title: ID_006700_dFoxI_rpoE_C

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

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

description: samples were grown to mid-exponetial phase and either treated for 30 min with anhydrotetracycline or left untreated

data_processing:
Reads from the RNA-seq experiments were trimmed and filtered using the FASTX toolkit (v.0.10.1; http://hannonlab.cshl.edu/fastx_toolkit). Mapping was performed using READemption (v.1.01)(Förstner et al., 2014) against the genome sequence for F. nucleatum subsp. nucleatum ATCC 23726 (NZ_CP028109.1) downloaded from the National Center for Biotechnology Information (NCBI). Differential gene expression analysis was carried using DEseq2 (v.1.18.01) (Love et al., 2014). All analysis for each was carried for biological triplicates and considered significant with a false-discovery rate ≤ 0.05. For the experiment concerning the σE expression, the genes had to additionally show a fold change either ≤ 1 or ≥ -1 to be marked as significantly changed. For the experiment concerning the pulse expression of FoxI or seed region mutants of the sRNA, the fold change of genes to be considered significantly changed was set to either ≤ 0.5 or ≥ -0.5.
Genome_build: NZ_CP028109.1
Supplementary_files_format_and_content: wiggle

organism: Fusobacterium nucleatum subsp. nucleatum ATCC 23726

growth_protocol: Growth was performed in Columbia broth at 37°C inside an anaerobic chamber. Pre-cultures were inoculated with a signel colony. After 24h, the working cultures were inoculated at a dilution 1:50 and samples taken during the mid-exponential growth phase.

extract_protocol:
Total RNA was extracted using the hot phenol protocol. Bacterial cultures were grown to the desired OD600, mixed with 0.2 volumes of STOP solution (95 % ethanol, 5 % phenol) and snap-frozen at – 80 °C if not directly processed. The bacterial solution was centrifuged for 20 min, 4500 rpm at 4 °C and the supernatant was completely discarded. Cells were suspended in 600 μl of 10 mg/ml lysozyme in TE buffer (pH 8.0) and incubated at 37 °C for 10 min. Next, 60 μl of 10 % w/v SDS was added and everything mixed by inversion. Samples were incubated in a water bath at 64 °C, 1-2 min before adding 66 μl 3 M NaOAc, pH 5.2. Next, 750 μl acid phenol (Roti-Aqua phenol) was added, followed by incubation for 5 min. at 64 °C. Samples were briefly placed on ice to cool before centrifugation for 15 min, 13,000 rpm at 4 °C. The aqueous layer was transferred into a 2 ml phase lock gel tube (Eppendorf), 750 μl chloroform (Roth, #Y015.2) was added, and everything centrifuged for 12 min, 13,000 rpm at room temperature. For ethanol precipitation, the aqueous layer was transferred to a fresh tube, 2 volumes of 30:1 mix (EtOH:3 M NaOAc, pH 6.5) was added and incubated overnight at -20 °C. Precipitated RNA was harvested by centrifugation, washed with cold 75 % v/v ethanol and air-dried. Purified RNA was resuspended in 50 µl RNase-free water and stored at -80 °C.
The cDNA library preparation was carried by Vertis (Munich, Germany). The first step consisted out of rRNA removal. The rRNA depleted RNA was then fragmented via ultrasound (1 pulse of 30 seconds; 4 °C). The fragmented RNA was then used to ligate an adapter to the 3’ end of the molecules. For first-strand cDNA synthesis, the M-MLV reverse transcriptase was used in conjunction with the introduced 3’-adapter serving as a primer. After purification, 5’ Illumina TruSeq sequencing adapters were ligated to the cDNA. The resulting cDNA was used as input for during PCR amplification (10 – 20 ng µl-1). The amplified cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and further evaluated via capillary electrophoresis. The cDNA was pooled further purified to include only cDNA from 200 – 600 bp using a preparative agarose gel. The finished pooled libraries were sequenced by the Core unit SysMed (University of Würzburg) using an Illumina NextSeq 500 system and 75 bp read length.

treatment_protocol: see description of samples

value: 30 min + 100ng/ml anhydrotetracycline

value: carries inducible plasmid for rpoE expression


title: Psoriatic skin from donor 6215A [PP-6215A]

status: Public on Sep 20 2022

type: SRA

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
Libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina).
Fastq files were generated using Cellranger mkfastq (version 4.0.0). The raw reads were mapped to the  human genome (hg38) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every cell

molecule: total RNA

organism: Homo sapiens

source_name: Psoriatic skin

extract_protocol:
6-mm punch biopsies were taken from healthy skin from healthy donors, lesional and non-lesional skin from psoriasis patients.
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 70μM mesh. Epidermal and dermal cells were combined in 1:1 ratio and libraries were constructed by the University of Michigan Advanced Genomics Core on the 10X Chromium system.

tag: subject id

value: donor 6215A

tag: subject status

value: psoriasis patient

tag: tissue type

value: Psoriatic skin

tag: cell type

value: Epidermal and dermal cells


title: Psoriatic skin from donor 31499 [PP-31499]

value: donor 31499


title: Psoriatic skin from donor 8659ED [PP-8659ED]

value: donor 8659ED


title: PD1: Proliferating Fibroblast DMSO

city: Madison

first: Christopher

last: Morrow

state: Wisconsin

address: 1111 Highlange Ave.

institute: University of Wisconsin - Madison

data_processing:
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 [2] to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/. The mapped reads of each sample were assembled using StringTie [3]. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie [3] and edgeR [4] was used to estimate the expression levels of all transcripts.
StringTie [3] was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [4].
Genome_build: Mus musculus (Version: v88)
Supplementary_files_format_and_content: Table S1 - RNA Sequencing TPM Normalized to ERCC

molecule: polyA RNA

organism: Mus musculus

source_name: tail

growth_protocol: Fibroblasts were cultured with 37°C/5% CO2 in RPMI with Glutamine (Invitrogen 11875-093), 10% FBS (Invitrogen 16000044), 55 µM β-Mercaptoethanol (Invitrogen 21985-023), 100 µM asparagine and 100 µg/ml Penicillin-Streptomycin (Invitrogen 15140122), 25 µg/mL Amphoterecin B (Sigma-Aldrich A9528)

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen 74104) according to the manufacturer’s instructions.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: All samples were treated to generate distinct cell states as indicated in each sample and additionally treated with either DMSO or MG132

tag: strain

value: Fibroblast

tag: cell state

value: Proliferating

tag: treatment

value: DMSO


title: Psoriatic skin from donor 31277 [PP-31277]

value: donor 31277


title: Psoriatic skin from donor  31170 [PP-31170]

value: donor  31170


title: Psoriatic skin from donor 30696V3 [PP-30696V3]

value: donor 30696V3


title: Patient nCounter 2

type: RNA

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

description: Total RNA samples runs were performed on the nCounter FLEX Analysis System based on the NanoString PanCancer Immuno-Oncology panel (IO360), made of 770 genes and a custom panel of 30 genes, in which we included genes from Hendrickx et al.’s Immunologic Constant of Rejection (ICR) signature.

hyb_protocol: According to Nanostring protocol

scan_protocol: Sample runs were performed on the nCounter FLEX Analysis System (automated nCounter® Prep station and the nCounter® Digital Analyzer optical scanner, NanoString Technologies, Seattle, WA, USA) according to the manufacturer’s protocol.

data_processing: We refined the 20-housekeeping gene list defined in NanoString IO360 panel using three independent datasets grouping triple negative breast cancer patients retrieved from xenaBrowser [TCGA BRCA primary tumors with 123 patients, Chin et al. 2006 : 41 patients and Hess et al. 2006  : 27 patients]. We computed gene expression variability as the inter-quantile (5%-95%) ratio in each dataset and selected 6 of the 20 genes showing ratios under 1.5 in all datasets: ERCC3, POLR2A, SF3A1, TBC1D10B, TMUB2, UBB.  We normalized the expression values using NanoStringNorm R package v1.2.1.1 with options CodeCount ='geo.mean', Background ='mean.2sd', SampleContent ='housekeeping.geo.mean', round.values = TRUE, take.log = TRUE.

