seq: D7-EA05-1


title: scRNA-seq: E12-EA05-1


title: scRNA-seq: D10-EA05-1


title: scRNA-seq: D12-EA05-1


title: scRNA-seq: D11-EA05-1


title: scRNA-seq: E3-EA05-1


title: scRNA-seq: D2-EA05-1


title: scRNA-seq: C9-EA05-1


title: scRNA-seq: C6-EA05-1


title: scRNA-seq: C3-EA05-1


title: scRNA-seq: C8-EA05-1


title: Kidney proximal tubules

city: Copenhagen

first: Søren

middle: Norge

last: Andreassen

state: Region Hovedstaden

address: Blegdamsvej 3

department: Department of Neuroscience

country: Denmark

institute: University of Copenhagen

description: Proximal tubules of the kidney

data_processing:
QC quality control and adapter removal was done by Novogene (UK) Company Limited.
Mapping to reference genome (rattus norvegicus Rnor_6.0.103) using STAR (v. 2.7.2a) (--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --quantMode TranscriptomeSAM)
Abundance quantified by RSEM (v. 1.3.3) (--bam --paired-end --forward-prob 0)
Genome_build: Rnor_6.0 (rn6) v.103
Supplementary_files_format_and_content: tab-delimited text files for gene abundance for each samples in TPM and FPKM

organism: Rattus norvegicus

source_name: Proximal tubules

extract_protocol:
Extraction was performed by Novogene (UK) Company Limited.
Done by Novogene (UK) Company using NEB Next® Ultra™ RNA Library Prep Kit, and sequenced on Illumina NovaSeq 6000, paired-end 150 bp, 12Gb output.

value: Sprague Dawley

value: 9 weeks

tag: Sex

value: Male

value: Proximal tubules

tag: animals pooled


title: scRNA-seq: C4-EA05-1


title: Female choroid plexus

description: Whole tissue

source_name: Choroid plexus

value: Female

value: Choroid plexus


title: Male choroid plexus

description: Whole tissue


title: Chroid plexus epithelial cells

description: Epithelial cells captured by NKCC1 labeling and FACS


title: scRNA-seq: C2-EA05-1


title: scRNA-seq: C12-EA05-1


title: scRNA-seq: C10-EA05-1


title: scRNA-seq: C5-EA05-1


title: Sup Control replicate3

city: Huai'an

first: Xiuqin

last: Ni

address: No.4 Mei Cheng Road, Higher Education Park

institute: Jiangsu Food and Pharmaceutical Science College

description: m6A methylation of mRNAs and long non-coding RNAs (lncRNAs) after PBS -sensitized and challenged

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar  Mouse mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 4 samples were retained for further analysis

source_name: RNAs that without binding to the magnetic beads with anti-N6-methyadenosine (m6A) antibody

label_protocol: Total RNAs were  immunoprecipitated with anti-N6-methyadenosine(m6A) antibody. The immunoprecipitated IP fraction contained enriched m6A methylated RNAs, and the supernatant  Sup fraction contained unmodified RNAs.IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit.

growth_protocol: The mice were housed in pathogen-free conditions.

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, USA) in accordance with the manufacturer’s instructions.

treatment_protocol: The mice were randomized into two groups: the control group and the asthma group. The mice in the asthma group were sensitized with 0.01% OVA by intraperitoneal injection on Day 0 and 7, and were subsequently challenged with 2.5% OVA aerosols three times weekly for seven weeks. The mice in the control group were injected and challenged with PBS.

value: BALB/c

value: whole lung

tag: gender

value: female


title: Sup Test replicate2

description: m6A methylation of mRNAs and long non-coding RNAs (lncRNAs) after OVA-sensitized and challenged


title: scRNA-seq: C1-EA05-1

value: Pancreas


title: Sup Control replicate2


title: Sup Test replicate1


title: scRNA-seq: B9-EA05-1


title: IP Test replicate3

source_name: RNAs that binded to the magnetic beads with anti-N6-methyadenosine (m6A) antibody


title: Sup Test replicate3


title: IP Control replicate1


title: Sup Control replicate1


title: DU145-PFOA10-6M-48h.2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: cRNA were then hybridized on 8×60K high density SurePrint G3 human gene expression Agilent microarrays according to manufacturer's instructions (Agilent Technologies). Agilent : 100.0 ng at 65 degree_C during 17 hours.

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: The data were quantile normalized using the Bioconductor package limma. Replicated probes were averaged after normalization and control probes were removed. Then we used a linear modeling approach to calculate log ratios, moderated t-statistics, and P-values. The Benjamini-Hochberg procedure was used to adjust the p-values for multiple gene comparisons.

source_name: DU145 cells PFOA 10-6M 48h replicate 2

label_protocol: The integrity of the RNA was assessed using an Agilent BioAnalyzer 2100 (Agilent Technologies). Amplification and labeling were performed with the LowInput QuickAmp Labeling Kit (Agilent Technologies).

growth_protocol: DU145 cells were seeded in DMEM medium without red phenol supplemented with 10% heat inactivated and charcoal stripped FBS at 37°C in 5% CO2. Addition of PFOA or EtOH was done the day after seeding.

extract_protocol: Trizol and RNeasy column (Qiagen) following manufacturer's recommendations

treatment_protocol: PFOA dissolved in EtOH was applied to cells for 48h before RNA extraction.

