title: RNAseq_60336


title: RNAseq_67272

status: Public on Dec 31 2020

type: SRA

city: Boston

first: Peter

last: Castaldi

state: Massachusetts

address: 181 Longwood Ave

country: USA

institute: Brigham and Women's Hospital

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

library_source: transcriptomic

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_32586

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_19158


title: RNAseq_67730


title: RNAseq_46798


title: RNAseq_06504


title: RNAseq_28956


title: RNAseq_11363


title: RNAseq_20840


title: RNAseq_53757


title: RNAseq_47652


title: RNAseq_17907


title: RNAseq_25802


title: RNAseq_23923


title: RNAseq_31132


title: RNAseq_07354


title: RNAseq_58852


title: RNAseq_07307


title: RNAseq_69298


title: RNAseq_35819


title: RNAseq_01019


title: RNAseq_92883


title: RNAseq_37284


title: RNAseq_95450


title: RNAseq_86319


title: RNAseq_99527


title: RNAseq_25559


title: RNAseq_14116


title: RNAseq_95653


title: RNAseq_60250


title: RNAseq_83007


title: RNAseq_93718


title: RNAseq_70151


title: RNAseq_26221


title: RNAseq_66841


title: RNAseq_50464


title: RNAseq_77288


title: RNAseq_67330


title: RNAseq_17376


title: RNAseq_87139


title: RNAseq_76871


title: RNAseq_15325


title: RNAseq_02741


title: RNAseq_89598


title: RNAseq_29905


title: RNAseq_34032


title: RNAseq_61584


title: RNAseq_98279


title: RNAseq_49014


title: RNAseq_00132


title: RNAseq_09353


title: RNAseq_83083


title: RNAseq_29213


title: RNAseq_04355


title: RNAseq_80264


title: RNAseq_12355


title: RNAseq_83664


title: RNAseq_03949


title: RNAseq_10784


title: RNAseq_16731


title: RNAseq_81649


title: RNAseq_43746


title: RNAseq_48807


title: RNAseq_64786


title: RNAseq_95034


title: RNAseq_44077


title: RNAseq_84183


title: RNAseq_01625


title: RNAseq_54569


title: RNAseq_15087


title: RNAseq_46417


title: RNAseq_76363


title: RNAseq_00642


title: RNAseq_72721


title: RNAseq_71424


title: RNAseq_67230


title: RNAseq_23972


title: RNAseq_31693


title: RNAseq_59527


title: RNAseq_81659


title: RNAseq_55637


title: RNAseq_27880


title: RNAseq_61585


title: RNAseq_72416


title: RNAseq_11587


title: RNAseq_81527


title: RNAseq_37381


title: RNAseq_64717


title: RNAseq_40005


title: RNAseq_22200


title: RNAseq_07340


title: RNAseq_81191


title: RNAseq_19660


title: RNAseq_82119


title: RNAseq_68572


title: RNAseq_09756


title: RNAseq_10231


title: RNAseq_96203


title: RNAseq_01616


title: RNAseq_86541


title: RNAseq_08607


title: RNAseq_92954


title: RNAseq_04307


title: RNAseq_93120


title: RNAseq_89093


title: RNAseq_18279


title: RNAseq_46093


title: RNAseq_45352


title: RNAseq_08496


title: RNAseq_54899


title: RNAseq_39061


title: RNAseq_75044


title: RNAseq_84324


title: RNAseq_43690


title: RNAseq_11478


title: RNAseq_79683


title: RNAseq_95893


title: RNAseq_47511


title: RNAseq_21879


title: RNAseq_55198


title: RNAseq_27588


title: RNAseq_28235


title: RNAseq_15270


title: RNAseq_99029


title: RNAseq_34882


title: RNAseq_53113


title: RNAseq_91002


title: RNAseq_82394


title: RNAseq_14325


title: RNAseq_78758


title: RNAseq_72430


title: RNAseq_53643


title: RNAseq_46598


title: RNAseq_22167


title: RNAseq_20508


title: RNAseq_03003


title: RNAseq_21702


title: RNAseq_05373


title: RNAseq_78392


title: RNAseq_12964


title: RNAseq_31785


title: RNAseq_32443


title: RNAseq_86511


title: RNAseq_70495


title: RNAseq_73235


title: RNAseq_40779


title: RNAseq_53016


title: RNAseq_01428


title: RNAseq_96571


title: RNAseq_69225


title: RNAseq_50373


title: RNAseq_44318


title: RNAseq_78865


title: RNAseq_08631


title: RNAseq_28208


title: RNAseq_65667


title: RNAseq_52904


title: RNAseq_62789


title: RNAseq_03151


title: RNAseq_72206


title: RNAseq_57012


title: RNAseq_88708


title: RNAseq_37769


title: RNAseq_60964


title: RNAseq_83819


title: RNAseq_76026


title: RNAseq_50441


title: RNAseq_81466


title: RNAseq_59873


title: RNAseq_49019


title: RNAseq_22728


title: RNAseq_15952


title: RNAseq_21320


title: RNAseq_22513


title: RNAseq_57295


title: RNAseq_47521


title: RNAseq_18324


title: RNAseq_13323


title: RNAseq_05574


title: RNAseq_58318


title: RNAseq_67294


title: RNAseq_79772


title: RNAseq_05802


title: RNAseq_93314


title: RNAseq_56721


title: RNAseq_35036


title: RNAseq_03659


title: RNAseq_68621


title: RNAseq_94912


title: RNAseq_84423


title: RNAseq_66573


title: RNAseq_84142


title: RNAseq_13656


title: RNAseq_53996


title: RNAseq_04782


title: RNAseq_80521


title: RNAseq_03886


title: RNAseq_18431


title: RNAseq_29325


title: RNAseq_65512


title: RNAseq_05662


title: RNAseq_29219


title: RNAseq_33741


title: RNAseq_59514


title: RNAseq_83388


title: RNAseq_10983


title: RNAseq_24668


title: RNAseq_41224


title: RNAseq_90261


title: RNAseq_92411


title: RNAseq_54991


title: RNAseq_07126


title: RNAseq_28238


title: RNAseq_58943


title: RNAseq_43562


title: RNAseq_72625


title: RNAseq_27997


title: RNAseq_07638


title: RNAseq_92030


title: RNAseq_47621


title: RNAseq_81334


title: RNAseq_01733


title: RNAseq_06539


title: RNAseq_96625


title: RNAseq_74206


title: RNAseq_96190


title: RNAseq_28264


title: RNAseq_79949


title: RNAseq_92318


title: RNAseq_48395


title: RNAseq_38038


title: VTL-81 -Dox [VTL-81-82_S12]

city: Clayton

first: Nicholas

middle: C

last: Wong

state: Victoria

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

country: Australia

institute: Monash University

data_processing:
Data was processed using https://laxy.io which wraps RNASik analysis pipeline together to generate a counts table for Degust ingestion.
Alignment with STAR v2.5.2b to mm10 reference genome
Gene counting with featureCounts
Differential Expression analysis with Degust (http://degust.erc.monash.edu).
Genome_build: mm10
Supplementary_files_format_and_content: Gene counts table containing genes, ENSMBL IDs, samples and read counts, CPM, log2(CPM)

organism: Mus musculus

source_name: T-ALL_Independent_Dox Minus

growth_protocol: Thymocytes equivalent to one quarter of a thymus were intravenously injected into sublethally irradiated C57BL/6-Ly5.1;FVB F1. VTL-induced leukemias cryopreserved cells were thawed and 1-2x10^5 cells intravenously injected into C57BL/6-Rag1-/-  recipients.

extract_protocol:
RNA was extracted from sorted donor (CD45.1/CD45.2 double positive) tumour cells derived from the spleen of secondary recipient mice using the RNeasy Kit (Qiagen) according to manufacturer's instructions.
Libraries were prepared from RNA with a RIN score of > 8.0 using NEBNext RNA Ultra II  RNA library preparation kit (NEB) according to manufacturer's instructions.

treatment_protocol: Where indicated, Doxycycline (Dox) was administered to mice via food pellets (600 mg/kg)

tag: host strain

tag: cell type

value: T-ALL Tumour cells derived from spleen

value: Independent

tag: dox

value: Minus


title: RNAseq_24152


title: RNAseq_31807


title: RNAseq_71607


title: RNAseq_52204


title: VTL-33 -Dox [VTL-33-87_S8]


title: VTL-81 +Dox [VTL-81-37_S11]

source_name: T-ALL_Independent_Dox Plus

value: Plus


title: replicate1_male_female

city: Stanford

first: Aaron

last: Gitler

state: California

address: Beckman Center

department: Genetics

institute: Stanford University

data_processing:
single-nucleus RNA seq analysis
illumina basecalling
10X cellranger (STAR alignment, UMI calls, etc)
Mitochondrial read removal (Seurat)
Read depth normalization (Seurat)
Batch correction by integration (Seurat)
PCA, graph-based clustering, and UMAP projection (Seurat)
Differential expression among clusters (Seurat, DEseq2 algorithm)
full analysis pipeline available as Jupyter-R notebook at github.com/neurojacob/blum_et_al_2020
Genome_build: mm10 (mm10-3.0.0-premrna)
Supplementary_files_format_and_content: .h5d expression matrices (output from cellranger) and CSV count files (output from Seurat integration, etc).

molecule: polyA RNA

source_name: FACS-sorted mouse spinal cord nuclei

extract_protocol:
Transgenic reporter mice were aged to P100-150
Nuclei were extracted and purified (see methods), then sorted using FACS fluorescence for GFP reporter at 60/40 ratio.
Nuclei were encapsulated in droplets using the 10X V3 oligo-dT kit.
Libraries prepared according to manufacturer (10X) instructions for V3 library.

tag: treatment

value: Chat-Cre;ROSAnT-nG

tag: tissue

value: spinal cord


title: replicate4_male


title: replicate3_female


title: replicate2b_male_female


title: VTL-33 +Dox [VTL-33-77_S7]


title: RNAseq_60172

tag: batch


title: RNAseq_42280

tag: current smoker


title: RNAseq_06496

tag: pack years


title: VTL-44 -Dox [VTL-44-8_S10]


title: replicate2a_male_female


title: RNAseq_88027

tag: age


title: VTL-24 -Dox [VTL-24-4-5_S4]

source_name: T-ALL_Dependent_Dox Minus

value: Dependent


title: VTL-19 -Dox [VTL-19-13_S1]


title: VTL-21 +Dox [VTL-21-4_S2]

source_name: T-ALL_Evolving_Dox Plus

value: Evolving


title: RNAseq_08961

tag: gender (1=male, 2=female)


title: RNAseq_37363

tag: race (1=white, 2=black)


title: RNAseq_15675

tag: fev1 % predicted


title: RNAseq_97847

tag: neutrophil percent


title: VTL-21 -Dox [VTL-21-15_S3]

source_name: T-ALL_Evolving_Dox Minus


title: RNAseq_76013

tag: lymphocyte percent


title: VTL-25 +Dox [VTL-25-7_S5]


title: RNAseq_13586

tag: eosinophil percent


title: VTL-44 +Dox [VTL-44-2_S9]


title: RNAseq_44063

tag: monocyte percent


title: RNAseq_77371

tag: basophil percent


title: VTL-153 +Dox [VTL-153-11_S13]

tag: host strain


title: VTL-25 -Dox [VTL-25-19_S6]

tag: cell type


title: RNAseq_88658


title: VTL-153 -Dox [VTL-153-23_S14]

tag: dox


title: RNAseq_41396


title: RNAseq_01240


title: RNAseq_25862


title: FD23

city: Melbourne

first: Loretta

last: Giummarra

address: c/o Psychological Science

department: Psychology & Counselling

institute: La Trobe University

description: After initiation of form deprivation myopia (FDM) for 7 days, occluders were removed to allow 6 hrs of normal light and FDM recovery (FDMR)

data_processing:
Read quality was assessed using FastQC
Adapter and low quality (Q-score <10) sequences removed using CutAdapt and Trimmomatic
Reads were mapped to the chick genome using Tophat2 and Bowtie2
The number of reads uniquely mapping to each gene was counted using existing gene models with HTSeq
Genome_build: GalGal4
Supplementary_files_format_and_content: The txt file contains processed data for all samples (raw counts)

organism: Gallus gallus

source_name: After form deprivation myopia (FDM) for 7 days, occluders removed to allow 6 hrs of normal light and FDM recovery (FDMR)

extract_protocol:
Total RNA was isolated from the retina/RPE/choroid using the miRNeasy Mini Kit (Qiagen) including DNase digestion. RNA quality and quantity was assessed on the 2100 Bioanalyzer. All samples had an RNA integrity number (RIN) of >8. RNA quantity was also assessed on the Qubit 2.0 Fluorometer.
Using an average of concentration measures obtained from Qubit and Bioanalyzer assays, 2.5μg of RNA from each sample was used for library preparation. Libraries were prepared using the TruSeq Stranded mRNA LS kit (Illumina) with dual indexing according to the manufacturer’s instructions. The generated libraries were assessed on the 2100 Bioanalyzer to ensure an average size distribution of approximately 280bps, then quantified on the Qubit 2.0 Fluorometer and by qPCR. Libraries were normalised to 10nM in Tris-HCl, pooled, and prepared for cluster generation on the Illumina cBot using the TruSeq SR Cluster Kit V3-cBot (Illumina) with denatured template DNA diluted to 7pM. The flow cell and sequencing reagents (TruSeq SBS Kit V3; Illumina) were loaded on the Illumina HiSeq 1500 and a dual-index, single-end, 100bp sequencing run performed.