label: biotin

source_name: Residual Triple Negative Breast Cancer

label_protocol: According to Nanostring protocol

extract_protocol: Total tumor RNA was extracted from four to six 10-micron tumor sections after identification of the residual tumor by a pathologist on a corresponding H&E section. RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche®), following the manufacturer’s instructions. RNA quantity and quality were assessed by Nanodrop 1000 spectrophotometer (ThermoFisher, Waltham, MA, USA) and 2100 Bioanalyser with Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). 200ng of total RNA was used from each sample for gene expression profiling (acceptation criteria 260/280 ratio: 1.8 -2.3, 230/280 ratio: 1.7-2.3).

tag: age

tag: lve

tag: tils

tag: metastasis


title: Patient nCounter 11


title: Psoriatic skin from donor 30696 [PP-30696]

value: donor 30696


title: ∆nhr-114-B12-1

city: Hangzhou

first: Shenlu

last: Qin

state: Zhejiang

address: No. 600 Dunyu Road

country: China

institute: Westlake University

description: Sequencing libraries were generated using an NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform, and 125 bp/150 bp paired-end reads were generated. The sequencing reads were demultiplexed (bcl2fastq) and quantified with kallisto 0.46.0 with the default parameters according to the WormBase reference genome (WS245).

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference transcripts and gene annotation files were downloaded from genome  website directly. Index of the reference transcripts was built using kallisto v0.46.0 and  paired-end clean reads were quantified to the reference transcripts using kallisto v0.46.0.
Sequencing reads were de-multiplexed (bcl2fastq) and quantified with kallisto 0.46.0 with default parameters to the appropriate WormBase reference genome (WS245).
Assembly: WormBase reference genome (WS245)
Supplementary files format and content: H5 files for each sample
Supplementary files format and content: CPM

organism: Caenorhabditis elegans

extract_protocol:
RNA was extracted with TRIzol (Life Technologies). The RNA quality and quantity were determined with a NanoPhotometer® spectrophotometer (IMPLEN) and a Qubit® RNA Assay Kit in a Qubit® 2.0 Fluorometer (Life Technologies). The integrity of the RNA was assessed using the RNA Nano 6000 Assay Kit of a Bioanalyzer 2100 system (Agilent).
Sequencing libraries were generated using an NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.Clustering of the index-coded samples was performed on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina NovaSeq 6000 platform, and 125 bp/150 bp paired-end reads were generated.

tag: cell line

value: Whole body

tag: genotype

value: Maternal supplied B12 (8 μM）

tag: developmental stage

value: Larva 4


title: ∆nhr-114-B12-3


title: ∆nhr-114-B12-2


title: 19R548: CU-REWIRE1.0-fig3-r1

city: Shanghai

first: zefeng

last: wang

address: 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology

data_processing:
For deep sequencing analysis of targeted sites, indexs were generated using the targeted site sequence(upstream and downstream 200-nt) of each transcript.
Reads were aligned and quantified using BWA(0.7.17-r1188). Alignment BAMs were then sorted by Samtools(1.9), and RNA editing sites were analyzed using REDitools(1.2) with the following parameters: -t 20 -p -u -m20 -T6-6 -W -v 1 -n 0.0 -e -d -l.
AWK scripts were used to filtered out all the A-to-I or C-to-U conversions within the REWIRE targeting region, which were considered significant if the Fisher’s exact test yielded a p-value less than 0.05.
The mutations that appeared in control and experimental groups simultaneously were considered to be due to single nucleotide polymorphism.
Supplementary_files_format_and_content: Matrix table with the editing rate (from RNA-seq and Sanger-seq) of the on-target site of each sample

source_name: HEK293T cell

growth_protocol: 293T human embryonic kidney cell line was cultured in DMEM (high glucose) medium containing 10% fetal bovine serum (FBS, Hyclone)

extract_protocol:
The RNAs were isolated with TRIzol reagent following the manufacturer’s instructions.
Libraries were generated  using the NEBNext RNA Library  Kit (NEB, cat#E6310X, E7760L, E6609L).

treatment_protocol: To transient transfect plasmids into cells, 2μg of plasmids were transfected into cells in 6 well plate, using lipofectamine 3000 (Invitrogen) according to the manufacturer’s instruction. After 48 h, cells were collected for further analysis of RNA and protein levels.

tag: tissue

value: embryonic kidney


title: 19R201: CU-REWIRE-NLS-r3


title: 19R550: CU-REWIRE1.0-fig3-r2


title: 19R200: CU-REWIRE1.0-fig3-r3


title: 19R549: CU-REWIRE-NLS-r1


title: 19R551: CU-REWIRE-NLS-r2


title: 19R167: AI-REWIRE2.1-r3


title: 19R552: Mut.CU-REWIRE1.0-r1


title: Peripheral normal skin from donor 9709PC [PN-9709PC]

source_name: Peripheral normal skin

value: donor 9709PC

value: Peripheral normal skin


title: 19R411: AI-REWIRE2.1-r2


title: ID_006698_dFoxI_rpoE_A

country: Germany

value: 30 min + 100ng/ml anhydrotetracycline

value: carries inducible plasmid for rpoE expression


title: ID_006696_dFoxI_rpoE_ctrl_B

value: untreated


title: ID_006699_dFoxI_rpoE_B


title: ID_006695_dFoxI_rpoE_ctrl_A


title: ID_006697_dFoxI_rpoE_ctrl_C


title: ID_006667_FoxI_C4A_C

value: carries inducible plasmid for sRNA FoxI seed region mutant (C4A) expression


title: Peripheral normal skin from donor 929 [PN-929]

value: donor 929

value: psoriasis patient

value: Epidermal and dermal cells


title: ∆nhr-114-veh-3

value: Maternal supplied vehicle


title: ∆nhr-114-veh-2


title: 19R405: AI-REWIRE2.1-r1


title: DMSO, rep 1

city: Philadelphia

first: Morgan

last: Basta

state: Pennsylvania

address: 1020 Locust Street

institute: Thomas Jefferson University

description: DMSO 1

data_processing:
Raw reads were processed through Novogene in-houser perl scripts. Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Q20, Q30, and GC content of clean data were calculated and downstream analyses were performed on clean data with high quality.
Reads were mapped using Hisat2. Mapped reads of each sample were assembled by StringTie (v1.3.3b). featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0). P-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Index of reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were laigned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: tab-delimited text files include counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Gallus gallus

source_name: ocular lens

growth_protocol: Post-cataract surgery lens explants were maintained in complete media supplemented with 10% fetal bovine serum (FBS), L-glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared following Novogene's protocols and sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: Cultures were treated with DMSO or GSK-J4 every day from day 1 to day 3 post-injury

value: ocular lens

value: Vehicle (DMSO)


title: GSK-J4, rep 1

description: GSK-J4 1


title: DMSO, rep 3

description: DMSO 3


title: DMSO, rep 2

description: DMSO 2


title: GSK-J4, rep 3

description: GSK-J4 3


title: ID_006666_FoxI_C4A_B


title: GSK-J4, rep 2

description: GSK-J4 2


title: ∆nhr-114-veh-1


title: 19R404: AI-REWIRE2.0-r3


title: Peripheral normal skin from donor 8940 [PN-8940]

value: donor 8940


title: Peripheral normal skin from donor 8659ED [PN-8659ED]

value: donor 8659ED


title: Peripheral normal skin from donor 7802ED [PN-7802ED]

value: donor 7802ED


title: ID_006665_FoxI_C4A_A


title: WT-veh-3

source_name: WT

value: Whole body

value: WT

value: Larva 4


title: ID_006664_FoxI_3xCtoA_C

value: carries inducible plasmid for sRNA FoxI seed region mutant (3xC to A) expression


title: WT-veh-2


title: 19R166: AI-REWIRE2.0-r1

value: embryonic kidney


title: ID_006663_FoxI_3xCtoA_B

value: 30 min + 100ng/ml anhydrotetracycline


title: Peripheral normal skin from donor 5851 [PN-5851]

value: donor 5851

value: Peripheral normal skin


title: WT-veh-1


title: 19R547: AI-REWIRE1.1-r3


title: Peripheral normal skin from donor 369PC [PN-369PC]

value: donor 369PC


title: 19R545: AI-REWIRE1.1-r2


title: Zfp503-DCKO, scRNA-seq

city: shanghai

first: song

last: xingrui

address: Dong An Road

department: institute of brain science

institute: fudan university

library_source: transcriptomic single cell

data_processing:
cellranger mkfastq demultiplexes raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode counting, and UMI counting.
Stringtie (vetrsion: 1.3.0) was used to count the read numbers mapped to each gene, and standardrized the counts using TMM (Trimmed mean of M values)
cellranger aggr aggregates outputs from multiple runs of cellranger count, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data.
Finally, Seurat (V3) were used for the following dimensionality reduction, clustering, and gene expression.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Striatum LGE

extract_protocol: The Chromium droplet-based sequencing platform (10X Genomics) was used to generate scRNA-seq libraries, following the manufacturer’s instructions (manual document part number: CG00052 Rev C).