tag: cell line

tag: cell type

value: prostate cancer cell line

value: male

value: after PFOA 10-6M treatment 48h


title: IP Test replicate1

tag: age


title: IP Test replicate2

tag: strain


title: scRNA-seq: B7-EA05-1

tag: embryonic stage


title: IP Control replicate2


title: IP Control replicate3


title: DU145-PFOA10-9M-48h.2

source_name: DU145 cells PFOA 10-9M 48h replicate 2

value: after PFOA 10-9M treatment 48h


title: scRNA-seq: B5-EA05-1

tag: plate code

value: endocrine


title: DU145-PFOA10-12M-48h.2

source_name: DU145 cells PFOA 10-12M 48h replicate 2

value: after PFOA 10-12M treatment 48h


title: scRNA-seq: B8-EA05-1

tag: tissue


title: Targeting_2

data_processing:
Library strategy: DNA-seq
Paired-end reads were merged using BBMerge (version 38.69) with parameters “qtrim2=t, ecco, trimq=20, -Xmx1g, mix=f”
reads with perfect matches were mapped to reference genome  with In-house python script
Genome_build: NC_000913.3
Supplementary_files_format_and_content: CSV, raw counts of gRNAs in each sample

source_name: DNA

extract_protocol:
Library was transformed in cells with or without Cas13a and backdiluted 1:100 in LB with antibiotics to reach OD 0.06 and let grow for 12 hours shaking at 37°C. Finally, the library was midi-prepped with ZymoPure II Plasmid Midiprep Kit (Zymo Research, D4200).
The library prep was amplified with Kapa Hifi polymerase (Kapa Biosystems- Roche, 7958889001) according to the provider protocol. The reactions were purified using Ampure beads and further amplified to add the appropriate indexes and illumina adaptors. The resulting product was again purified with Ampure beads and run on a gel to verify the presence of the correct amplicon. The samples were sent for Sanger sequencing to make sure to get the expected sequence and then their quality was checked at the Bioanalyzer. Finally, they were sent for sequencing at the Next Seq sequencer (Illumina) with a 150 bp paired-ends kit (130 million reads) to get 1000x coverage. To increase the library diversity, 20% of phiX phage was spiked-in.

value: bacterial culture

tag: sample

value: Sample with nuclease


title: scRNA-seq: B3-EA05-1

tag: genotype


title: scRNA-seq: B6-EA05-1


title: scRNA-seq: B4-EA05-1


title: Targeting_1


title: scRNA-seq: B2-EA05-1


title: DU145-EtOH-48h.2

source_name: DU145 cells EtOH control replicat 2

tag: treatment

value: after EtOH treatment 48h


title: Non_targeting_1

value: Sample without nuclease

tag: biological replicate


title: scRNA-seq: A9-EA05-1


title: scRNA-seq: B1-EA05-1


title: DU145-PFOA10-9M-48h.1

source_name: DU145 cells PFOA 10-9M 48h replicate 1


title: DU145-PFOA10-6M-48h.1

hyb_protocol: cRNA were then hybridized on 8×60K high density SurePrint G3 human gene expression Agilent microarrays according to manufacturer's instructions (Agilent Technologies). Agilent : 65 degree_C during 17 hours.

source_name: DU145 cells PFOA 10-6M 48h replicate 1


title: DU145-PFOA10-12M-48h.1

source_name: DU145 cells PFOA 10-12M 48h replicate 1


title: ME161_ADT

city: New Haven

first: Rong

last: Fan

state: Connecticut

address: 55 Prospect St.

department: Biomedical Engineering

institute: Yale University

description:
antibody-derived DNA   tags (ADT)
Integrated_object_of_mesothelin_3T3_condition.rds

data_processing:
Library strategy: CITE-seq
Reads from the mRNA libraries were aligned to the referece genome using STAR 2.6.1a
A UMI count matrix was built using the Drop-seq core computational protocol (Version 2.0.0)
For co-culture experiments we filtered out mouse cells by removing cells with more than a specified number of mouse associated UMIs
The mRNA expression data  was log normalized using Seurat, and the Seurat v3 anchor-based integration workflow was  used to integrate data from different experiments
Genome_build: human (hg38) and mouse  (mm10)
Supplementary_files_format_and_content: Seurat object with gene matrix

source_name: PBMCs

growth_protocol: CAR T cells were thawed and cultured in OpTmizer™ T-Cell Expansion Basal Medium supplemented with OpTmizer™ T-Cell Expansion Supplement and GlutaMAX™ Supplement (Gibco) in the humidified incubator on day 1 for overnight rest.

extract_protocol:
Cell suspension, barcoded beads, lysis buffer and fluorinated oil were loaded sequentially into  microwells. The device was placed in a petri dish and exposed to  three cycles of freeze-and-thaw, each of which included freezing at -80°C freezer or dry ice for 5  min followed by thawing at room temperature for 5 min. To capture mRNA onto beads, the device  was then incubated for 1h inside an aluminum foil covered wet chamber.
Library preparations were performed as described in the DropSeq protocol (version 3.1)
Single cell RNA-seq

treatment_protocol: For the stimulation with CD19-3T3 cells or mesothelin-3T3 cells, 1e6 CAR T cells were mixed  with the same number of target cells in 2mL medium; for the stimulation with anti-CD3/CD28  beads, 1e6 CAR T cells were mixed with 3e6 beads in 1mL medium