treatment_protocol: Male chicks (Leghorn/New Hampshire) were raised from post-hatch days 0-5 under a 12-hr day/night light cycle in groups of <25.  In the middle of the light cycle on day 5, chicks were randomly assigned to a lens condition (FD or No Lens) and occluders attached to Velcro were fixed to the periocular feathers of the right eye. Following a further 7 days, tissue was collected from no lens and FDM chicks. At the same time, occluders were removed from FDMR chicks. Tissue was collected from these FDMR chicks following 6hrs or 24hrs recovery. Description of tissue collection: Chicks were anaesthetized and right eye refraction and axial dimensions determined by retinoscopy and A-Scan ultrasonography. Chicks were euthanized and their right eyes were enucleated. The retina/RPE/choroid was immediately collected from the posterior eyecup and frozen in liquid nitrogen before being transferred to -80°C.

value: Post-hatch day 20

tag: time

value: 7 days (post-occlusion)

tag: lens type

value: FDMR (6hrs)

value: Retina, RPE, choroid


title: FD26

description: After initiation of form deprivation myopia (FDM) for 7 days, occluders were removed to allow 24hrs of normal light and FDM recovery (FDMR)

source_name: After form deprivation myopia (FDM) for 7 days, occluders removed to allow 24hrs of normal light and FDM recovery (FDMR)

value: Post-hatch day 21

value: 8 days (post-occlusion)

value: FDMR (24hrs)

tag: tissue


title: RNAseq_74680

tag: batch

tag: current smoker


title: FD29

tag: age


title: FD21


title: RNAseq_79918

tag: pack years

tag: gender (1=male, 2=female)


title: FD19


title: RNAseq_36879

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: RNAseq_29258

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_61947

tag: eosinophil percent

tag: monocyte percent


title: FD30


title: RNAseq_97502

tag: basophil percent


title: FD13

description: Form deprivation myopia (FDM) was initiated for 7 days

source_name: Form deprivation myopia (FDM) for 7 days

value: FDM (7 days)


title: RNAseq_90099


title: FD9


title: FD12


title: FD10


title: FD32


title: RNAseq_03700


title: RNAseq_89470


title: FD7

description: Chicks were raised normally (with no lenses) for 20 days

source_name: Chicks raised normally (with no lenses) for 20 days

value: No Lens


title: RNAseq_82561


title: FD4


title: FD6


title: RNAseq_08141


title: RNAseq_45120


title: FD3


title: RNAseq_26358


title: RNAseq_04626


title: RNAseq_73407


title: RNAseq_58511


title: RNAseq_56964


title: RNAseq_73302


title: RNAseq_40827


title: RNAseq_75281


title: RNAseq_27927


title: RNAseq_80418


title: RNAseq_96773


title: RNAseq_31859


title: RNAseq_33476


title: RNAseq_59727


title: RNAseq_25287


title: degradome-leaf

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

country: China

institute: Yunnan Agricultural University

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides
Keep the sequences with lengths are greater than or equal to 18 bp (the 3'adapter sequence of reads had been removed by the sequenceing faclility)
Sort and remove repetitive sequences
Calculate the counts of unique sequences
The unique sequences were aligned to  assembled genome with BLAST
Supplementary_files_format_and_content: sequences and count values

organism: Camellia sinensis

source_name: degradome-leaf

extract_protocol:
Total RNA was isolated from selected tissues using TRIzol reagent with the manufacture's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols with only ribosomal RNA removal.

value: leaf


title: RNAseq_02502


title: degradome-root

source_name: degradome-root

value: root


title: RNAseq_58453


title: EdgeSeq_miRXplore_2

city: Vestec

first: Šárka

last: Benešová

address: Prumyslova 595

department: Institute of Biotechnology

country: Czech Republic

institute: Czech Academy of Science

description: processed data file: count_matrix_miRXplore.txt

data_processing:
Raw reads of all samples were trimmed with cutadapt tool (version 1.18) according to the respective library preparation manual and bases with phred 33 quality lower than 20 were trimmed.
Reads longer than 16 bp and shorter than 29 bp were kept.
Reads of all samples were aligned to rRNA and Univec database (obtained from sortmerna github repository) using bowtie aligner  (version 1.2.2) with one mismatch allowed and only reads which did not align were kept.
Reads of all samples were further aligned to synthetic spike-ins reference using bowtie aligner (version 1.2.2) with zero mismatch allowed and only reads which did not align were kept.
Reads of plasma samples were aligned with STAR (version 2.7.0c) to human genome GRCh38.95 and only mapped reads were aligned to mature miRNAs from miRBase v22 with following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 15 --outFilterScoreMinOverLread 0   --outFilterMatchNminOverLread 0 --alignIntronMax 1 --alignEndsType EndToEnd.
Reads of miRxplore samples were aligned to the reference obtained from Miltenyi Biotec using STAR (version 2.7.0c) with the same parameters as plasma samples.
Only uniquely mapped reads of both types of samples were counted using Rsubread package version 1.32.4.
Genome_build: miRBase v22  - hsa mature sequences (GRCh38)
Supplementary_files_format_and_content: tab delimited text files include raw count values generated with featureCounts function (package - Rsubread_1.32.4)

organism: synthetic RNA

extract_protocol:
Blood samples were collected from four healthy volunteers into K2EDTA BD Vacutainer tubes (Beckman Dickinson) and centrifuged within 30 min from collection at 1500 x g for 15 min at room temperature. The plasma fraction was aspirated and transferred into 2 ml tubes and centrifuged again for 15 min at 3000 x g. The supernatant was transferred into new 2 ml tubes and stored at -80 °C until analysis. Total RNA was isolated starting from plasma aliquots of 250 µl using the miRNeasy Serum/Plasma Advanced Kit (Qiagen) according to manufacturer´s instructions. 1 µl of isolation spike-in mix and 1 µl of GlycoBlue Coprecipitant (Invitrogen) were added at the lysis step as described in (Androvic et al., 2019). RNA was eluted into 20 µl of nuclease-free water and stored at -80 °C. RNA eluates were then pooled together to produce standard plasma RNA sample used through the study.
Libraries were prepared in technical duplicates starting from 5 µl of plasma RNA pool and 5 µl of miRXplore Universal Reference (2x10^6 copies/µl) according to each manufacturer´s protocol using compatible set of sample indexes. Libraries generated by the same protocol were pooled and run on 5% TBE-PAGE on Mini-PROTEAN tetra cell (BioRad). A region representing fragments with RNA inserts of length 22 nt ± ~10 nt (i.e. fragments originating from miRNAs) was excised from the gel, DNA was eluted into nuclease-free water and purified with SPRIselect reagent (Beckman Coulter).

tag: sample type

value: equimolar pool of synthetic miRNAs

tag: sample origin

value: Synthetic - origin - human, mouse, rat and related viruses

tag: sample source

value: miRXplore Miltenyi Biotec

tag: library preparation protocol

value: HTG EdgeSeq miRNA Whole Transcriptome Assay

tag: technical replicate


title: RNAseq_06288

tag: batch


title: SMARTer_miRXplore_2

value: Takara:SMARTer smRNA-Seq kit for Illumina


title: RNAseq_80613

tag: current smoker


title: RNAseq_10283

tag: age


title: RNAseq_31083

tag: pack years


title: RNAseq_75666

tag: gender (1=male, 2=female)


title: RealSeq_miRXplore_2

value: Somagenics:RealSeq Biofluids Plasma/Serum miRNA


title: RealSeq_miRXplore_1


title: RNAseq_02048

tag: race (1=white, 2=black)


title: RNAseq_23412

tag: fev1 % predicted


title: NEXTflex_miRXplore_1

value: Bioo Scientific Corp. NEXTflex Small RNA-Seq Library Prep Kit v3


title: RNAseq_24910

tag: neutrophil percent


title: RNAseq_98334

tag: lymphocyte percent


title: QIAseq_miRXplore_1

value: Qiagen:QIAseq miRNA Library Kit


title: RNAseq_40299

tag: eosinophil percent


title: QIAseq_miRXplore_2


title: NEXTflex_miRXplore_2


title: Norgen_miRXplore _2

value: Norgen Biotek Copr.:Small RNA Library Prep Kit for Illumina


title: RNAseq_14547

tag: monocyte percent


title: RNAseq_40902

tag: basophil percent


title: Norgen_miRXplore _1

tag: sample type


title: Lexogen_miRXplore_2

tag: sample origin

value: Lexogen:Small RNA-Seq Library Prep Kit


title: RNAseq_78179


title: Lexogen_miRXplore_1

tag: sample source


title: EdgeSeq_miRXplore_1

tag: library preparation protocol


title: RNAseq_63493


title: SMARTer_miRXplore_1

tag: technical replicate


title: RNAseq_67064

tag: batch


title: RNAseq_56211

tag: current smoker


title: RNAseq_39918

tag: age


title: RNAseq_56283

tag: pack years


title: RNAseq_51274

tag: gender (1=male, 2=female)


title: RNAseq_85002

tag: race (1=white, 2=black)


title: 87E efgA mutant, 360 min after mock treatment

city: Austin

first: Jeffrey

middle: E.

last: Barrick

state: TX

address: 2500 Speedway, Stop A4800

department: Molecular Biosciences

institute: The University of Texas at Austin

description: counts.csv

data_processing:
Read trimming was performed using Trimmomatic v0.38 in paired-end mode, if applicable, and removing reads trimmed to fewer than 30 bases.
Read alignment was performed using Bowtie2 v4.8.2 with the -k option, in paired-end mode for reads paired after trimming and in single read mode for others
Raw counts were generated using HTSeq v0.11.4 with options to count read pairs or singleton reads that unambiguously overlapped each gene
Normalized read counts were generated using DeSeq2 in R version 3.6.
Genome_build: NC_010172.1
Supplementary_files_format_and_content: CSV

organism: Methylorubrum extorquens

source_name: Bacterial cells

growth_protocol: From individual colonies, wild-type (CM2730) and the ΔefgA mutant (CM3745) were inoculated into 2 mL MP medium (3.5 mM succinate) and grown at 30 °C with shaking for 32 hr. Cells were subcultured (1/64) into fresh MP media twice: first into 35 mL (3.5 mM succinate, 24 hr incubation) and then into 2 L (15 mM succinate). When OD600 of 2 L cultures = 0.2 (~8 hr), 100 mL of each culture was used to harvest “pretreatment” cells for transcriptomic analysis and remaining cultures were divided into 100 mL aliquots in 250 mL flasks for treatment.