treatment_protocol: Embryonic mouse (E14.5) brains were quickly collected and placed in HBSS. The LGE samples were dissected and incubated in 1 mg/ml papain in HBSS for 20 min at 37 °C. The tissues were gently dissociated into a single-cell suspension by pipetting. Cells were centrifuged and washed twice, filtered through Flowmi Tip 40 μM strainers, and resuspended in HBSS+ 0.04% BSA. Cell viability was assessed by trypan blue exclusion.

value: Striatum LGE

tag: development stage

value: Embryonic day 14.5


title: 19R543: AI-REWIRE1.1-r1


title: ID_006661_FoxI_WT_C

value: carries inducible plasmid for sRNA FoxI expression


title: Peripheral normal skin from donor 31277 [PN-31277]

value: donor 31277

value: psoriasis patient

value: Epidermal and dermal cells


title: THP1-CBD_plus_cGAMP-3

first: Anjie

last: Zhen

address: 615 Charles E Young Drive

department: Medicine- Hematology/ Oncology

institute: University of California, Los Angeles

data_processing:
Raw sequence data of different treatment conditions (in triplicate) were pre-processed for quality using Fastqc.
Trimmomatic was used for adaptors and quality trimming. After this, reads were aligned onto human genome (hg38) using STAR aligner.
SAMtools was used to convert SAM files BAM files.
Mapped reads were counted across human genes by using tool featureCounts that provided raw counts data by assigning mapped reads to genes.
Differential gene expression analysis with the raw read counts data using R package DESeq2 to estimate fold change and p values.
Assembly: hg38
Supplementary files format and content: All_samples_counts.txt
Supplementary files format and content: All_samples_counts.summary.txt

source_name: Peripheral blood

growth_protocol: THP1 cells were grown in RPMI complete medium.

extract_protocol: RNA was harvested using RNeasy mini kit (Qiagen).

treatment_protocol: Cells were treated with and without CBD in the presence and absence of 2'3' cGAMP.

value: Peripheral blood

value: Monocyte

value: CBD+ 2'3'cGAMP

tag: time


title: Peripheral normal skin from donor 30696V3 [PN-30696V3]

tag: subject id

value: donor 30696V3


title: 19R410: AI-REWIRE2.0-r2


title: 19R546: AI-REWIRE1.0-r3


title: THP1-CBD_plus_cGAMP-2

value: WT


title: ID_006662_FoxI_3xCtoA_A

value: carries inducible plasmid for sRNA FoxI seed region mutant (3xC to A) expression


title: Peripheral normal skin from donor 31170 [PN-31170]

value: donor 31170

tag: subject status


title: Peripheral normal skin from donor 3696 [PN-30696]

value: donor 3696

tag: tissue type


title: 19R542: AI-REWIRE1.0-r1

value: embryonic kidney


title: Normal skin from donor AR009 [NS-AR009]

source_name: Normal skin

value: donor AR009

value: healthy donor

value: Normal skin

tag: cell type


title: ID_006659_FoxI_WT_A

value: 30 min + 100ng/ml anhydrotetracycline


title: ID_006660_FoxI_WT_B

value: carries inducible plasmid for sRNA FoxI expression


title: 19R544: AI-REWIRE1.0-r2


title: 18R348: ADAR2-Ctrl-r1


title: THP1_plus_cGAMP-2

value: 2'3' cGAMP


title: THP1_plus_cGAMP-3


title: 18R347: ADAR1-Ctrl-r1


title: Normal skin from donor AR008 [NS-AR008]

value: donor AR008


title: THP1_plus_cGAMP-1


title: THP1-CBD_plus_cGAMP-1


title: Normal skin from donor AR007 [NS-AR007]

value: donor AR007

value: Epidermal and dermal cells


title: 19R412: PUF-Ctrl-r3


title: ID_006656_FoxI_ctrl_A

value: untreated


title: ID_006657_FoxI_ctrl_B


title: ID_006658_FoxI_ctrl_C


title: THP1-CBD-3

value: Peripheral blood

value: Monocyte

value: CBD (10ug/ml)


title: Normal skin from donor AR006 [NS-AR006]

value: donor AR006


title: 19R407: PUF-Ctrl-r2


title: THP1-CBD-2

value: WT


title: ID_006654_rpoE_B

value: carries inducible plasmid for rpoE expression


title: ID_006653_rpoE_A


title: 19R406: PUF-Ctrl-r1

value: embryonic kidney


title: ID_006655_rpoE_C


title: THP1-CBD-1


title: Normal skin from donor AR005 [NS-AR005]

value: donor AR005


title: Normal skin from donor AR003 [NS-AR003]

value: donor AR003

value: healthy donor


title: ID_006652_rpoE_ctrl_C


title: Normal skin from donor AR004 [NS-AR004]

value: donor AR004

value: Normal skin


title: ID_006651_rpoE_ctrl_B


title: THP1-3

value: Ethanol


title: 19R476: HEK293T-Mock-r2


title: THP1-2


title: 19R475: HEK293T-Mock-r1


title: THP1-1


title: ID_006650_rpoE_ctrl_A


title: RNA-seq_β-actin KO-NLS-beta-actin_1

status: Public on Sep 19 2022

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Raw reads quality trimmed using trimmomatic and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using hisat2 and counts generated with htseq_count
Assembly: GRCm38 (mm10)
Supplementary files format and content: txt files containing raw counts

source_name: Mouse Embronic Fibroblast

extract_protocol: RNA extraction protocol not provided.

value: fibroblast

value: Beta-actin KO-NLS


title: RNA-seq_β-actin KO-NLS-beta-actin_2


title: RNA-seq_β-actin KO-NLS-beta-actin_3


title: 19R170: HEK293T-Mock-r3


title: WT3

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: WT.bw

library_source: genomic

data_processing:
Sequenced samples were trimmed with Trimmomatic, mapped using Bowtie2 and replicate mapped files merged with SAM tools. Coverage files were generated with deepTools. Open chromatin chromatin was detected with MACS2 using a p value < 1x10-7 and a q value of less than 0.1 and differentially regulated regions identified with CSAW using a 2-fold enrichment threshold and lower than 0.01 p value. Bed files were analyzed with Bedtools, and visualized alongside coverage files on IGV. Transcription factor enrichment was done with HOMER.
Assembly: mm10
Supplementary files format and content: Genomic tracks as BigWig files

molecule: genomic DNA

source_name: Spleen and lymph node

extract_protocol:
Libraries were prepared using the Nextera DNA library Prep Kit (Illumina) adapting a published protocol. In vitro polarized Th17 cells were washed in PBS and then lysed for 3 min in 10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2 and 0.1% Igepal CA-630, 0.1% Tween-20, 0.01% Digitonin, 1% BSA (all SIGMA). Cold wash buffer (same as lysis buffer without Igepal and digitonin) was added to the lysate and mixed three times by inverting the tubes and immediately spun 500 x g for 5 min, 4°C. Supernatant was discarded and nuclei resuspended in 2.5 μl TDE1 (Nextera Tn5, 100 nM final), 0.5 μl 1% Digitonin (0.01% final), 0.5ul 10% Tween-20 (1% final) 16.5 μl PBS and 5 μl water and incubated for 30 min at 37°C with gentle mixing (1000 RPM).
DNA was purified with the QIAGEN MinElute PCR Purification Kit (Thermo Fisher Scientific). PCR amplification was performed with the NEBNext High-Fidelity 2x PCR Master Mix (New England Labs) using custom Nextera PCR Primers containing barcodes. Adaptors were removed with AMPure XP beads according to manufacturer’s protocol. Libraries were quantified with the Qubit and sequenced with a HISeq 3000 (Illumina) at the Deep-sequencing Facility at the Max-Planck-Institute for Immunobiology and Epigenetics.