value: Manufactured CAR T cells

tag: stimulation

value: Human mesothelin expressed 3T3 cells


title: Non_targeting_2


title: scRNA-seq: A5-EA05-1

source_name: Pancreas


title: ME157_ADT


title: ME167_ADT


title: ME158_ADT


title: scRNA-seq: B10-EA05-1


title: scRNA-seq: A4-EA05-1


title: DU145-EtOH-48h.1

source_name: DU145 cells EtOH control replicate 1


title: scRNA-seq: A6-EA05-1


title: ME111_ADT


title: scRNA-seq: A12-EA05-1


title: ME171_ADT


title: scRNA-seq: A8-EA05-1


title: ME139_ADT


title: scRNA-seq: A7-EA05-1


title: scRNA-seq: A2-EA05-1


title: ME110_ADT


title: scRNA-seq: H8-EA04

value: duct


title: scRNA-seq: A11-EA05-1


title: ME112_ADT


title: ME165_ADT


title: CD171A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 171
Integrated_object_of_CD19_3T3_condition.rds

value: Human CD19 expressed 3T3 cells


title: scRNA-seq: A10-EA05-1


title: ME151_ADT


title: scRNA-seq: H6-EA04


title: CD171B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 171
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: A1-EA05-1


title: ME117_ADT


title: CD165A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 165
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: H7-EA04


title: CD167B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 167
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: H2-EA04


title: scRNA-seq: H1-EA04


title: scRNA-seq: H5-EA04


title: CD165B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 165
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: H4-EA04


title: scRNA-seq: H3-EA04


title: scRNA-seq: H10-EA04


title: CD161B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 161
Integrated_object_of_CD19_3T3_condition.rds


title: CD161A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 161
Integrated_object_of_CD19_3T3_condition.rds


title: CD167A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 167
Integrated_object_of_CD19_3T3_condition.rds


title: CD158A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 158
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: G2-EA04


title: CD158B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 158
Integrated_object_of_CD19_3T3_condition.rds


title: CD157A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 157
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: G4-EA04


title: CD151B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 151
Integrated_object_of_CD19_3T3_condition.rds


title: CD151A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 151
Integrated_object_of_CD19_3T3_condition.rds


title: CD139B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 139
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: G9-EA04


title: scRNA-seq: G10-EA04


title: CD157B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 157
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: G12-EA04


title: CD117A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 117
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: F7-EA04


title: scRNA-seq: G3-EA04


title: CD112B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 112
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: F9-EA04


title: scRNA-seq: F6-EA04


title: scRNA-seq: F8-EA04


title: scRNA-seq: F3-EA04


title: CD117B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 117
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: F5-EA04


title: CD110A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 110
Integrated_object_of_CD19_3T3_condition.rds


title: CAR171_ADT

description:
antibody-derived DNA   tags (ADT)
Integrated_object_of_unstimulated_condition.rds

value: No stimulation


title: CD111B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 111
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: F11-EA04


title: CD111A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 111
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: F12-EA04


title: scRNA-seq: E9-EA04


title: scRNA-seq: E8-EA04


title: scRNA-seq: G1-EA04


title: CAR165_ADT


title: CAR158_ADT


title: CAR167_ADT


title: scRNA-seq: F4-EA04


title: scRNA-seq: E5-EA04


title: CAR161_ADT


title: scRNA-seq: E7-EA04


title: CD139A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 139
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: E3-EA04


title: scRNA-seq: E2-EA04


title: CD112A_ADT

description:
antibody-derived DNA   tags (ADT)
Library 1 from patient 112
Integrated_object_of_CD19_3T3_condition.rds


title: CD110B_ADT

description:
antibody-derived DNA   tags (ADT)
Library 2 from patient 110
Integrated_object_of_CD19_3T3_condition.rds


title: CAR139_ADT


title: CAR151_ADT


title: scRNA-seq: E11-EA04


title: CAR157_ADT


title: scRNA-seq: E10-EA04


title: scRNA-seq: E1-EA04


title: CAR111_ADT


title: scRNA-seq: D6-EA04


title: CAR112_ADT


title: scRNA-seq: D9-EA04


title: scRNA-seq: D4-EA04


title: BE171_ADT

description:
antibody-derived DNA   tags (ADT)
Integrated_object_of_CD3_CD28_beads_condition.rds

value: anti-CD3/CD28-coated beads


title: scRNA-seq: D12-EA04

value: Pancreas


title: CAR110_ADT


title: scRNA-seq: D3-EA04


title: BE165_ADT


title: BE167_ADT


title: BE161_ADT


title: scRNA-seq: C4-EA04


title: scRNA-seq: C3-EA04


title: BE151_ADT


title: scRNA-seq: C8-EA04


title: BE158_ADT


title: scRNA-seq: D1-EA04


title: BE157_ADT


title: CAR117_ADT


title: BE112_ADT


title: BE117_ADT


title: BE139_ADT


title: scRNA-seq: C12-EA04


title: scRNA-seq: C10-EA04


title: BE111_ADT


title: scRNA-seq: C2-EA04


title: BE110_ADT


title: scRNA-seq: B8-EA04


title: CKO5

city: Nanjing

first: chen

last: xiang

address: chunhua street

institute: nanjing medical university

data_processing:
Quality Control:  In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Mapping: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones
mm9
Assembly: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Brain

extract_protocol:
Cerebellar IV/V lobe Region tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Cereberal IV/V lobe