extract_protocol:
RNA was purified from cells for each sample using the RNAsnap method [1]. First, cell pellets were resuspended in 500 µl of RNA extraction buffer (18 mM EDTA, 0.025% w/v SDS, 1% v/v 2-mercaptoethanol, 95% v/v formamide) by vortexing. Following incubation at 95°C for 7 min, cell debris was pelleted by centrifugation at 16000 × g for 5 min at room temperature. The resulting supernatant was purified using the Clean & Concentrator kit incorporating the on-column DNase digestion step (Zymo Research). Yields were determined using a Qubit 2.0 fluorometer with the RNA BR assay kit (ThermoFisher). Then, 1.5 µg of purified RNA for each sample was processed using the Ribozero rRNA Removal Kit (Gram-negative bacteria) (Illumina) according to the manufacturer’s instructions except that reaction volumes were reduced by 50%. Depleted RNA samples were ethanol precipitated.
RNA-Seq library preparation from rRNA-depleted samples began by fragmenting them with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) for 110 s followed by ethanol precipitation. Fragmented RNA was treated with 10 U of T4 polynucleotide kinase (NEB) in 20 µl reactions containing 1 mM ATP. After another ethanol precipitation, the NEBNext small RNA Library Prep Set for Illumina (Multiplex Compatible) (New England Biolabs) was used to prepare samples according to recommended protocol, except all reaction volumes were reduced 50% and the SR RT primer concentration was reduced by an additional 50% in the RT primer hybridization step. After performing 15 cycles of PCR, samples were ethanol precipitated, and the DNA concentration was determined via the Qubit HS dsDNA assay kit (Thermofisher). For each sample, 200 ng of DNA was run on a 4% EX E-gel (ThermoFisher). DNA with a size of at least ~200 bases was excised and purified using a gel DNA recovery kit (Zymo Research) with elution in 50 µl of nuclease-free water.

treatment_protocol: When OD600 of 2 L cultures = 0.2 (~8 hr), 100 mL of each culture was used to harvest “pretreatment” cells for transcriptomic analysis and remaining cultures were divided into 100 mL aliquots in 250 mL flasks (18 hr for wild-type, 16 hr the ΔefgA mutant) and returned to the incubator for 30 min. All flasks were quickly removed from incubator and treated with i) 500 μL of 1 M formaldehyde (5 WT flasks, 4 ΔefgA mutant flasks), ii) 100uL of 50mg/mL kanamycin (4 flasks of each strain), or iii) left untreated (4 flasks of each strain). Flasks were well-sealed with foil and parafilm and returned to the shaker. Time of treatment is designated as t = 0, pretreatment therefore corresponds to -45 min. This growth regimen was executed on 6 consecutive days to obtain all treated samples in biological triplicate.

tag: strain

tag: genotype

value: efgA

tag: treatment

tag: time

tag: biological replicate


title: RNAseq_46816

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: 87W Wild type, 360 min after mock treatment

description: counts.csv

value: WT


title: 88W Wild type, 360 min after kanamycin treatment

description: counts.csv

value: kan


title: 89W Wild type, 360 min after formaldehyde treatment

description: counts.csv

value: form


title: 89E efgA mutant, 360 min after formaldehyde treatment

description: counts.csv


title: 88E efgA mutant, 360 min after kanamycin treatment

description: counts.csv


title: 79E efgA mutant, 180 min after formaldehyde treatment

description: counts.csv


title: 79W Wild type, 180 min after formaldehyde treatment

description: counts.csv


title: RNAseq_18175

tag: batch


title: RNAseq_28420

tag: current smoker


title: RNAseq_47538

tag: age


title: 78W Wild type, 180 min after kanamycin treatment

description: counts.csv


title: 78E efgA mutant, 180 min after kanamycin treatment

description: counts.csv


title: RNAseq_89002

tag: pack years


title: 77W Wild type, 180 min after mock treatment

description: counts.csv


title: 77E efgA mutant, 180 min after mock treatment

description: counts.csv


title: 49E efgA mutant, 40 min after formaldehyde treatment

description: counts.csv


title: 49W Wild type, 40 min after formaldehyde treatment

description: counts.csv


title: RNAseq_11775

tag: gender (1=male, 2=female)


title: RNAseq_15893

tag: race (1=white, 2=black)


title: 48W Wild type, 40 min after kanamycin treatment

description: counts.csv

tag: strain


title: RNAseq_97231


title: RNAseq_87015


title: RNAseq_14800


title: RNAseq_48056


title: 48E efgA mutant, 40 min after kanamycin treatment

description: counts.csv

tag: genotype


title: 142W Wild type, 720 min after formaldehyde treatment

description: counts.csv

tag: treatment


title: 47E efgA mutant, 40 min after mock treatment

description: counts.csv

tag: time


title: RNAseq_09294


title: RNAseq_28923


title: 13E efgA mutant, pretreatment

description: counts.csv

value: pre

tag: biological replicate


title: RNAseq_40336

tag: fev1 % predicted


title: RNAseq_04177

tag: neutrophil percent


title: 48hpf_Fli1a_Sox10_double_positive_ATAC_rep2

city: Los Angeles

first: Gage

last: Crump

state: CA

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

library_source: genomic

data_processing:
For ATACseq, reads were trimmed based on quality score and then aligned to reference mouse genome (mm10) using bowtie2. PCR-duplicates were removed by Sambamba, and then peaks were called by MACS2 from individual replicate using filter q value < 0.01.
Genome_build: danRer10
Supplementary_files_format_and_content: peak regions in narrowPeak format for ATACseq

molecule: genomic DNA

organism: Danio rerio

extract_protocol:
Cells were purified by FACS-sorting. chromatin were digested by tn5 transposase at 37°C for 20 minutes.DNA fragments were extracted using MiniElute columns (Qiagen), and then amplified by PCR.
FACS-sorted cells were centrifuged at 500 g for 20 m at 4 °C, and the pellet was suspended with 20 μL of lysis buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, 0.2% N-P40) by pipetting 6-10 times to release the nuclei without purification. The cell lysate was then mixed with 30 μL reaction buffer (10 mM Tris HCl (pH 7.4), 5 mM MgCl2, 10% DMF, and homemade Tn5 Transposase) by vortexing for 5 s. The reaction was incubated at 37°C for 20 minutes, followed by DNA purification using a Qiagen MinElute kit.
Libraries were amplified by PCR with indexed primers
DNA fragments are amplified by PCR for 5 cycles using NEBnext master mix, with primers containing various indexes. Additional cycles are determined by qPCR on 1/10 of the amplified libraries. After amplification, the libraries are cleaned using AMPURE beads, to only keep the fragments larger than 100bp. The libraries are pooled before sequencing.

tag: developmental stage

value: 48h post fertilization

tag: cell type

value: neural crest cell

tag: genotype/variation


title: 36hpf_Fli1a_Sox10_double_positive_ATAC_rep1

value: 36h post fertilization


title: RNAseq_99485

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_34024

tag: batch

tag: current smoker

tag: pack years

tag: age


title: 36hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC_rep2

value: dorsal intermediate domain neural crest cell


title: RNAseq_27494

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: 36hpf_Pou3f3b_Sox10_double_positive_ATAC_rep2


title: RNAseq_14786


title: 36hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC_rep1


title: 36hpf_Pou3f3b_Sox10_double_positive_ATAC_rep1


title: RNAseq_50744


title: 13W Wild type, pretreatment

description: counts.csv

tag: strain

tag: genotype

tag: treatment

tag: time


title: 47W Wild type, 40 min after mock treatment

description: counts.csv

tag: biological replicate


title: RNAseq_98195

tag: fev1 % predicted

tag: neutrophil percent


title: 48hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC_rep2

tag: developmental stage

tag: cell type

tag: genotype/variation


title: RNAseq_37564

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_64436

tag: batch

tag: current smoker

tag: pack years

tag: age


title: 36hpf_Fli1a_Sox10_double_positive_ATAC_rep2


title: 48hpf_Pou3f3b_Sox10_double_positive_ATAC_rep2


title: 48hpf_Pou3f3b_Sox10_double_positive_FoxC_mutant_ATAC_rep1


title: 48hpf_Fli1a_Sox10_double_positive_ATAC_rep1


title: RNAseq_18364

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: 48hpf_Pou3f3b_Sox10_double_positive_ATAC_rep1


title: RNAseq_12156


title: RNAseq_62882


title: 72hpf_Col2a1a_Sox10_double_negative_ATAC_rep1

value: 72h post fertilization

value: cartilage cell


title: RNAseq_64392


title: RNAseq_15309


title: 72hpf_Col2a1a_Sox10_double_positive_ATAC_rep1


title: RNAseq_71598


title: RNAseq_61171


title: RNAseq_15890


title: RNAseq_02252


title: RNAseq_13674


title: DNase-seq_EILP_Tcf7KO_rep4_GB7350

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

data_processing:
Library strategy: DNAase-seq
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) using Bowtie2 with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
For ChIC-seq samples, reads from replicates were merged for peak calling. Peak calling were performed using MACS2 with default parameters.
For scMNase-seq samples, reads with length between 140 and 180 bp were selected as nucleosome reads while reads with length less than 80 bp were selected as subnucleosomal reads.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIC-seq and DNase-seq samples, .wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization. For scMNase-seq samples, bed files provide genomic positions on chromosomes for nucleosomes (140-180 bp) and subnucleosomes (<80 bp).

growth_protocol: Samples were isolated by cell sorting from bone marrow single cell suspensions

extract_protocol:
For DNase I digestion, 300 cells from each cell type were collected by FACS sorting. 0.3 unit of DNase I (Roche, 04716728001) was added to each cell type and incubated at 37 °C for 5 minutes. Reaction were stop by adding 80 μl of stop buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 0.15% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 55 °C for overnight and DNA purified by phenol–chloroform extraction, followed by precipitation with ethanol in the presence of 20 μg glycogen.
The library was prepared using Illumina kits as described G. Hu et al. (Nature immunology 2013). The libraries were amplified using a two-step method to preferentially amplify the small DNA fragments derived from the DNA hypersensitive sites and to reduce non-specific amplification of the carrier DNA. The first amplification was done with index primers with the PCR condition: 98°C, 10"; 67°C, 30"; 72°C, 30" for 6 cycles. The second amplification was done with the P5 and P7 primers with the condition: 98°C, 10"; 68°C, 30"; 72°C, 30" for 22 cycles. The fragments between 160bp to 300bp were isolated on E-gel and sequenced on Illumina HiSeq3000.

tag: strain

tag: tissue

value: bone marrow

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ GFP+ Thy1-


title: DNase-seq_EILP_Tcf7KO_rep1_GB3047


title: DNase-seq_EILP_Tcf7KO_rep3_GB3061


title: DNase-seq_ILCP_rep3_GB7348 (duplicate GSM3677399)

source_name: ILCP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+


title: 72hpf_Col2a1a_Sox10_double_positive_ATAC_rep2


title: DNase-seq_EILP_Tcf7KO_rep2_GB3056


title: RNAseq_47134

tag: fev1 % predicted

tag: neutrophil percent


title: 72hpf_Col2a1a_Sox10_double_negative_ATAC_rep2

tag: developmental stage

tag: cell type


title: RNAseq_16233

tag: lymphocyte percent


title: DNase-seq_ILCP_rep2_GB3059 (duplicate GSM3677398)

tag: genotype/variation


title: DNase-seq_ILCP_rep1_GB3054 (duplicate GSM3677397)


title: RNAseq_45453

tag: eosinophil percent

tag: monocyte percent


title: DNase-seq_EILP_rep3_GB7347 (duplicate GSM3677396)

source_name: EILP

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: RNAseq_09485

tag: batch

tag: basophil percent


title: DNase-seq_EILP_rep2_GB3058 (duplicate GSM3677395)


title: RNAseq_11503

tag: current smoker

tag: pack years


title: RNAseq_38190

tag: age

tag: gender (1=male, 2=female)


title: DNase-seq_EILP_rep1_GB3053 (duplicate GSM3677394)

tag: strain


title: DNase-seq_ALP_rep3_GB7346  (duplicate GSM3677393)

source_name: ALP

tag: tissue

value: Lin- Kit+ 2B4+ a4b7- Flt3high IL-7Ra+


title: RNAseq_63660

source_name: blood

tag: race (1=white, 2=black)


title: RNAseq_40855

tag: fev1 % predicted


title: FD18

value: Post-hatch day 20

tag: time

value: 7 days (post-occlusion)

tag: lens type

value: FDMR (6hrs)

value: Retina, RPE, choroid


title: Normal5

type: RNA

city: Beijing

first: Xinxue

last: Zhang

state: Beijing

address: 8 Gongti South Street

institute: Beijing Chaoyang Hospital

description: SAMPLE 5_N

scan_protocol: After washing the slides, the arrays were scanned by the Agilent G2505C scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. A quantile normalization of the raw data was performed using R software. CircRNA samples with at least 3 out of 6 having flags in “P” or “M” (“All Targets Value”) were retained for further analyses. Limma package was applied to identify DE circRNAs between tumor and normal tissues (p<0.05 and |log2 FC|>1). Pheatmap package was used to visualize the DE circRNAs. Rcircos package was used to visualize the distribution of circRNAs in human chromosomes.