value: Spleen and lymph node

value: CD4+ T cell


title: WT2

description: WT.bw


title: SnRNAseq of striatum from SPF mice post exercise replicate 2

first: Patrick

last: Lundgren

state: PA

address: 302 Johnson Pavilion, 3610 Hamilton Walk

institute: University of Pennsylvania

data_processing:
Cellranger v3
Supplementary files format and content: mm10
Supplementary files format and content: matrix, barcodes, and gene files

source_name: Striatum

extract_protocol:
Nuclei were isolated as described in manuscript, sorted based on DAPI positivity, and loaded into 10X Genomics platform
10X Genomics according to manufacturers protocol

value: Striatum

value: Post exercise without antibiotics treatment


title: SnRNAseq of striatum from SPF mice post exercise replicate 1


title: SnRNAseq of striatum from mice treated with broad spectrum antibiotics post exercise replicate 2

value: Post exercise with antibiotics treatment


title: SnRNAseq of striatum from mice treated with broad spectrum antibiotics post exercise replicate 1


title: SnRNAseq of striatum from SPF mice without exercise replicate 1

value: Steady state without antibiotics treatment


title: OPA1_3


title: OPA1_2


title: SnRNAseq of striatum from mice treated with broad spectrum antibiotics without exercise replicate 2

value: Steady state with antibiotics treatment


title: SnRNAseq of striatum from mice treated with broad spectrum antibiotics without exercise replicate 1


title: WT_sgLKB1_3

description: Low input RNA libraries

data_processing:
Sequenced libraries were processed with deepTools, using STAR , for trimming and mapping, and featureCounts to quantify mapped reads. Raw mapped reads were processed in R (Lucent Technologies) with DESeq2.
Assembly: mm10
Supplementary files format and content: matrix of raw gene counts per sample

extract_protocol:
RNA was extracted using RNeasy Kit (QIAGEN) following the manufacturer’s instructions with an additional on-column DNase treatment using the RNAse-Free DNase set (Qiagen). RNA was quantified using Qubit 2.0 (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina) with a read depth of approximately 30 million aligned reads per sample by the Deep-sequencing Facility at the Max-Planck-Institute for Immunobiology and Epigenetics (Freiburg)

value: WT

tag: group


title: OPA1_1


title: WT_sgLKB1_1

description: Low input RNA libraries


title: w1118_embryo_oxidised_sRNA

city: Acton

first: Rippei

last: Hayashi

state: Australian Capital Territory

address: 131 Garran Road

department: John Curtin School of Medical Research

country: Australia

institute: The Australian National University

description: oxidised small RNAs (18-40nt) from w1118 embryos

data_processing:
genome_build:dm6/release 6.31
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting.  The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses.  Trimmed reads were mapped with bowtie v1.2.3 to the respective genomic sequences (allowing up to one mismatch) or transposon reference sequences (allowing up to three mismatches).  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.tile-coverage.txt: counts of piRNA (>22nt & <41nt) reads that uniquely mapped to the genomic 0.5kb tiles (allowing up to one mismatch), normalised to one million genome unique mappers
Supplementary files format and content: *.TE-mapping.txt: counts of piRNA (>22nt & <41nt) reads that mapped to the transposon reference sequences (allowing up to three mismatches, --all --best --strata option in bowtie), normalised to one million all genome mappers
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of piRNA reads (>22nt and <41nt) that are uniquely mapping to the genome

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: Flies were kept at standard conditions at room temperature.

extract_protocol:
Either ovaries or embryos were collected for the RNA extraction.  Ovaries were dissected from 3 -7 days old female flies. Embryos were collected between zero to two hours after fertilisation. Embryos were further dechorionated by 20% bleach and further rinsed by water.  Total RNA was extracted from ovaries/embryos using TRIZOL.
For oxidised small RNA libraries: Small RNAs were first size-selected by 12% w/v UREA-PAGE, and oxidised using sodium periodate.  For non-oxidised small RNA libraries: 2S rRNA was first removed from the total RNA using a biotinylated DNA ligo 'TACAACCCTCAACCATATGTAGTCCAAGCA'. 2S-rRNA-depleted total RNA was then size-selected by 12% w/v UREA-PAGE to yield the pool of small RNA.  The oxidised or unoxidised small RNAs were further size-selected by PAGE before 3' and 5' adapters were ligated.  The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the library was amplified using KAPA LongRange DNA polymerase (Sigma) with TruSeq compatible primers.

value: embryos

tag: Sex

value: pooled male and female

tag: strain

value: Oregon R

value: wild type

value: 0 - 2 hr post-fertlisation

value: unoxidised

tag: condition

value: standard food


title: tj-g4_yb-shmiR_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from ovaries depleted of Yb in the soma

source_name: ovaries

value: ovaries

value: female

value: traffic-jam::gal4 x shmiR[yb]

tag: age

value: 2 - 7 days old

tag: treatment

value: oxidised


title: WT_Control_3

description: Low input RNA libraries

value: Spleen and lymph node

value: CD4+ T cell

value: Control


title: WT_Control_2

description: Low input RNA libraries


title: tj-g4_control_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from ovaries of a control knockdown

value: traffic-jam::gal4 x w1118


title: w1118_ovary_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from w1118 ovaries


title: OPA1_sglkB1_3

description: Low input RNA libraries


title: WT_Control_1

description: Low input RNA libraries

value: WT


title: OPC Neuroepithelium, Ventral, rep3

city: Mississauga

first: Priscilla

last: Valentino

state: ON

address: 3359 Mississauga Rd

country: Canada

institute: University of Toronto

description: processed read counts in column "V3" of supplementary files.

data_processing:
Nextera adaptors and low quality bases were trimmed with trimmomatic (Galaxy, 0.36.6) using the following parameters: SLIDINGWINDOW:4:20, LEADING:20, TRAILING:20, MINLEN:30.
Reads were mapped with RNA Star (Galaxy, 2.6.0b-1) to the dm6 genome using the BDGP 6.31 gene model and the following parameters: --sjdbOverhang 125.
featureCounts (Galaxy, version 1.6.3+galaxy2) was used to assign reads to genes using the BDGP 6.31 gene model and the following parameters: -s no -Q 10. Multi-mapped reads were discarded from downstream analysis.
DESeq2 (Galaxy, version 2.11.40.2) was used to normalize read counts and perform comparative analyses between samples.
Assembly: D.melanogaster genome assembly model: BDGP 6.31
Supplementary files format and content: featurecounts_allsamples_rawcounts.txt.gz - tab delimited file of raw counts (featurecounts output)
Supplementary files format and content: DESeq2_allsamples_normalizedcounts.txt.gz - tab delimited file of normalized counts (DESeq2 output)

source_name: larval OPC neuroepithelium

growth_protocol: raised at 25°C on standard cornmeal food

extract_protocol:
Late L2 female larval brains were dissected in 1xPBS and mounted in a dish, and kept immersed in 1xPBS. GFP-labeled OPC neuroepithelial cells were manually extracted from brains using a glass micropipette over the course of 1h. Cells were ejected into a PCR tube containing PBS and flash frozen after collection. Cell samples from 3-4 brains were pooled together for mRNA extraction and library preparation. mRNA was extracted and purified using the SMART-Seq v4 Ultra Low Input RNA kit (Takara, #634894).
Nextera XT DNA Library Preparation kit (Illumina, FC-131-1024) was used to prepare the library from the extracted mRNA.