value: AAV-L7-EGFP injected


title: CKO6


title: CKO3


title: CKO2


title: ME171

description: Integrated_object_of_mesothelin_3T3_condition.rds

data_processing:
Reads from the mRNA libraries were aligned to the referece genome using STAR 2.6.1a
A UMI count matrix was built using the Drop-seq core computational protocol (Version 2.0.0)
For co-culture experiments we filtered out mouse cells by removing cells with more than a specified number of mouse associated UMIs
The mRNA expression data  was log normalized using Seurat, and the Seurat v3 anchor-based integration workflow was  used to integrate data from different experiments
Genome_build: human (hg38) and mouse  (mm10)
Supplementary_files_format_and_content: Seurat object with gene matrix


title: CKO4


title: CKO1


title: scRNA-seq: B6-EA04


title: CON5


title: ME165


title: ME161


title: scRNA-seq: B5-EA04


title: CON4


title: CON1


title: scRNA-seq: B4-EA04


title: ME158


title: scRNA-seq: C11-EA04


title: scRNA-seq: B9-EA04


title: ME157


title: T3-2

city: Shijiazhuang

first: Bing

last: Xie

state: Hebei

address: Tiyubei street

institute: Hebei Medical University

data_processing:
Illumina Casava1.7 software used for basecalling
Raw data (raw reads) of fastq format were firstly processed through custom perl  and python scripts. In this step, clean datas(clean reads) were obtained by  removing reads containing ploy-N, with 5’ adapter contaminants, without 3’  adapter or the insert tag, containing ploy A or T or G or C and low quality reads  from raw data.

source_name: nucleus accumben

extract_protocol:
nucleus accumbens were removed, flash frozen on dry ice, and RNA was harvest using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: nucleus accumben

value: Morphine injection  T3


title: T3-3


title: T3-1


title: T1-3

value: Morphine injection  T1


title: scRNA-seq: B7-EA04


title: CON3


title: scRNA-seq: B1-EA04


title: T1-1


title: T1-2


title: ME167


title: ME151


title: scRNA-seq: A9-EA04


title: ME139


title: CON2


title: scRNA-seq: B2-EA04


title: scRNA-seq: A8-EA04


title: ME117


title: scRNA-seq: B12-EA04


title: Liver FigS16-TTR_NaCl_rep4

city: Cambridge

first: Joseph

last: Barry

state: MA

address: 675 West Kendall St

institute: Alnylam Pharmaceuticals

data_processing:
Raw RNAseq reads were filtered with minimal mean quality scores of 25 and minimal remaining length of 36, using the ea-utils software fastq-mcf.
Filtered reads were aligned to the Rattus norvegicus genome (Rnor_6.0) [rat liver and primary hepatocyte samples], or combined Human (hgl9/GRCh37) and HBV (GenBank nucleotide ID U95551; NCBI GeneID: 7276) genomes using STAR (ultrafast universal RNAseq aligner) [HepG2.2.15 samples].
Differential gene expression analysis was performed by the R package DESeq2 v1.16.1 with the betaPrior parameter set to TRUE to shrink log2 fold-change estimates for noisy, low-count genes.
Assembly: Rnor_6.0, GRCh37

source_name: Liver

growth_protocol: HepG2.2.15 cells, a HepG2 derived cell line stably transfected with full genome HBV, were diluted with culture media to a final concentration of 187,500 cells/mL, and 80 µL was pipetted into 96-well collagen coated plates (BD Biocoat, Cat#356407) to give a final concentration of 15,000 cells/well.  RNAiMAX (ThermoFisher, Cat#13778150) was diluted with Opti-MEM (ThermoFisher Cat#31985062) at a concentration of 0.3 µL RNAiMAX/10 µL Opti-MEM and incubated for 5 minutes at room temperature.  After incubation, 10 µL/well was added to each well of 96-well collagen coated plates (BD Biocoat, Cat#356407), along with 10 µL/well of the appropriate dsRNA agent dilution (as appropriate in 1x PBS), mixed gently and incubated for 20 minutes at room temperature.  80 µL of prepared cell suspension was added to each well to give final cell density of 15,000 cells/well and final dsRNA agent concentrations of 10 nM.  Cells were incubated in a 37 °C incubator with 5% CO2 for 16-22 hours. Primary Rat Hepatocyte cells followed a similar protocol, but were incubated for 48 hours.

extract_protocol:
Rat livers collected at the end of the toxicity studies were snap-frozen, powdered, and RNA was extracted with the miRNeasy kit (Qiagen). HepG2.2.15 RNA was isolated using the ThermoFisher RNAqueous-96 Total RNA Isolation Kit, as per the protocol.
cDNA libraries were prepared with the TruSeq Stranded Total RNA Library Prep Kit (Illumina) and sequenced on a NextSeq500 sequencer (Illumina), all according to manufacturers’ instructions.