source_name: Normal

extract_protocol:
Paired tumor and adjacent normal fresh tissues were placed in liquid nitrogen for 2 h, then stored at -80°C.
Total RNA from each sample was extracted with TRIzol reagent (Invitrogen, Carlsbad, CA, USA), and quantified using the NanoDrop ND-1000. The products were digested with Rnase R (Epicentre, Madison, WI, USA) and the linear RNAs were removed. The enriched circRNAs were amplified and transcribed into fluorescent cRNA utilizing a random primer method (Super RNA Labeling Kit, Arraystar, Rockville, MD, USA). Labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K) and incubated for 17 h at 65°C in a hybridization oven (Agilent, Santa Clara, CA, USA).

tag: disease state

value: distal cholangiocarcinoma

value: adjacent normal sample

tag: histology

value: adenocarcinoma

tag: grade

value: moderate

tag: Sex

value: M

tag: Stage

value: IIA


title: RNAseq_01597

tag: batch

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_49730

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: basophil percent


title: RNAseq_38145

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: DNase-seq_ALP_rep2_GB3057  (duplicate GSM3677392)

tag: strain

tag: genotype/variation

tag: tissue

tag: sorting profile


title: RNAseq_61910


title: DNase-seq_ALP_rep1_GB3052 (duplicate GSM3677391)


title: RNAseq_64694


title: RNAseq_57382


title: ChIC-seq_H3K27ac_EILP_Tcf7KO_rep4_GB6955

description: EILP_KO_H3K27ac_6948_6955.150l.NR.se.sorted-W200-normalized.wig.gz

data_processing:
Library strategy: small cell ChIC-seq
Basecalling by RTA 1.18.66.3, Illumina instrument run time analysis software
Sequencing reads were aligned to mouse genome (mm9) using Bowtie2 with default parameters.
Reads from replicates were merged and redundant reads were removed from further analysis.
For ChIC-seq samples, reads from replicates were merged for peak calling. Peak calling were performed using MACS2 with default parameters.
For scMNase-seq samples, reads with length between 140 and 180 bp were selected as nucleosome reads while reads with length less than 80 bp were selected as subnucleosomal reads.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIC-seq and DNase-seq samples, .wig files contain normalized tag density, which can be uploaded to UCSC genome browser for visulization. For scMNase-seq samples, bed files provide genomic positions on chromosomes for nucleosomes (140-180 bp) and subnucleosomes (<80 bp).

extract_protocol:
Cells were fixed by adding 1:15 volume of 16%w/v formaldehyde solution (Thermo Fisher Scientific) and incubating at RT for 10 minutes. Reaction was terminated by adding 1:10 volume. 1ml RIPA buffer (10 mM Tris-Cl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.2% sodium dodecyl sulfate, 1% Triton X-100) added to each sorted 500 ALP, EILP, and ILCP cells, and incubated at room temperature for 30 minutes. Cells were rinsed with 500 μl binding buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM sodium chloride, 0.1% Triton X-100) twice and re-suspended in 50 μl binding buffer. To prepare TCF1 bounded PA-MNase (Ab+PA-MNase), TCF1 and the PA-MNase at a molecular ratio of 1:2 were pre-incubated at 4 °C for 30 minutes in 50 μl binding buffer. TCF1+PA-MNase were add to 50 μl binding buffer re-suspended cells and incubated one hour at 4 °C with rotation. Cells were washed using 200 μl wash buffer (10 mM Tris-Cl, 1 mM EDTA, 150 mM sodium chloride, 0.1%w/v SDS, 0.1%w/v sodium deoxycholate and 1%v/v Triton X-100) three times and pelleted by centrifugation at 600g for 2 minutes. Next, cells were rinsed using 200 μl rinsing buffer (10 mM Tris-Cl and 10 mM sodium chloride, 0.1%v/v Triton X-100). The MNase digestion was initiated by re-suspending the rinsed cells in 40 μl reaction solution buffer (10 mM Tris-Cl, 10 mM sodium chloride, 0.1%v/v Triton X-100, 2 mM CaCl2) and incubated at 37 °C for 3 minutes. The reaction was stopped by adding 80 μl stop buffer (20 mM Tris-Cl (pH 8.0), 10 mMethylenedioxy-bis-(ethylenenitrilo)-tetraacetic acid (EGTA), 20 mM sodium chloride, 0.2%w/v SDS) and 1 μl proteinase K (SigmaAldrich), then incubating at 65 °C for overnight. DNAs were purified by using phenol-chloroform extraction and ethanol precipitation. The purified DNA is ready for library preparation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. The ligation reaction was performed by adding 2 μM Illumina's adapters to each sample and incubated at RT one hour. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments from 180bp to 300bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Hi-seq3000 following the manufacturer's protocols.

tag: antibody name, manufacturer and catalog number

value: H3K27ac (cat# ab4729, abcam)


title: ChIC-seq_H3K27ac_EILP_Tcf7KO_rep3_GB6948


title: ChIC-seq_H3K4me3_EILP_Tcf7KO_rep2_GB6954

description: EILP_KO_H3K4me3_6947_6954.150l.NR.se.sorted-W200-normalized.wig.gz

value: H3K4me3 (cat# cs200580, millipore)


title: Normal4

description: SAMPLE 4_N

hyb_protocol: Labeled cRNAs were hybridized onto the Arraystar Human circRNA Array V2 (8x15K) and incubated for 17 h at 65°C in a hybridization oven (Agilent, Santa Clara, CA, USA).

label_protocol: The products were digested with Rnase R (Epicentre, Madison, WI, USA) and the linear RNAs were removed. The enriched circRNAs were amplified and transcribed into fluorescent cRNA utilizing a random primer method (Super RNA Labeling Kit, Arraystar, Rockville, MD, USA).

tag: disease state

tag: histology

tag: grade

tag: Sex

tag: Stage


title: ChIC-seq_H3K4me3_EILP_Tcf7KO_rep1_GB6947

value: bone marrow


title: Normal3

description: SAMPLE 3_N

value: IV


title: RNAseq_49348

tag: batch

tag: current smoker

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: Normal1

description: SAMPLE 1_N

tag: age

value: IB


title: Tumor3

description: SAMPLE 3_T

source_name: Tumor

value: primary distal cholangiocarcinoma


title: Tumor6

description: SAMPLE 6_T

value: poor

value: F

value: IIB


title: ChIC-seq_IgG_EILP_rep4_GB6248_tech2

description: EILP_IgG_GB3042-3051-6240-6248.se.nr-W100-normalized.wig.gz

tag: strain

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: RNAseq_85348

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Tumor5

description: SAMPLE 5_T

tag: disease state

tag: tissue

tag: histology


title: serpini1-/-

city: SHANGHAI

first: SHA

last: HAN

state: SHANGHAI

address: 12 Wulumuqi Zhong Road,

department: Department of Neurology

institute: Huashan Hospital, Fudan University

data_processing:
sequenced by Illumina HiSeq 4000 platform
mapped clean reads to reference genome using HISAT
performed gene expression analysis via StringTie and Biowite.
detected DEG via DESeq2
performed GO classification and functional enrichment, as well as KEGG pathway classification and functional enrichment for different expression genes using phyper
Genome_build: NC_007129.7 Reference GRCz11 Primary Assembly
Supplementary_files_format_and_content: DESeq2 output

source_name: larvae

extract_protocol:
Total RNA was extracted from 7dpf larvae in each group (n=30 per group) using RNeasy Plus Mini Kit (Qiagen 74132) according to its protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: zebrafish larvae were bathed in E3 medium with 40μg/mL Doxycycline [DOX] (sigma D9691) from 3dpf to 7dpf, and we changed E3 with DOX every day before executing

tag: strain background

value: AB

tag: genotype/variation

value: Tg (serpini1-/-)

value: whole larvae


title: Normal2

description: SAMPLE 2_N

value: distal cholangiocarcinoma

value: adjacent normal sample

value: adenocarcinoma

tag: grade

value: moderate-poor

tag: Sex

tag: Stage


title: ChIC-seq_H3K27me3_EILP_Tcf7KO_rep6_GB6956

description: EILP_KO_H3K27me3_6949_6956.150l.NR.se.sorted-W200-normalized.wig.gz

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ GFP+ Thy1-

tag: antibody name, manufacturer and catalog number

value: H3K27me3 (cat# 07-449, millipore )


title: Tumor4

description: SAMPLE 4_T

value: moderate

tag: age

value: M

value: IIA


title: ChIC-seq_IgG_EILP_rep4_GB6248_tech1

tag: strain

value: bone marrow


title: control

value: wild type


title: RNAseq_03657

tag: batch

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent


title: ChIC-seq_H3K27me3_EILP_Tcf7KO_rep5_GB6949

tag: tissue


title: RNAseq_01416

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: Rat liver, Imazalil+Clothianidin_rep4

city: Berlin

first: Heike

last: Sprenger

address: Max-Dohrn-Strasse 8-10

department: Food Safety

country: Germany

institute: German Federal Institute for Risk Assessment

data_processing:
Adapters were trimmed by Skewer version 0.2.2.
Data quality was assessed by FastQC version 0.11.5.
Reads were mapped to the rat reference genome Rnor_5.0 and counted per gene ID using STAR version 2.5.2b.
After removing genes with low expression (sum of reads across all samples below two), 19904 genes were retained and analyzed by the R-package DESeq2 version 1.15.1 using default settings estimation of size factors and dispersion.
Negative Binomial GLM fitting and Wald statistics were applied to test for differential gene expression between each treatment and control conditions, respectively. False discovery rate (FDR) was used to control for multiple testing. Only genes with a q-value ≤ 0.05 were included in the further analyses.
Genome_build: Rnor_5.0

organism: Rattus norvegicus

source_name: liver

growth_protocol: Young adult female Wistar rats (Crl:WI) were acclimatized to the laboratory conditions for at least 1 week and were weighed and monitored for their health status. Rats were allocated in a randomized manner to the different treatment groups and were maintained under conventional laboratory conditions: constant 12/12-hour light/dark cycle with controlled temperature at 22°C ± 2°C and humidity at 55% ± 15%.

extract_protocol:
Total RNA was isolated from approximately 20-40 mg frozen rat tissue sample using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using TruSeq Stranded Total RNA Sample Preparation-Kit from Illumina

treatment_protocol: The chosen doses of the test compounds (imazalil, thiacloprid and clothianidin) were daily administered to the rats by oral gavage through 28-day treatment. Test compounds were suspended in 0.5% aqueous carboxymethyl-cellulose, whereby the specified dosing volume was 7.5 ml/kg bw. Rats of the control group were treated with the vehicle only (0.5% aqueous carboxymethyl-cellulose in deionized water). Dose selection was based on studies from draft assessment report (DAR). Equipotent mixtures were established following the relative potency factors (RPF) approach.