value: larval OPC neuroepithelium

value: late L2


title: OPC Neuroepithelium, Ventral, rep2

description: processed read counts in column "V2" of supplementary files.


title: OPC Neuroepithelium, Ventral, rep1

description: processed read counts in column "V1" of supplementary files.


title: WT1

description: WT.bw


title: SnRNAseq of striatum from SPF mice without exercise replicate 2

value: Striatum

value: Steady state without antibiotics treatment


title: OPC Neuroepithelium, Dorsal, rep3

description: processed read counts in column "D3" of supplementary files.


title: OPC Neuroepithelium, Dorsal, rep2

description: processed read counts in column "D2" of supplementary files.


title: OPA1_Control_3

description: Low input RNA libraries


title: OPA1_sgLKB1_2

description: Low input RNA libraries


title: OPC Neuroepithelium, Dorsal, rep1

description: Processed read counts in column "D1" of supplementary files.


title: OPA1_sgLKB1_1

description: Low input RNA libraries


title: WT_sgLKB1_2

description: Low input RNA libraries


title: OPA1_Control_2

description: Low input RNA libraries


title: Whole ovarian tissue [96h Upd+lgl-KD replicate 2]

city: New Orleans

first: Wu-Min

last: Deng

state: LA

address: 1700 Tulane Avenue

department: School of Medicine, Department of Biochemistry

institute: Tulane University

data_processing:
Illumina Casava1.7 software used for base-calling
Single-ended fastq files for the whole-tissue RNA-Seq samples were aligned to Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using STAR (v2.7) aligner. featureCounts (Subread package) was run on individual bam files for the generation of count-matrix.
Genome index for single-cell analysis was built using the Drosophila melanogaster Release 6 (Drosophila_melanogaster.BDGP6.28.100.chr_filtered.gtf) reference genome assembly using 10X genomics cellranger (version 3.0.1) mkref pipeline. Sequenced reads were then mapped to this reference genome index. The cellranger count pipeline for alignment, filtering, barcode counting and UMI counting was used to generate the multidimensional feature-barcode matrix for single-cell RNA-Seq datasets.
Genome_build: dm6
Supplementary_files_format_and_content: csv files contain raw counts for each whole-genome RNA Seq sample.
Supplementary_files_format_and_content: Loom file generated after velocyto processing of the 3 files (barcodes.tsv, features.tsv and matrix.mtx) obtained from the standard cellranger pipeline for each single-cell RNA-Seq dataset. All these files are readable in R and were processed using the Seurat pipeline which resulted in the individual rds files for each dataset.

source_name: Whole ovarian tissue

growth_protocol: 100 adult ovaries from 50 female Drosophila melanogaster flies maintained at 25°C, with access to males and yeast supplements for 3 days

extract_protocol:
For bulk-RNA sequencing: Whole ovaries were extracted from 40 females in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS. The anterior part of the ovaries were carefully removed before stage 10 egg chambers. Samples were transferred to a steril Eppendorf tube and media was aspirated. Samples were flash frozen using liquid nitrogen and stored until day of the library preparation in -80°C. Total RNA was extracted using Trizol. For single-cell RNA sequencing: Whole ovaries were extracted from female flies that were dissected in complete medium (Grace’s Insect Basal Medium supplemented with 15% FBS) and were transferred to a tube containing 300 μL EBSS (no calcium, magnesium, and phenol red), followed by a gentle wash for 2 minutes. The EBSS was then removed and the tissue was dissociated in 100 μL Papain (50 U/mL in EBSS and previously heat activated in 37°C for 15 minutes) for 30 minutes. The suspension was mechanically dissociated every 3 minutes by gentle pipetting up and down. To quench the digestion, 500 μL complete medium was added to dissociated cells. The suspension was then passed through a 40 μL sterile cell strainer and centrifuged for 10 minutes at 700 RCF to remove large eggs with intact eggshell which cannot be dissociated and debris. Supernatant was removed and single cells were re-suspended in 100 μL. Cell viability was assayed using Trypan Blue and estimates of cell concentration were made using a hemocytometer. Cells were then further diluted to an approximate, final concentration of 2,000 cells/μL according to 10X Genomics recommendations.
Bulk sequencing libraries were made using the Ultra II Directional RNA library prep kit for Illumina using the protocol for NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB#E7490). Single-cell libraries were prepared using the Single Cell 3’ Library & Gel Bead Kit v2 and Chip Kit according to the recommended 10X Genomics protocol. Single cell suspension was loaded onto the Chromium Controller (10X Genomics). Library quantification assays and quality check analysis was performed using the 2100 Bioanalyzer instrument (Agilent Technologies). The library samples were then diluted to a 10nM concentration and loaded onto two lanes of the Illumina Hi-Seq 2500 (bulk RNA-Seq) and Illumina NovaSeq 6000 (single-cell RNA-Seq) instrument flow cell for a 100-cycle sequencing run.

treatment_protocol: Flies were transferred to 29°C incubator for 1 (24h), 3 (72h) and 4 (96h) days depending on the dataset, and were subsequently dissected.

value: Ovary

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-Upd, UAS-Dcr2

value: 4 day in 29°C


title: Whole ovarian tissue [24h Upd+lgl-KD replicate 2]

value: 1 day in 29°C


title: Whole ovarian tissue [96h Upd+lgl-KD replicate 1]


title: 24_Th17_OPA1_4

data_processing:
Sequenced libraries were processed with deepTools, using STAR, for trimming and mapping, and feature Counts to quantify mapped reads.
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 to generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute) and determine differentially expressed genes with greater than 2 fold change and lower than 0.05 adjusted P value.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is a matrix with raw counts for features in samples, obtained with featureCounts.

growth_protocol: CD4+ T cells were isolated from cell suspensions from spleen and peripheral lymph nodes (LN) from mice from the indicated genotypes. Pooled spleen and LN single cell suspensions were incubated with biotinylated antibodies against mouse CD44, CD25, CD8, IgM, B220, CD19, Gr-1, MHC-II, F4/80, CD11c, CD11b and DX5 (Biolegend), followed by negative selection using magnetic beads (Stem cell Technology). Approximately 0.3 x 106 naive CD4+ T cells were plated into 48-well-plates coated with 5 μg ml−1 anti-mouse CD3 (clone 17A2, BioXcell), 2 μg ml−1 soluble anti-mouse CD28 (clone 37.51, BioXcell) in RPMI 1640 (Gibco) supplemented with 10% fetal calf serum (Gibco), 1% (v/v) penicillin–streptomycin (Invitrogen), 55 μM β-mercaptoethanol (Sigma), 1 mM Sodium Pyruvate, 2 mM glutamine and 5 mM Hepes.

extract_protocol:
RNA was extracted using RNeasy Kit (QIAGEN) following the manufacturer’s instructions with an additional on-column DNase treatment using the RNAse-Free DNase set (Qiagen). RNA was quantified using Qubit 2.0 (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq stranded mRNA kit (Illumina) and sequenced in a HISeq 3000 (Illumina)

treatment_protocol: For Th17 conditions, TGF-β (5 ng ml-1), IL-6 (10 ng ml-1), IL-1β (10 ng ml-1), anti-mouse IFN-γ (10 μg ml-1) and anti-mouse IL-4 (10 μg ml-1) were included in cell cultures.