value: Sprague Dawley

value: 6-8 weeks

value: male


title: scRNA-seq: A7-EA04


title: Liver FigS16-TTR_NaCl_rep8


title: Liver FigS16-TTR_NaCl_rep7


title: Liver FigS16-TTR_NaCl_rep6


title: ME111


title: Liver FigS16-TTR_NaCl_rep5


title: Liver FigS16-TTR_NaCl_rep3


title: ME112


title: ME110


title: Liver FigS16-TTR_D4_30mkg_rep4


title: CD171B

description:
Library 2 from patient 171
Integrated_object_of_CD19_3T3_condition.rds


title: Liver FigS16-TTR_D4_30mkg_rep2


title: Liver FigS16-TTR_NaCl_rep2


title: scRNA-seq: A3-EA04


title: Liver FigS16-TTR_D11_30mkg_rep4


title: scRNA-seq: A4-EA04


title: Liver FigS16-TTR_NaCl_rep1


title: CD171A

description:
Library 1 from patient 171
Integrated_object_of_CD19_3T3_condition.rds


title: Liver FigS16-TTR_D4_30mkg_rep3


title: CD167B

description:
Library 2 from patient 167
Integrated_object_of_CD19_3T3_condition.rds


title: Liver FigS16-TTR_D1_30mkg_rep3


title: Liver FigS16-TTR_D11_30mkg_rep1


title: scRNA-seq: A2-EA04


title: scRNA-seq: A1-EA04


title: Liver FigS16-TTR_D1_30mkg_rep1


title: scRNA-seq: A11-EA04


title: Liver FigS16-TTR_D11_30mkg_rep2


title: CD161B

description:
Library 2 from patient 161
Integrated_object_of_CD19_3T3_condition.rds


title: Liver FigS16-TTR_D4_30mkg_rep1


title: Liver FigS16-TTR_D1_30mkg_rep4


title: scRNA-seq: A10-EA04


title: Liver FigS16-TTR_D1_30mkg_rep2


title: Liver FigS16-GO1_D12_30mkg_rep4


title: CD165A

description:
Library 1 from patient 165
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: H3-EA03


title: Liver FigS16-GO1_D12_30mkg_rep2


title: Liver FigS16-GO1_D12_30mkg_rep3


title: scRNA-seq: G9-EA03


title: Primary Rat Hepatocytes Fig4_mock_rep4

source_name: Primary Rat Hepatocytes

value: PRH


title: CD167A

description:
Library 1 from patient 167
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: A12-EA04


title: scRNA-seq: H1-EA03


title: Primary Rat Hepatocytes Fig4_mock_rep3


title: CD158B

description:
Library 2 from patient 158
Integrated_object_of_CD19_3T3_condition.rds


title: Liver FigS16-GO1_D12_30mkg_rep1


title: scRNA-seq: G8-EA03


title: scRNA-seq: G7-EA03


title: CD158A

description:
Library 1 from patient 158
Integrated_object_of_CD19_3T3_condition.rds


title: CD165B

description:
Library 2 from patient 165
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_mock_rep1


title: Primary Rat Hepatocytes Fig4_mock_rep2


title: Primary Rat Hepatocytes Fig4_D9_50nM_rep4


title: Primary Rat Hepatocytes Fig4_D9_50nM_rep3


title: CD157B

description:
Library 2 from patient 157
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: G6-EA03


title: CD157A

description:
Library 1 from patient 157
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D6_50nM_rep4


title: Primary Rat Hepatocytes Fig4_D6_50nM_rep3


title: scRNA-seq: G5-EA03


title: Primary Rat Hepatocytes Fig4_D6_50nM_rep2


title: CD161A

description:
Library 1 from patient 161
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D9_50nM_rep1


title: scRNA-seq: G4-EA03


title: Primary Rat Hepatocytes Fig4_D6_50nM_rep1


title: scRNA-seq: G3-EA03


title: CD151A

description:
Library 1 from patient 151
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D4_50nM_rep4


title: Primary Rat Hepatocytes Fig4_D4_50nM_rep3


title: CD139B

description:
Library 2 from patient 139
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D4_50nM_rep1


title: Primary Rat Hepatocytes Fig4_D4_50nM_rep2


title: CD139A

description:
Library 1 from patient 139
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D20_50nM_rep4


title: scRNA-seq: G12-EA03


title: CD151B

description:
Library 2 from patient 151
Integrated_object_of_CD19_3T3_condition.rds


title: scRNA-seq: G11-EA03


title: Primary Rat Hepatocytes Fig4_D20_50nM_rep3


title: Liver FigS16-TTR_D11_30mkg_rep3


title: scRNA-seq: G10-EA03


title: Primary Rat Hepatocytes Fig4_D20_50nM_rep2


title: Primary Rat Hepatocytes Fig4_D16_50nM_rep3


title: CD112B

description:
Library 2 from patient 112
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D9_50nM_rep2


title: CD117B

description:
Library 2 from patient 117
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D16_50nM_rep1


title: scRNA-seq: G1-EA03


title: Primary Rat Hepatocytes Fig4_D1_50nM_rep3


title: CD112A

description:
Library 1 from patient 112
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D20_50nM_rep1


title: scRNA-seq: F7-EA03


title: scRNA-seq: F8-EA03


title: Primary Rat Hepatocytes Fig4_D16_50nM_rep2


title: Primary Rat Hepatocytes Fig4_D1_50nM_rep4


title: Primary Rat Hepatocytes Fig4_D1_50nM_rep2


title: CD111B

description:
Library 2 from patient 111
Integrated_object_of_CD19_3T3_condition.rds


title: Primary Rat Hepatocytes Fig4_D1_50nM_rep1


title: CD111A

description:
Library 1 from patient 111
Integrated_object_of_CD19_3T3_condition.rds


title: Liver Fig3-TTR-2_Mock_rep4


title: Liver Fig3-TTR-2_Mock_rep3


title: scRNA-seq: F5-EA03


title: CD110B

description:
Library 2 from patient 110
Integrated_object_of_CD19_3T3_condition.rds