value: liver

tag: treatment

value: Imazalil+Clothianidin

tag: dose

tag: dose unit

value: mg/kg bw/day

tag: way of administration

value: oral gavage

tag: days of administration

value: Wistar (Crl:WI)

tag: Sex

value: F


title: Rat liver, Imazalil+Clothianidin_rep3

tag: strain


title: Rat liver, Imazalil+Clothianidin_rep2


title: Tg(serpini1)

tag: strain background

value: AB

tag: genotype/variation

tag: age

value: whole larvae


title: Normal6

description: SAMPLE 6_N

tag: disease state

value: distal cholangiocarcinoma

value: adjacent normal sample

tag: histology

value: adenocarcinoma

tag: grade

value: poor

tag: Stage

value: IIB


title: ChIC-seq_IgG_EILP_rep2_GB3051

tag: tissue

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: ChIC-seq_IgG_EILP_rep3_GB6240_tech1


title: Rat liver, Imazalil+Clothianidin_rep1


title: RNAseq_41363

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_05832

tag: age


title: ChIC-seq_H3K27me3_EILP_rep6_GB6953

description: EILP_WT_H3K27me3_3041-3050-6238-6246-6946-6953.se.sorted-W200-normalized.wig.gz

tag: strain

tag: genotype/variation

tag: antibody name, manufacturer and catalog number

value: H3K27me3 (cat# 07-449, millipore )


title: Rat liver, Thiacloprid+Clothianidin_rep4

tag: tissue

tag: treatment

value: Thiacloprid+Clothianidin

tag: dose

tag: dose unit

tag: way of administration

tag: days of administration

tag: Sex


title: ChIC-seq_IgG_EILP_rep1_GB3042

value: bone marrow

tag: sorting profile


title: Rat liver, Thiacloprid+Clothianidin_rep3

value: liver


title: Tumor2

description: SAMPLE 2_T

tag: disease state

value: primary distal cholangiocarcinoma

tag: histology

tag: grade

value: moderate-poor

value: M

tag: Stage

value: IB


title: ChIC-seq_H3K27me3_EILP_rep5_GB6946


title: Rat liver, Thiacloprid+Clothianidin_rep2

value: mg/kg bw/day

value: oral gavage

value: Wistar (Crl:WI)

value: F


title: RNAseq_59898

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: ChIC-seq_IgG_EILP_rep3_GB6240_tech2

tag: strain

tag: genotype/variation

tag: tissue


title: RNAseq_59436

tag: age


title: ChIC-seq_H3K27me3_EILP_rep4_GB6246_tech2

tag: sorting profile

tag: antibody name, manufacturer and catalog number


title: Rat liver, Thiacloprid+Imazalil_rep4

tag: treatment

value: Thiacloprid+Imazalil

tag: dose

tag: dose unit

tag: way of administration

tag: days of administration

tag: Sex


title: RNAseq_91617

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: Rat liver, Thiacloprid+Clothianidin_rep1

tag: tissue

tag: strain


title: ChIC-seq_H3K27me3_EILP_rep4_GB6246_tech1

tag: genotype/variation

tag: sorting profile


title: RNAseq_95505

tag: age

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_95882


title: Rat liver, Thiacloprid+Imazalil_rep3

tag: treatment

tag: dose

tag: dose unit

tag: way of administration

tag: days of administration

tag: Sex


title: ChIC-seq_H3K27me3_EILP_rep3_GB6238_tech2

tag: antibody name, manufacturer and catalog number


title: Rat liver, Thiacloprid+Imazalil_rep2


title: RNAseq_02996

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: RNAseq_25754

tag: age

tag: lymphocyte percent

tag: eosinophil percent


title: ChIC-seq_H3K27me3_EILP_rep2_GB3050

tag: strain

tag: genotype/variation

tag: tissue

tag: sorting profile


title: RNAseq_69006

tag: monocyte percent

tag: basophil percent


title: Rat liver, Thiacloprid+Imazalil_rep1

tag: treatment

tag: dose

tag: dose unit

tag: way of administration

tag: days of administration

tag: Sex


title: ChIC-seq_H3K27me3_EILP_rep1_GB3041

tag: antibody name, manufacturer and catalog number


title: RNAseq_84689

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: Rat liver, Clothianidin_rep3

tag: tissue

value: Clothianidin

tag: strain


title: Rat liver, Clothianidin_rep2


title: ChIC-seq_H3K27ac_EILP_rep6_GB6245_tech2

description: EILP_WT_H3K27ac_3040-3049-6237-6245.se.sorted-W200-normalized.wig.gz

tag: genotype/variation

tag: sorting profile

value: H3K27ac (cat# ab4729, abcam)


title: RNAseq_87594

tag: age

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: ChIC-seq_H3K27ac_EILP_rep5_GB6245_tech1

tag: antibody name, manufacturer and catalog number


title: Rat liver, Clothianidin_rep1

tag: treatment

tag: dose

tag: dose unit

tag: way of administration

tag: days of administration

tag: Sex


title: RNAseq_44509

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: ChIC-seq_H3K27ac_EILP_rep4_GB6237_tech2

tag: strain

tag: genotype/variation

tag: tissue

tag: sorting profile


title: ChIC-seq_H3K27ac_EILP_rep3_GB6237_tech1

tag: antibody name, manufacturer and catalog number


title: Rat liver, Imazalil_rep4

tag: treatment

value: Imazalil

tag: dose


title: ChIC-seq_H3K27ac_EILP_rep2_GB3049

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-


title: ChIC-seq_H3K27me3_EILP_rep3_GB6238_tech1

value: H3K27me3 (cat# 07-449, millipore )


title: Rat liver, Imazalil_rep2

tag: dose unit

tag: way of administration


title: RNAseq_00776

tag: age

tag: lymphocyte percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_89570

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: race (1=white, 2=black)


title: ChIC-seq_H3K27ac_EILP_rep1_GB3040

tag: strain

tag: genotype/variation

tag: tissue


title: Rat liver, Imazalil_rep3

tag: treatment

tag: days of administration

tag: Sex


title: ChIC-seq_H3K4me3_EILP_rep2_GB6951

description: EILP_WT_H3K4me3_6944_6951.150l.NR.se.sorted-W200-normalized.wig.gz

tag: sorting profile

tag: antibody name, manufacturer and catalog number

value: H3K4me3 (cat# cs200580, millipore)


title: RNAseq_76390

tag: age

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: Rat liver, Imazalil_rep1

tag: dose

tag: dose unit

tag: way of administration


title: Rat liver, Thiacloprid_rep4

value: Thiacloprid


title: RNAseq_16236

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: ChIC-seq_H3K4me3_EILP_rep1_GB6944

tag: strain

tag: genotype/variation

tag: tissue

value: bone marrow


title: RNAseq_96462

tag: age

tag: race (1=white, 2=black)


title: RNAseq_42458

tag: fev1 % predicted

tag: neutrophil percent


title: ChIC-seq_IgG_ILCP_rep2GB6261

tag: sorting profile

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+


title: Rat liver, Thiacloprid_rep2

value: liver

tag: treatment

tag: dose

tag: dose unit

tag: days of administration

tag: Sex


title: RNAseq_85233

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: lymphocyte percent


title: ChIC-seq_IgG_ILCP_rep1_GB6257

tag: strain

tag: genotype/variation


title: RNAseq_23386

tag: age

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Rat liver, Thiacloprid_rep1

tag: tissue

tag: way of administration


title: RNAseq_28573

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: Tumor1

description: SAMPLE 1_T

tag: disease state

value: distal cholangiocarcinoma

value: primary distal cholangiocarcinoma

tag: histology

value: adenocarcinoma

tag: grade

value: moderate

tag: Sex

value: M

tag: Stage


title: RNAseq_44905

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: lymphocyte percent


title: Rat liver, Control_rep7

tag: treatment

value: Control

tag: dose

tag: dose unit

value: mg/kg bw/day

value: oral gavage

tag: days of administration

tag: strain

value: Wistar (Crl:WI)

value: F


title: ChIC-seq_H3K27me3_ILCP_rep3_GB8028

tag: genotype/variation

tag: tissue

tag: sorting profile

tag: antibody name, manufacturer and catalog number


title: Rat liver, Control_rep6

tag: way of administration


title: ChIC-seq_H3K27me3_ILCP_rep2_GB6260


title: RNAseq_44142

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_65831

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: lymphocyte percent


title: Rat liver, Control_rep5

tag: treatment

tag: dose

tag: dose unit

tag: days of administration

tag: strain

tag: Sex


title: Rat liver, Control_rep4

tag: tissue

tag: way of administration


title: RNAseq_50080

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent


title: ChIC-seq_H3K27ac_ILCP_rep4_GB8025

tag: genotype/variation

tag: sorting profile

tag: antibody name, manufacturer and catalog number

value: H3K27ac (cat# ab4729, abcam)


title: Rat liver, Thiacloprid_rep3


title: RNAseq_01786

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: Rat liver, Control_rep3

tag: treatment

tag: dose

tag: dose unit

tag: days of administration

tag: strain

tag: Sex


title: Rat liver, Control_rep2

tag: tissue

tag: way of administration


title: RNAseq_78914

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: ChIC-seq_H3K27ac_ILCP_rep2_GB6259

tag: genotype/variation

tag: sorting profile

tag: antibody name, manufacturer and catalog number


title: Rat liver, Control_rep8


title: ChIC-seq_H3K27me3_ILCP_rep4_GB8029

value: H3K27me3 (cat# 07-449, millipore )


title: Rat liver, Control_rep1


title: ChIC-seq_H3K27ac_ILCP_rep1_GB6255


title: ChIC-seq_H3K4me3_ILCP_rep2_GB8027

value: H3K4me3 (cat# cs200580, millipore)


title: ChIC-seq_H3K4me3_ILCP_rep1_GB8026


title: RNAseq_51019

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: eosinophil percent

tag: monocyte percent

tag: basophil percent


title: ChIC-seq_IgG_ALP_rep2_GB6268

tag: strain

tag: tissue

value: Lin- Kit+ 2B4+ a4b7- Flt3high IL-7Ra+


title: RNAseq_05801

tag: age


title: RNAseq_58661

tag: race (1=white, 2=black)


title: ChIC-seq_H3K27me3_ILCP_rep1_GB6256

value: bone marrow


title: RNAseq_64732

tag: fev1 % predicted


title: ChIC-seq_IgG_ALP_rep1_GB6253


title: RNAseq_44946

tag: neutrophil percent


title: ChIC-seq_H3K27me3_ALP_rep1_GB7214


title: ChIC-seq_H3K27ac_ALP_rep2_GB7242


title: ChIC-seq_H3K27ac_ALP_rep1_GB7215


title: RNAseq_74542

tag: lymphocyte percent


title: RNAseq_17518


title: ChIC-seq_H3K4me3_ALP_rep1_GB7213

source_name: ALP (all lymphoid progenitors)

tag: genotype/variation


title: RNAseq_10634


title: ChIC-seq_H3K4me3_ALP_rep2_GB7240

tag: sorting profile


title: RNAseq_80816


title: RNAseq_18632


title: RNAseq_44803


title: ChIC-seq_TCF1_EILP_rep6_GB6950_tech2

description: EILP_TCF1_3039_3048_6236_6244_6943_6950.se.sorted-W100-normalized.wig.gz