tag: strain background

value: spleen and peripheral lymph nodes (LN)

value: CD4+ T cells


title: Whole ovarian tissue [24h Upd+lgl-KD replicate 1]


title: 21_Th17_OPA1_1


title: 20_Th17_WT4

value: Wt


title: 22_Th17_OPA1_2


title: Whole ovarian tissue [96h NICD+lgl-KD replicate 1]

value: tj>GAL4, UAS-Gal80TS>UAS-lglRNAi, UAS-NICD, UAS-Dcr2


title: 18_Th17_WT2


title: Whole ovarian tissue [24h NICD+lgl-KD replicate 1]


title: Whole ovarian tissue [96h NICD replicate 1]

value: tj>GAL4, UAS-Gal80TS>UAS-NICD


title: Whole ovarian tissue [24h NICD replicate 2]


title: 19_Th17_WT3


title: Whole ovarian tissue [24h NICD+lgl-KD replicate 2]


title: 17_Th17_WT1


title: OPA1_Control_1

description: Low input RNA libraries

value: Spleen and lymph node

value: CD4+ T cell

value: Control


title: Whole ovarian tissue [24h Upd replicate 2]

value: tj>GAL4, UAS-Gal80TS>UAS-Upd


title: C6 Control rep2

city: Haikou City

first: Jianqiang

last: Chen

state: Hainan Province

address: 43 People's Avenue, Meilan District, Haikou City, Hainan Province

institute: Haikou People 's Hospital

data_processing:
The sequencing quality was examined using FastQC software (v0.11.2). Reads containing adapter, reads containing ploy-N and low-quality reads from raw reads were removed to obtain filtered reads with Trimmomatic (v0.36) (Bolger, Lohse et al. 2014). All the downstream analyses were based on the filtered reads with high quality and at least 75 bp.
The paired-end filtered reads were aligned to the rat reference genome (rn6) using STAR (v2.5.1b) (Dobin, Davis et al. 2013).
The gene expression quantification was conducted using RSEM (v1.2.29) (Li and Dewey 2011). Only genes with average TPM (Transcripts Per Million) value greater than 1 in at least one group of samples were considered expressed and used for the differential expression analysis.
Differentially expressed genes (DEGs), defined as genes with fold change (FC) > 2 and FDR < 0.05, were identified using DESeq2 package (v 1.14.1) (Love, Huber et al. 2014).
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited gene expression values (RSEM read counts)

organism: Rattus norvegicus

source_name: C6 cell line

extract_protocol:
Total RNA was extracted using Trizol (Invitrogene, Lot# 15596-018) and genomic DNA contamination removed with RNase-free DNase I (Transgen, Code#GD201-01) following the manufacturer’s protocols. RNA degradation and contamination were monitored on 1% agarose gels. RNA was reverse-transcribed into cDNA using the M-MLV Reverse Transcriptase (Promega, Lot# M5301).
10ng of total RNA were reverse transcribed and amplified using the Ovation RNA-seq System V2 (Nugen). Libraries were constructed from 100ng of sonicated cDNA (Covaris) using the Ovation Ultra Low DR Multiplex system (Nugen). The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina HiSeq 2500 platform, obtaining 100-nucleotide single reads.

tag: cell line

value: control


title: C6 Control rep1

tag: genotype


title: Whole ovarian tissue [24h Upd replicate 1]


title: C6 AQP1 rep1

value: overexpress Aqp1


title: C6 Control rep3


title: Whole ovarian tissue [96h Upd replicate 1]


title: 23_Th17_OPA1_3


title: Whole ovarian tissue [96h Upd replicate 2]


title: C6 AQP1 rep2


title: C6 AQP1 rep3


title: Whole ovarian tissue [96h NICD+lgl-KD replicate 2]


title: E9H1_rep2

city: Piscataway

last: Rongo

state: NJ

address: 190 Frelinghuysen Road, #163

department: Waksman Institute

institute: Rutgers University

data_processing:
Libraries were sequenced across two lanes on an Illumina HiSeq2000 (GeneWiz) or an Illumina HiSeq 2500 in Rapid Run Mode (RUCDR).
Raw sequences were aligned using STAR 2.5.1a and gene counts, normalization and statistical analysis on gene counts were performed with EdgeR using generalized linear model functionality and tagwise dispersion estimates. Likelihood ratio tests were conducted in a pairwise fashion between genotypes with a Benjamini and Hochberg correction. Genes were considered to be HIF-1-dependent if they were differentially expressed with an FDR<0.01 in the same direction (up or down) in all four of the following pairwise comparisons: (1) egl-9 vs. N2; (2) egl-9 vs. egl-9 hif-1; (3) odIs131; egl-9 vs. N2; (4) odIs131; egl-9 vs. egl-9 hif-1. These pairwise comparisons are in the attached .xlsx file named "DEGenes_All samples and comparisons.xlsx" . This file includes ALL gene fold changes (log2FC) and corresponding p-values and FDR vaues.
Genome_build: WS245/WbCel235
Supplementary_files_format_and_content: EdgeR Excel File with differential gene expression

source_name: Whole Worm RNA extract

growth_protocol: Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults and embryos hatched overnight for 15-17 hours in M9.  Starvation-arrested L1s were plated on NGM plates and grown at 20°C until L4 stage.

extract_protocol:
Total RNA was isolated from animals using Trizol (Invitrogen) combined with Bead Beater lysis in four biological replicates for each genotype.
An mRNA library (single-end, 50-bp reads) was prepared for each sample/replicate using Illumina Truseq with PolyA selection

tag: gentoye


title: Whole ovarian tissue [96h NICD replicate 2]

tag: tissue


title: Whole ovarian tissue [96h lgl-KD replicate 1]


title: Whole ovarian tissue [24h lgl-KD replicate 2]


title: E9_rep2


title: E9H1_rep1


title: Whole ovarian tissue [24h NICD replicate 1]


title: Papaya, 1B, Unripe, bio rep 3

city: Brisbane

first: ziwei

last: zhou

state: QUEENSLAND

address: 170 Kessels Rd, Nathan

institute: Griffith University

data_processing:
The raw sequencing data was processed to remove adaptors, as well as low quality bases/reads using bbduk (from BBMap v38.34) followed with Trimmomatic (v0.40) and FastQC (v0.11.9)
Assembly: Trinity (v2.11.0) was then applied on the clean reads to de novo assemble the full transcriptome of ‘RB1’ and ‘1B’
Supplementary files format and content: Sample-related biases were identified through variance-stabilising transformation of the raw counts of reads and plotted into a between-sample distance matrix.

organism: Carica papaya

source_name: fruit

extract_protocol:
RNA was extracted from papaya flesh using NucleoZOL (Machery-Nagel Inc. USA) from approximately 50 mg of fruit flesh per sample according to the manufacturer’s instructions.
A total amount of 2 µg of the high-quality RNA per sample of ‘RB1’ and ‘1B’ were sequenced using an Illumina Sequencing platform. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.

value: fruit

tag: cultivar

tag: phenotype

value: bitter flavour and musty aroma

value: Unripe stage


title: Whole ovarian tissue [96h control replicate 1]

value: Ovary

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-GFP


title: Hif1_rep2


title: Whole ovarian tissue [24h control replicate 2]

value: 1 day in 29°C


title: Whole ovarian tissue [24h control replicate 1]


title: Whole ovarian tissue [96h lgl-KD replicate 2]

value: 4 day in 29°C


title: N2_rep2

value: wild-type


title: Papaya, 1B, Unripe, bio rep 1

tag: time


title: N2_rep1

value: Wild-type


title: Papaya, 1B, Unripe, bio rep 2


title: E9_rep1


title: Papaya, 1B, Ripe, bio rep 2

value: Ripe stage


title: G_b

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
The read pairs were mapped to the human reference genome (GRCh38) with STAR aligner (Dobin et al., 2013).
Gene expression was counted from read pairs mapping to exons using featureCount in Rsubreads (Liao, Smyth and Shi, 2019). Duplicates, chimeric and multimapping reads were excluded, as well as reads with low mapping score (MAPQ < 10).
The read count data was analyzed with DESeq2 (Love, Huber and Anders, 2014).
We analyzed the effect differentiation as a function of time (from stage1, stage4 to stage7). We omitted the graft samples as those were deemed physiologically dissimilar to prior graft samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: DE_ultradeep.csv: DESeq2 results and read counts.