title: CD110A

description:
Library 1 from patient 110
Integrated_object_of_CD19_3T3_condition.rds


title: CD117A

description:
Library 1 from patient 117
Integrated_object_of_CD19_3T3_condition.rds


title: Liver Fig3-TTR-2_D4_60mkg_rep4


title: Liver Fig3-TTR-2_Mock_rep1


title: Liver Fig3-TTR-2_D4_60mkg_rep3


title: Liver Fig3-TTR-2_D4_60mkg_rep2


title: Liver Fig3-TTR-2_D4_60mkg_rep1


title: CAR171

description: Integrated_object_of_unstimulated_condition.rds


title: scRNA-seq: F2-EA03


title: CAR167


title: scRNA-seq: F3-EA03


title: scRNA-seq: F6-EA03


title: CAR165


title: Liver Fig3-TTR-2_D4_30mkg_rep2


title: Liver Fig3-TTR-2_D4_30mkg_rep1


title: Liver Fig3-TTR-2_D4_30mkg_rep3


title: Liver Fig3-TTR-2_D4_30mkg_rep4


title: Liver Fig3-TTR-2_D4_120mkg_rep4


title: CAR161


title: scRNA-seq: F12-EA03


title: Liver Fig3-TTR-2_D4_120mkg_rep3


title: scRNA-seq: F11-EA03


title: Liver Fig3-TTR-2_Mock_rep2


title: Liver Fig3-TTR-2_D4_120mkg_rep2


title: scRNA-seq: F10-EA03


title: scRNA-seq: F4-EA03


title: CAR157


title: Liver Fig3-TTR-2_D1_60mkg_rep4


title: Liver Fig3-TTR-2_D4_120mkg_rep1


title: scRNA-seq: E9-EA03


title: Liver Fig3-TTR-2_D1_60mkg_rep3


title: CAR151


title: scRNA-seq: E7-EA03


title: Liver Fig3-TTR-2_D1_60mkg_rep2


title: CAR139


title: scRNA-seq: E6-EA03


title: Liver Fig3-TTR-2_D1_60mkg_rep1


title: Liver Fig3-TTR-2_D1_30mkg_rep4


title: Liver Fig3-TTR-2_D1_30mkg_rep3


title: CAR112


title: MSF25

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

data_processing:
BGISEQ-500 platform
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: RNA from monocyte-derived macrophages treated with LPS for 4h in the presence of an anti-IL-10 blocking antibody (donor #B5)

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml M-CSF to generate M-CSF-polarized macrophages.

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Monocyte-derived macrophages (at day 7 along the differentiation protocol) were treated with an anti-IL-10 blocking antibody (anti-IL10) or an isotype-matched antibody (IgG2b) at 2.5 micrograms/ml for 1 hour, and exposed to LPS (10 ng/ml). After 4 hours of LPS treatment, cells were lysed and RNA isolated for transcriptional analysis.

value: Monocyte-derived M-CSF macrophages

value: Blocking anti-IL-10 antibody; LPS


title: Liver Fig3-TTR-2_D1_30mkg_rep2


title: MSF26

source_name: RNA from monocyte-derived macrophages treated with LPS for 4h in the presence of an anti-IL-10 blocking antibody (donor #B3)


title: CAR117

value: Manufactured CAR T cells


title: Liver Fig3-TTR-2_D1_30mkg_rep1


title: CAR111


title: scRNA-seq: E5-EA03


title: MSF24

source_name: RNA from monocyte-derived macrophages treated with LPS for 4h in the presence of an anti-IL-10 blocking antibody (donor #B4)


title: scRNA-seq: F1-EA03


title: scRNA-seq: E8-EA03


title: scRNA-seq: E4-EA03


title: CAR110


title: MSF23

source_name: RNA from monocyte-derived macrophages treated with LPS for 4h in the presence of IgG2b (donor #B3)

value: Control IgG2B; LPS


title: Liver Fig3-TTR-2_D1_120mkg_rep3


title: BE171

description: Integrated_object_of_CD3_CD28_beads_condition.rds


title: MSF22

source_name: RNA from monocyte-derived macrophages treated with LPS for 4h in the presence of IgG2b (donor #B5)


title: scRNA-seq: E12-EA03


title: BE167


title: scRNA-seq: E11-EA03


title: Liver Fig3-TTR-1_Mock_rep4


title: MSF21

source_name: RNA from monocyte-derived macrophages treated with LPS for 4h in the presence of IgG2b (donor #B4)


title: Liver Fig3-TTR-2_D1_120mkg_rep1


title: BE161


title: scRNA-seq: D4-EA03


title: BE165


title: Liver Fig3-TTR-1_Mock_rep3


title: scRNA-seq: E10-EA03


title: monocyte-derived macrophages 48 hours after transfection with a STAT3-specific siRNA and exposure to LPS for 4 hours #2

source_name: macrophages

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures.monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells).monocytes (0.5 x 10e6 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 1000 U/ml M-CSF to generate M-CSF-polarized macrophages.

treatment_protocol: Monocyte-derived macrophages (at day 5 along the differentiation protocol) were transfected with STAT3-specific siRNA or control siRNA, kept in culture for 48 hours, and then stimulated (or not) with LPS (10 ng/ml). After 4 hours, cells were lysed and RNA isolated for transcriptional analysis.