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1-

tag: antibody name, manufacturer and catalog number

value: TCF1/TCF7 (C46C7) Rabbit mAb #2206 from CST


title: RNAseq_81115

tag: batch


title: RNAseq_46899

tag: current smoker


title: ChIC-seq_TCF1_EILP_rep6_GB6950_tech1


title: RNAseq_14539

tag: pack years


title: RNAseq_87064

tag: gender (1=male, 2=female)


title: ChIC-seq_TCF1_EILP_rep5_GB6943_tech2


title: ChIC-seq_H3K27me3_ALP_rep2_GB7241


title: ChIC-seq_TCF1_EILP_rep4_GB6244


title: RNAseq_52318

tag: eosinophil percent


title: ChIC-seq_TCF1_EILP_rep5_GB6943_tech1


title: RNAseq_42243

tag: monocyte percent


title: ChIC-seq_H3K27ac_ILCP_rep3_GB8024

value: Lin- Kit+ 2B4+ a4b7+ Tcf7+ Thy1+ IL-7Ra+


title: ChIC-seq_TCF1_EILP_rep3_GB6236


title: RNAseq_56444

tag: basophil percent


title: ChIC-seq_TCF1_EILP_rep2_GB3048

tag: strain


title: ChIC-seq_TCF1_EILP_rep1_GB3039

source_name: EILP (early innate lymphoid progenitors)

tag: tissue


title: RNAseq_96547

tag: age


title: RNAseq_06848

tag: race (1=white, 2=black)


title: RNAseq_50442

tag: fev1 % predicted


title: RNAseq_23255

tag: neutrophil percent


title: RNAseq_92756

tag: lymphocyte percent


title: RNAseq_21756


title: RNAseq_45457


title: SKOV3-MDSC1

city: Shanghai

first: Xiaoqing

last: Guo

address: 2699 west gaoke road

department: Obstetrics and Gynecology

institute: Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine

description: Gene expression after 24h with MDSCs

hyb_protocol: Each slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: EOC cells with MDSCs

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: SKOV3 cells were obtained from the American Type Culture Collection (ATCC) and were cultured and passaged according to the manufacturer’s instructions. All cell lines were cultured in RPMI-1640 medium (HyClone, USA) containing 10% foetal bovine serum (FBS; Gibco, USA), 100 units/mL penicillin, and 100 mg/mL streptomycin at 37°C in a humidified 5% CO2 incubator.

extract_protocol: Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: SKOV3 cells cultured with or without MDSCs were collected for microarray analysis. SKOV3 cells (2.5×105) were co-cultured with freshly sorted EOC-associated MDSCs (5×105) or medium in a transwell system (Corning, USA) for 24 hours.

tag: cell line

tag: cell type

value: epithelial ovarian cancer (EOC) cell line

tag: treatment

value: Myeloid-derived suppressor cells (MDSCs)


title: SKOV3-MDSC3

description: Gene expression after 24h with MDSCs


title: SKOV3-MDSC2

description: Gene expression after 24h with MDSCs


title: RNAseq_68915

tag: batch


title: SKOV3-Control2

description: Gene expression after 24h without MDSCs

source_name: EOC cells without MDSCs

value: none (control)


title: SKOV3-Control3

description: Gene expression after 24h without MDSCs


title: SKOV3-Control1

description: Gene expression after 24h without MDSCs


title: RNAseq_81048

tag: current smoker


title: RNAseq_51577

tag: pack years


title: RNAseq_45642

tag: gender (1=male, 2=female)


title: RNAseq_70185

tag: eosinophil percent


title: RNAseq_40887

tag: monocyte percent


title: ROR+ 20,23(OH)2D3

city: Birmingham

first: Andrzej

middle: T

last: Slominski

state: AL

address: 1720 2nd Avenue South

department: Dermatology

institute: UAB

data_processing:
BGI used SOAPnuke to create the FASTQ files by filtering reads by removing reads with adaptors, removing reads in which unknown bases (N) are more than 10%, and remove low quality reads (percentage of base which quality is lesser than 15 is greater than 50% in a read).
FASTQ files were aligned to genome using STAR version 2.5.4b with parameters --outReadsUnmapped Fastx; --outSAMtype BAM SortedByCoordinate; --outSAMattributes All --outFilterIntonMotifs RemoveNoncanonicalUnannotated
Transcript abundances were calculated with Cufflinks version 2.2.1 with parameters -G; -L; --library-type fr-firststrand
Cuffmerge with default settings was used to merge the data
Cuffdiff with default settings was used to calculate differentially expressed genes
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: Tab delimited Excel file containing FPKM values for each gene

source_name: Fibroblasts

growth_protocol: Skin tissue from newborn mice, RoRγ wild type (RORγ+/+), heterozygotes (RORγ-/+) or knock out (RORγ-/-) was collected. Fibroblasts were isolated from the skin of 1-2 day old mice. The dermis was separated from the epidermis and a suspension of single fibroblasts cells was prepared from dermis. Cells were grown in complete DMEM media containing 10% serum, mouse FGF and 1% antibiotic.Cells in their early passage were used for experiments and were treated with compounds diluted in DMEM and 10% charcoal-stripped fetal bovine serum. In addition, cells isolated from different mice were pooled together to provide more representative samples.

extract_protocol:
After 24 h of incubation, cells were harvested for RNA isolation (RNAeasy Micro kit, Qiagen) following the manufacturers’ protocol. At least 200 ng of RNA for each sample was used for RNASeq processing and analysis  done by BGI Americas Corporation Service (Cambridge, MA). Sample quality and concentration were determined using Agilent 2100.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine fibroblasts were treated with the following vitamin D3 derivatives: 1,25(OH)2D3 (from Sigma) or 20(OH)D3 synthesized chemically, or 20,23(OH)2D3, 1,20(OH)2D3 or 1,20,23(OH)3D3 synthesized enzymatically , diluted in ethanol in DMEM medium containing charcoal-treated serum. Final concentration of the vitamin D hydroxyderivatives was 100 nM, with the final ethanol concentration being 0.1% which was also used as a vehicle control.

value: fibrobroblast cells from skin

value: skin

tag: mice genotype

value: wild type (RORγ+/+)


title: RNAseq_22137

tag: basophil percent


title: ROR+ 1,20,23(OH)3D3

tag: tissue


title: ROR+ 20(OH)Chol


title: ROR+ 1,25(OH)2D3


title: ROR+ 1,20(OH)2D3


title: RNAseq_97141

tag: age


title: ROR- 20(OH)D3

value: knock out (RORγ-/-)


title: RNAseq_22366

tag: race (1=white, 2=black)


title: ROR+ 20(OH)D3


title: RNAseq_81946

tag: fev1 % predicted


title: ROR- 1,20(OH)2D3


title: RNAseq_66031

tag: neutrophil percent


title: RNAseq_33784

tag: lymphocyte percent


title: RNAseq_97195


title: RNAseq_09538


title: RNAseq_01043


title: ROR- control ethanol

value: ethanol


title: ROR+ control ethanol


title: RNAseq_67284


title: RNAseq_29993


title: RNAseq_67395


title: RNAseq_32256


title: RNAseq_78721


title: RNAseq_43626


title: RNAseq_69473


title: T1_WGS

city: Guangzhou

first: zhiwu

last: jiang

address: 190 Kai Yuan Avenue, Science Park

institute: GIBH

data_processing:
Library strategy: WGS
Sequencing-derived raw image files were processed by BGISEQ-500  basecalling Software for base-calling with default parameters and the sequence data of each  individual is generated as paired-end reads, which is defined as "raw data" and stored in FASTQ  format.
Burrows-Wheeler Aligner  (BWA)\[1\]\[2\] software was used to do the alignment.
Best Practices for variant analysis with the Genome Analysis Toolkit(GATK,  https://www.broadinstitute.org/gatk/guide/best-practices).
The genomic variations, including SNPs and InDels were detected by the state-of-the-art  software, such as HaplotypeCaller of GATK(v3.3.0). After that, the variant quality score recalibration  (VQSR) method, which uses machine learning to identify annotation profiles of variants that are likely  to be real, was applied to get high-confident variant calls. The Copy Number Variants ( CNVs ) were  called using the CNVnator\[6\] v0.2.7 read-depth algorithm. The structural variations ( SV ) were  detected using Breakdancer\[7\]\[8\] or CREST\[9\]. Then the SnpEff tool  (http://snpeff.sourceforge.net/SnpEff_manual.html) was applied to perform a series of annotations for  variants.
Genome_build: HG19

source_name: T cells

growth_protocol: cells cultured in T551 H3 (Takara, Japan) medium supplemented with 5% heat-inactivated fetal bovine serum (FBS), 1000 IU/ml recombinant human IL-2, 10 mM HEPES, 2 mM glutamine and 1% penicillin/streptomycin.

extract_protocol:
To extract genomic DNA, sorted cells were incubated in 400 μl of lysis buffer (50mM Tris with pH 8.0, 100mM NaCl, 25 mM EDTA with pH 8.0, 0.5% SDS, and 0.5 mg/ml Proteinase K) at 65 oC for 2 hrs. Genomic DNA was precipitated by adding 500 μl of isopropanol into cell lysis buffer. After centrifugation, DNA was washed once with 500 μl 70% ethanol and air dried before being re-suspended as template for PCR.
The qualified genomic DNA sample was randomly fragmented by Covaris technology and the
fragment of 350bp was obtained after fragment selection

value: Cord blood

value: T cells


title: NK_3_RNA-seq

data_processing: Sequenced reads were trimmed for adaptor sequence and masked for a low complexity or low-quality sequence. The number of raw reads mapped to genes was calculated by RSEM(rsem-1.2.4), and the sample results were put together and normalized by EDAseq (1.99.1).

source_name: NK cells

extract_protocol:
Retinas 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

treatment_protocol: Sorted T, ITNK and NK cells was prepared according to the TruSeqTM RNA Sample Preparation Guide

value: NK cells


title: RNAseq_14508

data_processing:
alignment: STAR, 2-pass
gene quantification: Salmon v0.12.0 and tximport
exon quantification: Rsubread v1.32.2
isoform quantification: Salmon v0.12.0
Genome_build: HG38 (GTF: Ensembl Homo_sapiens.GRCh38.94.gtf.gz)
Supplementary_files_format_and_content: count matrices

extract_protocol:
Total RNA was extracted from PAXgene TM Blood RNA tubes using the Qiagen PreAnalytiX PAXgene Blood miRNA Kit (Qiagen, Valencia, CA).
Globin reduction and cDNA library preparation for total RNA was performed with the Illumina TruSeq Stranded Total RNA with Ribo-Zero Globin kit (Illumina, Inc., San Diego, CA).


title: RNAseq_52834


title: RNAseq_85684


title: NK_5p_RNA-seq

value: PBMC


title: RNAseq_16461


title: NK_6p_RNA-seq


title: RNAseq_73274


title: RNAseq_23700


title: NK_4_RNA-seq


title: T3_WGS


title: TK_7p_RNA-seq

source_name: ITNK cells

value: ITNK cells


title: RNAseq_96138


title: TK_5p_RNA-seq


title: TK_6p_RNA-seq


title: TK_4_RNA-seq


title: TK3_WGS


title: TK_2_RNA-seq


title: RNAseq_86221


title: RNAseq_77488


title: TK_3_RNA-seq


title: RNAseq_39725


title: RNAseq_46966


title: RNAseq_77696


title: RNAseq_85326


title: T_7p_RNA-seq


title: T_6p_RNA-seq


title: T_4_RNA-seq


title: RNAseq_75358


title: T_5p_RNA-seq


title: T_3_RNA-seq


title: Leaf protoplast scRNA seq- Library 2

city: Düsseldorf

first: Jiyun

last: Kim

address: Universitätsstr. 1

department: Biology

institute: HHU

description:
Arabidopsis Col-0 leaf protoplasts- replicate 2
barcodes.tsv
matrix.mtx
features.tsv

data_processing:
Reads were aligned to the Arabidopsis thaliana reference genome (Araport 11) using Cell Ranger 3.0.2 (10X Genomics, California) with default parameters. The output files for the two replicates were aggregated into one gene-cell expression matrix using Cell Ranger aggregate with the mapped read depth normalization option.
Genome_build: Arabidopsis thaliana reference genome (Araport 11)
Supplementary_files_format_and_content: 2 biological replicates  were sequenced three times each and processed in a single Cellranger run

organism: Arabidopsis thaliana

source_name: leaf protoplasts

growth_protocol: Col-0 plants were grown under short-day (8 h light / 16 h dark) conditions at a PAR of 60 µmol m-2 s-1.