source_name: iPS derived pancreatic cells

growth_protocol: Human iPSC line HEL46.11 (derived from human neonatal foreskin fibroblast) were reprogrammed using Sendai virus technology as described elsewhere (Trokovic et al., 2015). The cells were differentiated using a 17-day protocol (see Figure 1A) described earlier (Toivonen et al., 2013).

extract_protocol:
RNA was purified using AllPrep DNA/RNA Mini Kit according to manufacturer’s guide (Qiagen).
Directional RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacturer’s guide.
Sequencing was performed using Illumina HiSeq 2500 (with chemistry v4) at Eurofins Genomics.

treatment_protocol: We performed bulk RNA-seq analysis for the HEL46.11 derived stage 1 (DE), stage 4 (PP) and stage 7 (SC-islets).

tag: developmental stage

value: graft

tag: replicate

value: b


title: Papaya, 1B, Ripe, bio rep 3


title: G_c

tag: cell type

value: c


title: G_a

value: a


title: S7_e

value: control

value: stage 7

value: SC-islets

value: e


title: SLO_P3_memB_IGHC

city: Leiden

first: Mirjam

last: van der Burg

address: Albinusdreef 2

country: Netherlands

institute: LUMC

data_processing:
454 sequences were demultiplexed based on their multiplex identifier sequence and 40 nucleotides trimmed from both sides to remove the primer sequence using the ARGalaxy demultiplex tool. Illumina FASTQ files were paired (PEAR), demultiplexed, trimmed with cutadapt  and converted into FASTA files. FASTA files from both 454 and Illumina data were analyzed using IMGT/High-V-Quest (Alamyar E, Duroux P, Lefranc MP, Giudicelli V. IMGT((R)) tools for the nucleotide analysis of immunoglobulin (IG) and T cell receptor (TR) V-(D)-J repertoires, polymorphisms, and IG mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS. Methods Mol Biol. 2012;882:569-604)
Assembly: GRCh38
Supplementary files format and content: IMGT-HighVQuest output Summary file:
Library strategy: Amplicon-seq

source_name: Secondary Lymphoid organ

extract_protocol:
RNA was isolated using RNeasy Plus Kits (Qiagen) and transcribed into cDNA using random hexamer primers and Superscript III® (both Invitrogen).
Amplicon-seq: IGH transcripts of the SLO samples were amplified from 5µl cDNA per reaction in a multiplex PCR using the forward VH1-6 FR1 (BIOMED-2) primers and the CgCH1, the IGHA or the IGHM reverse primer (sequence available upon request). These PCR products were purified and sequenced using Roche 454 sequencing as previously described
Amplicon-seq: IGH transcripts of the PBMC samples were amplified using the forward VH1-6 FR1 (BIOMED-2) primers and costum IGHG, IGHA and IGHM reverse primers (sequence available upon request). PCR products were purified and sequenced using 2x300 Illumina sequencing (Illumina).

treatment_protocol:
Secondairy Lymphoid Organ samples of 3 CVID patients (P1-3) and 3 healthy donors (HAD, HDB, HDC) were flow sorted into 5 B-cell subsets: naïve, centroblasts (CB), centrocytes (CC), memory B-cells (Mem B) and plasmablasts (PB)
Peripheral blood mononuclear cell samples of 2 CVID patients (P1,2) and 3 healthy donors (HDL, HDM, HDR) were flow sorted into 4 B-cell subsets: naïve, natural effector B-cells (NE),  memory B-cells (Mem B) and plasmablasts (PB)

value: Secondary Lymphoid organ

value: memory B cells

tag: primers

value: IGM and IGG and IGA


title: G_d

value: d


title: SLO_P3_PB_IGHC

value: plasmablasts


title: S7_d


title: Whole ovarian tissue [96h control replicate 2]

value: Ovary

value: 3 days after eclosion

value: tj>GAL4, UAS-Gal80TS>UAS-GFP

value: 4 day in 29°C


title: Hif1_rep1

first: Christopher


title: S7_c


title: Papaya, RB1, Unripe, bio rep 3

value: fruit

value: sweet flavour and floral aroma

value: Unripe stage


title: SLO_P3_CC_IGHC

value: centrocytes


title: S7_b

value: control

value: b


title: Papaya, 1B, Ripe, bio rep 1

value: bitter flavour and musty aroma

value: Ripe stage


title: G_e

value: graft

value: e


title: S4_e

value: stage 4

value: pancreatic progenitor


title: S4_d

value: d


title: S7_a

value: stage 7

value: SC-islets

value: a


title: SLO_P3_CB_IGHC

value: Secondary Lymphoid organ

value: centroblasts

value: IGM and IGG and IGA


title: Papaya, RB1, Unripe, bio rep 2

value: fruit

value: sweet flavour and floral aroma

value: Unripe stage


title: S4_c

value: control

value: c


title: S4_b

value: b


title: Papaya, RB1, Unripe, bio rep 1


title: S4_a


title: DE_e

value: stage 1

value: DE


title: Whole ovarian tissue [24h lgl-KD replicate 1]

value: Ovary

value: 3 days after eclosion

value: 1 day in 29°C


title: Papaya, RB1, Ripe, bio rep 3

value: Ripe stage


title: DE_d

value: d


title: DE_b


title: SLO_P2_PB_IGHC

value: plasmablasts


title: SLO_P2_Naive_IGHCM

value: Secondary Lymphoid organ

value: naive

value: IGM


title: SLO_P2_CC_IGHC

value: centrocytes

value: IGM and IGG and IGA


title: DE_c


title: Papaya, RB1, Ripe, bio rep 1

value: fruit

value: sweet flavour and floral aroma


title: Papaya, RB1, Ripe, bio rep 2


title: DE_a

value: control

value: a


title: SLO_P1_naive_IGHM


title: SLO_P2_CB_IGHC

value: centroblasts


title: RIP_Input

city: Jinan

first: Zixiang

last: Wang

state: Shandong

address: No.44 Wenhuaxi Road

department: Cheeloo College of Medicine

institute: Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were filtered to obtain clean reads after removal of reads containing adapter and at low quality using Trimmomatic. rRNA sequences were removed before alignment.
High-quality reads were mapped to the human reference genome hg19 using Tophat (v2.0.13).
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded.
FeatureCounts was used to perform expression level for RNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts and FPKM for every gene.

source_name: HEY

extract_protocol:
RNA was extracted with Phenol/Chloroform/Isoamyl Alcohol (125:24:1 Mixture).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEY cells were collected for the RIP assay, which was performed using the EZ-Nuclear RIP Kit (17-701, Merck Millipore) following the manufacturer's instructions.

value: HEY

value: serous ovarian cancer cell line


title: TYK2-S6-2

data_processing:
The raw data was filtered with cutadapt (Martin, 2011) to remove adapter sequences, ambiguous (N) and low quality bases (Phred score < 25). We also excluded read pairs that were too short (<25bp) after trimming.
The filtered reads were mapped to the human reference genome (GRCh38) with STAR aligner (Dobin et al., 2013).
Gene expression was counted from read pairs mapping to exons using featureCount in Rsubreads (Liao, Smyth and Shi, 2019). Duplicates, chimeric and multimapping reads were excluded, as well as reads with low mapping score (MAPQ < 10).
The read count data was analyzed with DESeq2 (Love, Huber and Anders, 2014). We analyzed the effect of TYK2 knockout separately for each developmental stage (iPS, stage4, stage5, stage6).
Genome_build: GRCh38
Supplementary_files_format_and_content: DE_results.csv: DESeq2 results and read counts.

treatment_protocol: We performed bulk RNA-seq analysis for stage 0 (iPSCs), stage 4 (PP), stage 5 (EP) and stage 6 (EC). For TYK2 knockout the ATG starting codon containing third exon was deleted using two CRISPR/Cas9 guides.