value: STAT3 knockdown

value: Exposed to LPS


title: Liver Fig3-TTR-1_Mock_rep2


title: BE158

value: anti-CD3/CD28-coated beads


title: monocyte-derived macrophages 48 hours after transfection with a STAT3-specific siRNA and exposure to LPS for 4 hours #1


title: monocyte-derived macrophages 48 hours after transfection with a STAT3-specific siRNA #3

value: untreated


title: BE157


title: scRNA-seq: C9-EA03

value: Pancreas


title: scRNA-seq: E3-EA03


title: Liver Fig3-TTR-2_D1_120mkg_rep2


title: scRNA-seq: C8-EA03


title: scRNA-seq: C7-EA03


title: monocyte-derived macrophages 48 hours after transfection with a STAT3-specific siRNA #2


title: Liver Fig3-TTR-1_D4_3mkg_rep4


title: BE139


title: BE151


title: Liver Fig3-TTR-1_D4_3mkg_rep3


title: monocyte-derived macrophages 48 hours after transfection with a STAT3-specific siRNA and exposure to LPS for 4 hours #3


title: monocyte-derived macrophages 48 hours after transfection with a STAT3-specific siRNA #1


title: BE117


title: scRNA-seq: C6-EA03


title: scRNA-seq: C5-EA03


title: Liver Fig3-TTR-1_Mock_rep1


title: Liver Fig3-TTR-1_D4_3mkg_rep2


title: monocyte-derived macrophages 48 hours after transfection with a control siRNA and exposure to LPS for 4 hours #3

value: Control


title: scRNA-seq: C4-EA03


title: monocyte-derived macrophages 48 hours after transfection with a control siRNA and exposure to LPS for 4 hours #2


title: BE112


title: BE111


title: scRNA-seq: C3-EA03


title: Liver Fig3-TTR-1_D4_10mkg_rep2


title: monocyte-derived macrophages 48 hours after transfection with a control siRNA and exposure to LPS for 4 hours #1


title: Liver Fig3-TTR-1_D4_10mkg_rep3


title: BE110


title: monocyte-derived macrophages 48 hours after transfection with a control siRNA #3


title: scRNA-seq: C2-EA03


title: monocyte-derived macrophages 48 hours after transfection with a control siRNA #2


title: scRNA-seq: C12-EA03


title: monocyte-derived macrophages 48 hours after transfection with a control siRNA #1


title: Liver Fig3-TTR-1_D4_10mkg_rep1


title: Liver Fig3-TTR-1_D1_3mkg_rep4


title: Liver Fig3-TTR-1_D1_3mkg_rep3


title: scRNA-seq: C11-EA03


title: Liver Fig3-TTR-1_D4_3mkg_rep1


title: scRNA-seq: C10-EA03


title: scRNA-seq: C1-EA03


title: Liver Fig3-TTR-2_D1_120mkg_rep4


title: Ds noni 2

city: Middletown

last: Coolon

state: CT

address: 52 Lawn Ave.

department: Biology

institute: Wesleyan University

data_processing:
FASTQC on each of the 6 raw fastq files
Bowtie2 alignment using the D. sechellia reference genome available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa)
Cuffdiff for quantification and differential expression analysis using the D. sechellia reference genome available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa) and gene file available at the time of analysis (Drosophila_sechellia.dsec_caf1.42.gff3) with geometric library normalization
Assembly: Drosophila_sechellia.dsec_caf1.dna.toplevel.fa
Supplementary files format and content: Tab-delimited Cuffdiff output in csv format

organism: Drosophila sechellia

source_name: Whole adults

growth_protocol: Flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20 degrees Celsius

extract_protocol:
Total RNA was extracted from whole female adults using Promega SV Total RNA Isolation System
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were exposed to 1g of rotten M. cirtrifolia fruit pulp mixed into instant Drosophila food or control food for a period of 24 hours