extract_protocol:
Two biological replicates were performed with the aim of capturing ~7,000 leaf protoplasts for each replicate. Freshly isolated protoplasts were adjusted to 700-900 cells/μL and loaded into the 10X Genomics Chromium single cell microfluidics device according to the Single Cell 3’ Reagent Kit v2 protocol (10x Genomics, California). scRNA-seq library sequencing was performed on a NextSeq platform (Illumina Inc, California), using the sequencing parameters 26,8,0,98.
Libraries were quantified using the NEBNext Library Quantification Kit for Illumina (New England Biolabs, Massachusetts). Libraries were made  according to the Single Cell 3’ Reagent Kit v2 protocol (10x Genomics, California).

treatment_protocol: Seven to nine abaxial epidermis-peeled and cut leaves attached to time tape were immediately immersed in the petri dish containing 15 mL freshly prepared protoplast isolation solution (1% Cellulase Onuzuka R-10 (Duchefa, Haarlem), 0.3% macerozyme R-10, (Duchefa, Haarlem), 0.6 M Mannitol, 20 mM MES pH 5.7, 20 mM KCL, 1 mM DTT, 10 mM CaCl2, and 0.1 % BSA). The protoplasts were washed four times with 20 mL washing buffer. After the final wash step, protoplasts were slowly resuspended in 1 mL wash buffer and gently filtered twice using a 40 m Flowmi cell strainer (Bel-Art SP Scienceware, New Jersey).

tag: ecotype

tag: genotype

value: Wild type

value: leaf protoplasts

tag: growth condition

value: Grown under SD conditions


title: RNAseq_46115

tag: batch


title: T_2_RNA-seq

tag: cell type


title: RNAseq_59001

tag: current smoker

tag: pack years


title: RNAseq_56844

tag: gender (1=male, 2=female)

tag: eosinophil percent


title: Leaf protoplast scRNA seq- Library 1

description:
Arabidopsis Col-0 leaf protoplasts- replicate 1
barcodes.tsv
matrix.mtx
features.tsv


title: RNAseq_45273

tag: monocyte percent


title: T_1_RNA-seq


title: D3-Control-h-3

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: embryonic stem cell

data_processing:
RNA-seq reads were mapped to the mouse genome and human genome using HISAT2 (version 2.1.0)32 with parameters “-k 1 --no-unal --dta --rna-strandness R”.
The gene expression levels were then calculated using StringTie (v1.3.3b)33 with parameters “--rf -t -e -B -A”.
A 2-fold variance in expression levels, a P value less than 0.05 and an adjusted P value less than 0.1 were used as cutoffs to define differentially expressed genes. The P value and adjusted P value were calculated using DESeq234.
GO analysis preformed on DAVID (https://david-d.ncifcrf.gov/home.jsp).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: FPKMs of 45,962  genes detected by RNA-seq

source_name: embryonic stem cell

growth_protocol: Primed human PSCs were either cultured on Matrigel (BD Biosciences) coated plates in mTeSR1 medium (StemCell Technologies) or on mitotically inactived mouse embryonic fibroblasts (MEFs) in NBFR medium, which contains DMEM/F12 (Invitrogen) and Neurobasal medium (Invitrogen) mixed at 1:1 ratio, 0.5x N2 supplement (Invitrogen), 0.5x B27 supplement (Invitrogen), 2 mM GlutaMax (Gibco); 1x NEAA (Gibco), 0.1mM 2-Mercaptoethanol (Sigma-Aldrich), 20 ng/ml FGF2 (Peprotech), 2.5µM IWR1 (Sigma-Aldrich), and 1mg/ml BSA (Low fatty acid, MP Biomedicals New Zealand Ltd, Cat No# ABFF).

extract_protocol:
RNA extraction was performed using a RNeasy Mini Kit (QIAGEN) using DNase treatment (QIAGEN). RNA was analyzed using a 2100 Bioanalyzer (Aglient Technologies). (Transcripts per Kilobase Million).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cells

tag: passages

tag: cell line


title: RNAseq_93161

city: Boston

first: Peter

last: Castaldi

address: 181 Longwood Ave

institute: Brigham and Women's Hospital

tag: age

tag: basophil percent


title: TK_1_RNA-seq

tag: tissue


title: salt+paraquat+highlight+heat_stress [S-PQ-HL-HS_48]

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

data_processing:
Illumina's two-channel SBS sequencing
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample

growth_protocol: Seeds of Arabidopsis thaliana wild type Col-0 were sterilized and placed on 1% agar plates (0.5x Murashige and Skoog (MS) medium, pH 5.8) as controls. Similarly, sterilized seeds were placed on 1% agar MS medium supplemented by: Salt (50 mM NaCl); PQ (0.05 µM paraquat); Salt + PQ (50 mM NaCl + 0.05 µM paraquat). After being stratified at 4ºC for 12 hours in dark, seeds were germinated horizontally under controlled conditions (21°C, 50 µmol m-2 s-1). 10 days after germination, seedlings growing in the different plates were subjected to high light (700 µmol m-2 s-1), heat stress (33ºC) and the combination of high light and heat stress (700 µmol m-2 s-1; 33ºC) for 1.5 h. Immidiately after that, seedlings were frozen in liquid nitrogen.

extract_protocol:
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Col-0 seedlings were subjected to salt, paraquat, high light, heat stress, and a combination of 2, 3 or 4 of those stresses as described in the groth protocol

value: wild type

tag: treatment

value: Seedlings

tag: repeat


title: salt+paraquat+highlight+heat_stress [S-PQ-HL-HS_47]

tag: ecotype


title: RNAseq_80110

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_53241

tag: batch

tag: current smoker


title: RNAseq_37096

tag: pack years

tag: gender (1=male, 2=female)


title: paraquat+highlight+heat_stress [PQ-HL-HS_44]

tag: genotype


title: RNAseq_41999

tag: eosinophil percent

tag: monocyte percent


title: paraquat+highlight+heat_stress [PQ-HL-HS_45]


title: D2-Co-h-3

description: embryonic stem cell

tag: cell type

tag: passages

tag: cell line


title: D2-Co-h-1

description: embryonic stem cell


title: salt+highlight+heat_stress [S-HL-HS_42]

tag: treatment

tag: tissue


title: RNAseq_84041

tag: age

tag: basophil percent


title: RNAseq_75796

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: D1-Co-h-3

description: embryonic stem cell


title: RNAseq_58292

tag: neutrophil percent

tag: lymphocyte percent


title: salt+highlight+heat_stress [S-HL-HS_41]

tag: ecotype

tag: repeat


title: RNAseq_38793

tag: batch

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)


title: D1-Co-h-2

description: embryonic stem cell

tag: cell type


title: RNAseq_57322

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_94433


title: salt+highlight+heat_stress [S-HL-HS_40]

tag: genotype

tag: treatment


title: D3-Control-h-2

description: embryonic stem cell

tag: passages

tag: cell line


title: salt+paraquat+highlight+heat_stress [S-PQ-HL-HS_46]

tag: tissue


title: highlight+heat_stress [HL-HS_39]


title: RNAseq_19706

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: basophil percent


title: ALDH1A2 sgRNA plus_1

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

data_processing:
RNA-seq datasets of control samples, knockout samples for ALDH1A2 were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 control vs 2 knockout samples.
Genome_build: hg19
Supplementary_files_format_and_content: fold change

source_name: Jurkat

growth_protocol: Jurkat cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and sequencing of single-end, 100-bp-long reads by the BGISEQ were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: Jurkat cells expressing the dCas9-KRAB and an inducible sgRNA were treated with doxycycline for 72 hrs.  Total RNA was harvested followed by RNA-sequencing.

value: Jurkat

tag: knockout

value: knockout


title: D3-Co-h-2

description: embryonic stem cell


title: highlight+heat_stress [HL-HS_38]

tag: ecotype

tag: repeat


title: D3-Co-h-1

description: embryonic stem cell


title: paraquat+highlight+heat_stress [PQ-HL-HS_43]


title: RNAseq_53760

tag: batch

tag: current smoker

tag: pack years

tag: neutrophil percent

tag: lymphocyte percent


title: ALDH1A2 sgRNA minus_2

value: control


title: ALDH1A2 sgRNA minus_1


title: highlight+heat_stress [HL-HS_37]

tag: genotype


title: RNAseq_66293

tag: gender (1=male, 2=female)

tag: eosinophil percent

tag: monocyte percent


title: RNAseq_13430


title: RNAseq_99050


title: RNAseq_34074


title: RNAseq_09983


title: salt+paraquat+heat_stress [S-PQ-HS_34]

tag: treatment

tag: tissue


title: ALDH1A2 sgRNA plus_2

tag: cell line


title: salt+paraquat+heat_stress [S-PQ-HS_35]


title: paraquat+heat_stress [PQ-HS_32]


title: RNAseq_99597

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 13-3-E Wild type, 360 min after formaldehyde treatment

description: counts.csv

source_name: Bacterial cells

tag: strain

value: efgA

value: form

tag: time

tag: biological replicate


title: RNAseq_68006

source_name: blood

tag: batch

tag: current smoker

tag: basophil percent


title: paraquat+heat_stress [PQ-HS_31]

tag: ecotype

tag: repeat


title: paraquat+heat_stress [PQ-HS_30]

tag: genotype


title: salt+heat_stress [S-HS_29]


title: RNAseq_13879

tag: pack years

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: 7-3-E Wild type, 180 min after formaldehyde treatment

description: counts.csv

tag: treatment


title: 8-3-E Wild type, 360 min after formaldehyde treatment

description: counts.csv


title: 12-9-E Wild type, 180 min after formaldehyde treatment

description: counts.csv


title: salt+heat_stress [S-HS_28]

tag: tissue


title: 11-3-E Wild type, 40 min after formaldehyde treatment

description: counts.csv


title: RNAseq_67267

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: monocyte percent


title: salt+heat_stress [S-HS_27]


title: RNAseq_25909

tag: batch


title: salt+paraquat+heat_stress [S-PQ-HS_36]


title: heat_stress [HS_26]


title: 4-3-E Wild type, 40 min after formaldehyde treatment

description: counts.csv

tag: strain

tag: time

tag: biological replicate


title: 10-9-E Wild type, 20 min after formaldehyde treatment

description: counts.csv


title: heat_stress [HS_25]

tag: ecotype

tag: repeat


title: RNAseq_09652

tag: current smoker

tag: pack years

tag: basophil percent


title: RNAseq_69204

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent


title: RNAseq_27932

tag: eosinophil percent


title: 3-9-E Wild type, 20 min after formaldehyde treatment

description: counts.csv

tag: genotype

tag: treatment


title: RNAseq_98801

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 3-3-E Wild type, 20 min after formaldehyde treatment

description: counts.csv

tag: strain


title: salt+paraquat+highlight [S-PQ-HL_33]

value: salt+paraquat+highlight

tag: tissue


title: RNAseq_83668

tag: batch

tag: monocyte percent


title: salt+paraquat+highlight [S-PQ-HL_22]

tag: ecotype

tag: repeat


title: salt+paraquat+highlight [S-PQ-HL_11]


title: 2-9-E Wild type, 5 min after formaldehyde treatment

description: counts.csv

tag: time

tag: biological replicate


title: RNAseq_56298

tag: current smoker

tag: pack years

tag: gender (1=male, 2=female)

tag: basophil percent


title: RNAseq_18220

tag: neutrophil percent

tag: lymphocyte percent

tag: eosinophil percent


title: 8-2-E efgA mutant, 360 min after kanamycin treatment

description: counts.csv

tag: genotype

tag: treatment

value: kan


title: paraquat+highlight [PQ-HL_21]

value: paraquat+highlight


title: 2-3-E Wild type, 5 min after formaldehyde treatment

description: counts.csv

tag: strain


title: RNAseq_73315

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted


title: 7-2-E efgA mutant, 180 min after kanamycin treatment

description: counts.csv


title: paraquat+highlight [PQ-HL_20]