tag: diet


title: Ds noni 3

value: 1g of rotten M. cirtrifolia fruit pulp mixed into instant Drosophila food


title: Liver Fig3-TTR-1_D1_3mkg_rep2


title: Ds noni 1


title: Liver Fig3-TTR-1_D1_3mkg_rep1


title: Liver Fig3-TTR-1_D1_10mkg_rep3


title: Ds Control 3

value: control


title: scRNA-seq: B7-EA03


title: Ds Control 1


title: scRNA-seq: B6-EA03


title: Liver Fig3-TTR-1_D1_10mkg_rep1


title: Liver Fig3-GO1_NaCl_rep8


title: Liver Fig3-GO1_NaCl_rep7


title: scRNA-seq: B4-EA03


title: Liver Fig3-GO1_NaCl_rep6


title: scRNA-seq: B5-EA03


title: scRNA-seq: B3-EA03


title: Liver Fig3-GO1_NaCl_rep5


title: scRNA-seq: B2-EA03


title: scRNA-seq: B9-EA03


title: scRNA-seq: B8-EA03


title: Liver Fig3-GO1_NaCl_rep4


title: Ds Control 2


title: Liver Fig3-TTR-1_D1_10mkg_rep2


title: scRNA-seq: B11-EA03


title: Liver Fig3-GO1_NaCl_rep2


title: Liver Fig3-GO1_NaCl_rep3


title: Liver Fig3-GO1_NaCl_rep1


title: scRNA-seq: B10-EA03


title: scRNA-seq: A9-EA03


title: scRNA-seq: B1-EA03


title: Liver Fig3-GO1_D9_60mkg_rep4


title: Liver Fig3-GO1_D9_60mkg_rep3


title: scRNA-seq: B12-EA03


title: scRNA-seq: A8-EA03


title: scRNA-seq: A7-EA03


title: Liver Fig3-GO1_D9_60mkg_rep2


title: Liver Fig3-GO1_D9_60mkg_rep1


title: Liver Fig3-GO1_D9_3mkg_rep4


title: scRNA-seq: A3-EA03


title: scRNA-seq: A5-EA03


title: scRNA-seq: A4-EA03


title: Liver Fig3-GO1_D9_3mkg_rep3


title: scRNA-seq: A6-EA03


title: Liver Fig3-GO1_D9_3mkg_rep2


title: Liver Fig3-GO1_D9_3mkg_rep1


title: scRNA-seq: A11-EA03


title: human_methylation_NTP_rep7

type: genomic

city: ChangSha

first: ZhaoQian

last: Liu

state: China

address: xiangya road 110

institute: Xiangya Hospital, Central South University

description: DNA Methylation of human brain tissue in TLE+HS and NTP

hyb_protocol: The labeled product is purified by the Nucleospin® Extract II kit in an elution volume of about 30 µL. 100µL of hybridization solution was added to the hybridization cover fence. The hybridization box is installed on the rotor of the hybridization furnace, Meanwhile, after adding appropriate amount of ultrapure water in the tray, hybridize at 45°C overnight.

scan_protocol: Agilent G2565CA Microarray Scanner was used to scan the slides.

data_processing: Agilent Feature Extraction Software v10.7 was used to analyze the scanned pictures of the microarray.

source_name: Brain tissue, normal temporal or parietal cortices

label_protocol: The volume of cDNA product obtained after reverse transcription and purification was concentrated to 14µL, mixed with 4µL Random Primer, briefly centrifuged and placed on a PCR instrument, denatured at 95°C for 3 minutes and ice bath for 5 minutes. Add the reagents (5 µL 5×Klenow Buffer; 1 µL Cy3-dCTP; 1.2 µL Klenow Fragmen) in sequence and mix well by blowing 2-3 times with a pipette. After a short centrifugation, place on a PCR instrument and react for 1.5 h at 37°C and 5 min at 70°C. Hold at 4°C. After the fluorescent dye labeling reaction, cDNA was purified using the Nucleospin® Extract II (MN, Cat. No. 740609.250) kit, and the purified fluorescently labeled products were quantified for fluorescence admixture and nucleic acid using a UV spectrophotometer.

extract_protocol: MirVana miRNA Isolation Kit was used to purify total microRNA. The DNA sample was bisulfite converted using the Zymo EZ DNA Methylation Kit (Zymo Research) as directed. The Illumina 450k BeadChip was used to measure methylation.

treatment_protocol: All of the tissue was taken from Hippocampus or cerebral cortex (temporal or parietal cortices). Tissues were obtained and kept at –80°C until microarray analysis.

value: Parietal lobe

value: Male


title: human_methylation_NTP_rep9


title: scRNA-seq: A10-EA03

data_processing:
Raw reads passed quality control using FastQC
Reads were aligned to a custom reference genome consisting of Fasta files for mm10, ERCC knock in, and three transgenes: eGFP, tdTomato, and cre. STAR was used to create the custom genome and read alignment
BAM/SAM files created a counts table using ht-seq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes a matrix of normalized tag counts for each sample


title: Liver Fig3-GO1_D9_30mkg_rep4

value: Sprague Dawley

value: 6-8 weeks


title: Liver Fig3-GO1_D9_30mkg_rep3

value: male


title: human_methylation_NTP_rep8

value: Temporal lobe


title: human_methylation_NTP_rep4


title: human_methylation_NTP_rep5


title: scRNA-seq: A12-EA03


title: scRNA-seq: A1-EA03


title: scRNA-seq: H3-EA02

value: endocrine


title: scRNA-seq: H4-EA02


title: CAR158

value: Manufactured CAR T cells

value: No stimulation


title: Liver Fig3-GO1_D9_120mkg_rep4


title: scRNA-seq: H1-EA02


title: Liver Fig3-GO1_D9_120mkg_rep3


title: human_methylation_NTP_rep6


title: Liver Fig3-GO1_D9_30mkg_rep2


title: Liver Fig3-GO1_D9_120mkg_rep2


title: human_methylation_NTP_rep1

value: Female


title: human_methylation_TLE+HS_rep4

source_name: Brain tissue, TLE+HS

value: Hippocampus


title: scRNA-seq: G9-EA02


title: Liver Fig3-GO1_D9_120mkg_rep1


title: human_methylation_TLE+HS_rep6


title: scRNA-seq: G8-EA02


title: scRNA-seq: G7-EA02


title: scRNA-seq: G5-EA02


title: human_methylation_NTP_rep2


title: Liver Fig3-GO1_D9_10mkg_rep3


title: scRNA-seq: G6-EA02


title: Liver Fig3-GO1_D9_10mkg_rep2


title: Liver Fig3-GO1_D9_10mkg_rep1


title: Liver Fig3-GO1_D9_30mkg_rep1


title: human_methylation_NTP_rep3


title: scRNA-seq: G4-EA02


title: Liver Fig3-GO1_D9_10mkg_rep4


title: Liver Fig3-GO1_D6_60mkg_rep4


title: Liver Fig3-GO1_D6_60mkg_rep3


title: scRNA-seq: G10-EA02


title: Liver Fig3-GO1_D6_60mkg_rep1