tag: ecotype

tag: tissue


title: 11-2-E efgA mutant, 40 min after kanamycin treatment

description: counts.csv

tag: time


title: RNAseq_77483

tag: batch

tag: monocyte percent


title: RNAseq_38161

tag: current smoker

tag: pack years


title: salt+highlight [S-HL_18]

value: salt+highlight

tag: repeat


title: salt+highlight [S-HL_19]


title: 4-2-E efgA mutant, 40 min after kanamycin treatment

description: counts.csv

tag: biological replicate


title: heat_stress [HS_24]


title: 10-3-E Wild type, 5 min after formaldehyde treatment

description: counts.csv


title: RNAseq_48941

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent

tag: basophil percent


title: 8-1-E efgA mutant, 360 min after mock treatment

description: counts.csv

tag: strain

tag: genotype

tag: treatment


title: RNAseq_82205

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: salt+highlight [S-HL_17]

tag: ecotype

tag: tissue


title: M_FU-1-1-lib1 scRNA-seq

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
quality control, Cell Ranger Single Cell Software Suite (v3.0.2)
sample de-multiplexing,  Cell Ranger Single Cell Software Suite (v3.0.2)
barcode processing, Cell Ranger Single Cell Software Suite (v3.0.2)
single-cell 3′ gene counting , Cell Ranger Single Cell Software Suite (v3.0.2)
alignment, Cell Ranger Single Cell Software Suite (v3.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

source_name: CD3-CD19-SiglecH+GFP–, SiglecH+GFPlow/int and SiglecH–GFPhigh isolated from inguinal and axillary LN of Zbtb46-GFP x CLEC4C-DTR+ untreated mice

extract_protocol:
Mice were aged to 8-12 weeks in a SRF facility. Cell suspensions of spleen and LN were prepared by collagenase D digestion for 45 minutes and passage through nylon mesh cell strainers (BD Biosciences). Cells were sorted on an Aria II and preserved in 10% FCS RPMI until input into 10X  Genomics Single Cell Protocol.
Cell-barcoded cDNA was generated from single cells via an oligo-dT priming approach. Single cells were captured into droplets utilizing the 10X Chromium system.  A sequencing library was generated from the 3' fragments containing the barcode.

tag: mouse genotype

value: DTR+

value: inguinal and axillary skin


title: highlight [HL_16]

value: highlight


title: RNAseq_22919

tag: batch

tag: current smoker

tag: pack years

tag: monocyte percent


title: 12-7-E efgA mutant, 180 min after mock treatment

description: counts.csv

data_processing:
Read trimming was performed using Trimmomatic v0.38 in paired-end mode, if applicable, and removing reads trimmed to fewer than 30 bases.
Read alignment was performed using Bowtie2 v4.8.2 with the -k option, in paired-end mode for reads paired after trimming and in single read mode for others
Raw counts were generated using HTSeq v0.11.4 with options to count read pairs or singleton reads that unambiguously overlapped each gene
Normalized read counts were generated using DeSeq2 in R version 3.6.
Genome_build: NC_010172.1
Supplementary_files_format_and_content: CSV

extract_protocol:
RNA was purified from cells for each sample using the RNAsnap method [1]. First, cell pellets were resuspended in 500 µl of RNA extraction buffer (18 mM EDTA, 0.025% w/v SDS, 1% v/v 2-mercaptoethanol, 95% v/v formamide) by vortexing. Following incubation at 95°C for 7 min, cell debris was pelleted by centrifugation at 16000 × g for 5 min at room temperature. The resulting supernatant was purified using the Clean & Concentrator kit incorporating the on-column DNase digestion step (Zymo Research). Yields were determined using a Qubit 2.0 fluorometer with the RNA BR assay kit (ThermoFisher). Then, 1.5 µg of purified RNA for each sample was processed using the Ribozero rRNA Removal Kit (Gram-negative bacteria) (Illumina) according to the manufacturer’s instructions except that reaction volumes were reduced by 50%. Depleted RNA samples were ethanol precipitated.
RNA-Seq library preparation from rRNA-depleted samples began by fragmenting them with the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) for 110 s followed by ethanol precipitation. Fragmented RNA was treated with 10 U of T4 polynucleotide kinase (NEB) in 20 µl reactions containing 1 mM ATP. After another ethanol precipitation, the NEBNext small RNA Library Prep Set for Illumina (Multiplex Compatible) (New England Biolabs) was used to prepare samples according to recommended protocol, except all reaction volumes were reduced 50% and the SR RT primer concentration was reduced by an additional 50% in the RT primer hybridization step. After performing 15 cycles of PCR, samples were ethanol precipitated, and the DNA concentration was determined via the Qubit HS dsDNA assay kit (Thermofisher). For each sample, 200 ng of DNA was run on a 4% EX E-gel (ThermoFisher). DNA with a size of at least ~200 bases was excised and purified using a gel DNA recovery kit (Zymo Research) with elution in 50 µl of nuclease-free water.

tag: time

tag: biological replicate


title: RNAseq_05844

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent

tag: basophil percent


title: 7-1-E efgA mutant, 180 min after mock treatment

description: counts.csv

tag: strain

tag: genotype

tag: treatment


title: highlight [HL_15]

tag: repeat


title: highlight [HL_14]

tag: ecotype


title: WT scRNA-seq

source_name: CD3-CD19-CD11c+MHCII+ and CD3-CD19-CD11c+SiglecH+ cells isolated from inguinal and axillary LN of DT treated CLEC4C-DTR- mice 48h after epicutaneous treatment with FITC Hapten

value: DTR-

tag: tissue


title: RNAseq_78794

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: DTR scRNA-seq

source_name: CD3-CD19-CD11c+MHCII+ and CD3-CD19-CD11c+SiglecH+ cells isolated from inguinal and axillary LN of DT treated CLEC4C-DTR+ mice 48h after epicutaneous treatment with FITC Hapten

tag: mouse genotype


title: RNAseq_31153

tag: batch

tag: current smoker

tag: pack years

tag: monocyte percent


title: RNAseq_39526

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent


title: salt+paraquat [S-PQ_13]

tag: genotype

value: salt+paraquat


title: Salmonella-timecourse_TCR

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description:
GEX-Timecourse-Salmonella.txt
Feature-Timecourse-Salmonella.txt
processed data files are found on GSM4859317.

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
Cellranger mkfastq
Cellranger count
Genome_build: mm10
Supplementary_files_format_and_content: filtered read counts>1000 UMIs
Supplementary_files_format_and_content: GEX* : filtered RNA UMI counts
Supplementary_files_format_and_content: Feature*: raw feature read counts

source_name: CD4+ Colonic LP SPF and S. typhimurium infection day3,5,7,10,13, 17

growth_protocol: Live CD4+ TCRb+ cells were sorted by flow cytometry from the colon LP

extract_protocol:
Colons were enzymatically dissociated and digested with collagenase/dispase to single cell suspensions. Live CD4+ TCRb+ cells were sorted using the MoFlo Astrios. Single cells were then encapsulated in nanodroplets according to the 10x Genomics protocol.
10X Genomics library prep (3' V1, V2 or 5' V1) Library were sequenced using a NextSeq500.

tag: strain

tag: Sex

value: Male

tag: age (weeks)

value: Colon LP

tag: cell type

value: CD4+ TCRb+


title: 4-1-E efgA mutant, 40 min after mock treatment

description: counts.csv

tag: treatment

tag: time

tag: biological replicate


title: 13-1-E efgA mutant, 360 min after mock treatment

description: counts.csv


title: salt+paraquat [S-PQ_12]

tag: ecotype

value: wild type

tag: tissue

value: Seedlings

tag: repeat


title: M_FU-2-2-lib2 scRNA-seq

tag: mouse genotype


title: Salmonella_atac

source_name: CD4+ Colonic LP S. Typhimurium infection day13


title: 10-7-E efgA mutant, 20 min after mock treatment

description: counts.csv


title: Salmonella-timecourse_GEX


title: salt+paraquat [S-PQ_10]


title: RNAseq_94126

description:
gene_TMM_counts.csv
exon_TMM_counts.csv
isoform_TMM_counts.csv

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent

tag: basophil percent


title: paraquat [PQ_9]

tag: genotype

value: paraquat


title: 3-7-E efgA mutant, 20 min after mock treatment

description: counts.csv

tag: strain

value: efgA


title: 10-1-E efgA mutant, 5 min after mock treatment

description: counts.csv

tag: treatment


title: paraquat [PQ_8]


title: salmonella-day13-single lane

description: Salmonella.txt

tag: Sex

tag: age (weeks)

tag: cell type


title: paraquat [PQ_7]

tag: ecotype

tag: tissue


title: 11-1-E efgA mutant, 40 min after mock treatment

description: counts.csv

tag: time

tag: biological replicate


title: RNAseq_68025

tag: current smoker

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent

tag: monocyte percent


title: RNAseq_74492

tag: batch

tag: pack years

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: eosinophil percent


title: citronacter-single lane

description: Citrobacter.txt

source_name: CD4+ Colonic LP C. Rodentium infection day13

tag: strain

tag: Sex

tag: age (weeks)


title: Salt [S_6]

tag: ecotype

tag: genotype

tag: treatment

value: Salt

tag: tissue

tag: repeat


title: 2-7-E efgA mutant, 5 min after mock treatment

description: counts.csv

tag: time

tag: biological replicate


title: RNAseq_71151

tag: current smoker

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent

tag: monocyte percent

tag: basophil percent


title: RNAseq_53223

tag: batch

tag: age

tag: race (1=white, 2=black)


title: RNAseq_57513

tag: pack years

tag: fev1 % predicted

tag: eosinophil percent


title: 1-5-E efgA mutant, pretreatment

description: counts.csv

tag: strain

tag: genotype

tag: treatment

value: pre


title: Salt [S_5]

tag: ecotype

tag: tissue

tag: repeat


title: 2-1-E efgA mutant, 5 min after mock treatment

description: counts.csv

tag: time

tag: biological replicate


title: Salt [S_4]


title: RNAseq_69148

tag: current smoker

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent


title: 1-1-E efgA mutant, pretreatment

description: counts.csv


title: All_infections-hashed

description:
GEX-Hash-all_infections.txt
Feature-Hash-all_infections.txt

source_name: Hashed_all_infections: CD4+ Colonic LP SPF, C. Rodentium, S. Typhimurium, N. Brasiliensis, H. Polygyrus

tag: Sex

tag: age (weeks)

tag: cell type


title: RNAseq_17572

tag: batch

tag: pack years

tag: age

tag: race (1=white, 2=black)

tag: fev1 % predicted

tag: monocyte percent

tag: basophil percent


title: GF_10x_v1-2

description:
GF-V1.txt
GF-V1.txt is found on GSM4859310.

source_name: CD4+ Colonic LP GF

tag: strain

tag: tissue


title: Salmonella-timecourse_hash

description:
GEX-Timecourse-Salmonella.txt
Feature-Timecourse-Salmonella.txt


title: N.brasiliensis-single lane

description: Nippo.txt

source_name: CD4+ Colonic LP N. Brasiliensis infection day11


title: RNAseq_63854

tag: eosinophil percent


title: Control [CT_3]

tag: ecotype

tag: genotype

tag: treatment

value: Control

tag: repeat


title: 3-1-E efgA mutant, 20 min after mock treatment

description: counts.csv

tag: time

tag: biological replicate


title: GF_10x_v1-1

tag: Sex

tag: age (weeks)

tag: cell type


title: 13-3-W Wild type, 360 min after formaldehyde treatment

description: counts.csv

value: WT

value: form


title: RNAseq_85902

tag: batch

tag: current smoker

tag: pack years

tag: age

tag: gender (1=male, 2=female)

tag: neutrophil percent

tag: lymphocyte percent


title: Control [CT_1]

tag: tissue


title: 8-3-W Wild type, 360 min after formaldehyde treatment

description: counts.csv

tag: strain


title: SPF_10x_v2-single lane

description: SPF.txt

source_name: CD4+ Colonic LP SPF


title: SPF_10x_v1-2

description:
SPF-V1.txt
SPF-V1.txt is found on GSM4859308.


title: SPF_10x_v1-1