value: TYK2 knockout

value: endocrine cells


title: RIP_BUD31

tag: antibody


title: CNT-S6-3


title: TYK2-S6-1


title: TYK2-S6-3


title: CNT-S6-1


title: CNT-S6-2


title: SLO_P1_memB_IGH

value: memory B cells


title: Lx8-SINE B2_KD_batch1 rep2

city: Tianjin

first: Xuan

last: Zhao

state: Tianjin

address: No. 38 Tongyan Road, Haihe Education Park, Tianjin

department: State Key Laboratory of Medicinal Chemical Biology

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Hisat2.
Raw count were generated by featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include raw count values for each Sample.

source_name: Embryonic stem cell

growth_protocol: Mouse E14 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with 15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara) and was subjected to DNase Ｉ(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: We used pSuper puro to knockdown Lx8-SINE B2 in embryonic stem cells. The shRNA of Lx8-SINE B2 was cloned into pSuper puro vector. WT ESCs were transfected with 1000ng pSuper puro vector. After transfection for 24h, the cells were selected with 1ug/ml puromycine for 3days and the medium were changed every 24h.

tag: strain

value: knocked down


title: SLO_P2_memB_IGHC


title: TYK2-S5-3

value: endocrine progenitor


title: TYK2-S5-2


title: TYK2-S5-1


title: SLO_P1_PB_IGHMA

value: Secondary Lymphoid organ

value: plasmablasts

value: IGM AND IGA


title: Lx8-SINE B2_Control rep2

value: wild type


title: SLO_P1_PB_IGHCG

value: IGG


title: CNT-S5-2


title: Lx8-SINE B2_KD_batch1 rep1


title: SLO_P1_CC_IGH

value: centrocytes

value: IGM and IGG and IGA


title: CNT-S5-1

value: control


title: TYK2-S4-3

value: pancreatic progenitor


title: SLO_P1_CB_IGH

value: centroblasts

value: IGG and IGG and IGA


title: TYK2-S4-1


title: TYK2-S4-2


title: Normal skin from donor AR001 [NS-AR001]

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

institute: UCLA

data_processing:
Libraries were sequenced using a NovaSeq6000 SP 100-cycle flow cell (Illumina).
Fastq files were generated using Cellranger mkfastq (version 4.0.0). The raw reads were mapped to the  human genome (hg38) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with raw gene counts for every gene and every cell

extract_protocol:
6-mm punch biopsies were taken from healthy skin from healthy donors, lesional and non-lesional skin from psoriasis patients.
Samples were incubated overnight in 0.4% dispase (Life Technologies) in Hank’s Balanced Saline Solution (Gibco) at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.25% Trypsin-EDTA (Gibco) with 10U/mL DNase I (Thermo Scientific) for 1 hour at 37°C, quenched with FBS (Atlanta Biologicals), and strained through a 70μM mesh. Dermis was minced, digested in 0.2% Collagenase II (Life Technologies) and 0.2% Collagenase V (Sigma) in plain medium for 1.5 hours at 37°C, and strained through a 70μM mesh. Epidermal and dermal cells were combined in 1:1 ratio and libraries were constructed by the University of Michigan Advanced Genomics Core on the 10X Chromium system.

tag: subject id

value: donor AR001

tag: subject status

value: healthy donor

tag: tissue type

value: Normal skin

value: Epidermal and dermal cells


title: CNT-S4-3


title: Lx8-SINE B2_Control rep1


title: SLO_HDC_naive_IGHM

value: naive B cells

value: IGM


title: CNT-S4-1


title: SLO_HDC_memB_IGHG

value: Secondary Lymphoid organ

value: memory B cells


title: CNT-S4-2


title: Itgb1-WT-Transitional B cells - LY294002-144

city: Freiburg

first: Senthilkumar

last: Ramamoorthy

address: Stübeweg 51

department: Cellular & Molecular Immunology

institute: Max Planck Institute of Immunobiology and Epigenetics

description: Gene expression profile of Itgb1-wt transitional B cells cultured on OP9-Dll1 cells and treatedd with LY294002 -Rep1

data_processing:
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.20.0.422).
The paired-end RNA-seq datasets were were trimmed using trimgalore and mapped to the mouse reference genome (mm10) using STAR aligner (2.5.3a).
The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm10) was calculated by Cuffquant. The differential gene expression between the conditions was calculated by using Cuffdiff.
The differentially expressed genes were filtered with the q-value cut-off <0.05 following Benjamini–Hochberg multiple testing correction of the original p-values. The gene sets were further filtered for more than two-fold up or down regulation.
Assembly: mm10
Supplementary files format and content: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) are provided in TXT format.

source_name: Spleen

growth_protocol: OP9-Dll1 or control OP9 cells were grown to 80% confluence in 24-well plates in optimized medium (α-MEM supplemented with 20% FCS). For the PI3K inhibitor assay, CD93+ (AA4.1+) transitional B cells were incubated with DMSO or PI3K inhibitor (10 μM) (LY294002; Cell signaling Technology) for 30 min at 37°C. For enrichment of transitional B cells, red cell lysis was performed first on spleen suspensions. Cells were washed, incubated first with anti-CD19 magnetic beads, sorted using LS columns, and later incubated with anti-CD93 magnetic beads to be sorted again with LS columns (beads and columns from Miltenyi Biotec). Subsequently, 5x105 magnetically enriched CD19+CD93+ (AA4.1+)transitional B cells were added to the OP9 cells, in a new optimized medium (IMDM supplemented with 10% FCS). The B cell growth and survival factor BAFF (10 ng/ml; R&D Systems) was added to maintain cell survival, and cells were harvested for flow cytometry analysis 3 days later.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
The total mRNA was enriched by OligodT magnetic beads. The libraries were prepared by using a TruSeq Stranded mRNA library preparation kit using the NEB Next Low Input RNA Library preparation protocol.

treatment_protocol: For the PI3K inhibitor experiments, CD93+ (AA4.1+) transitional B cells were incubated with DMSO or PI3K inhibitor (10 μM) (LY294002; Cell signaling Technology) for 30 min at 37°C. Cells were washed and cultured in OP9-DLL1 cells as described.

value: Spleen

value: Transitional B cells cultured on OP9-Dll1 stromal cells

value: Itgb1+/+ Cd21Cre

tag: treatment


title: Itgb1-KO-Transitional B cells - LY294002-162

description: Gene expression profile of Itgb1-ko transitional B cells cultured on OP9-Dll1 cells and treatedd with LY294002 -Rep2

value: Itgb1fl/fl Cd21Cre


title: Itgb1-KO-Transitional B cells - LY294002-156

description: Gene expression profile of Itgb1-ko transitional B cells cultured on OP9-Dll1 cells and treatedd with LY294002 -Rep1


title: Itgb1-WT-Transitional B cells - LY294002-150

description: Gene expression profile of Itgb1-wt transitional B cells cultured on OP9-Dll1 cells and treatedd with LY294002 -Rep2


title: TYK2-D0-2

value: TYK2 knockout

value: stage0 (undifferentiated)

value: iPSC


title: SLO_HDC_CC_IGHC

value: centrocytes

value: IGM and IGG and IGA


title: TYK2-D0-3


title: TYK2-D0-1


title: CNT-D0-3

value: control


title: Itgb1-KO-Transitional B cells - DMSO-162

description: Gene expression profile of Itgb1-ko transitional B cells cultured on OP9-Dll1 cells and treatedd with DMSO -Rep2

value: DMSO


title: CNT-S5-3

value: endocrine progenitor


title: CNT-D0-1


title: SLO_HDB_memB_IGHC


title: Spy_re1

description: nuclear RNA

data_processing:
The adaptor sequence or low-quality reads was removed with trimgalore (version 0.6.1). Quality of clean reads were checked with FastQC (version 0.11.9).
rRNA sequences were removed with bowtie (1.2.3)(Langmead et al., 2009).
The remaining reads were mapped to the human genome (hg38) using STAR program (2.7.1a) (Dobin et al., 2013) with -outFilterMultimapScoreRange 1 -outFilterScoreMin 10 -outFilterMultimapNmax 1.
PCR duplicates of uniquely mapped reads were removed using Picard (version 2.25.5) (http://broadinstitute.github.io/picard/) with MarkDuplicates REMOVE_DUPLICATES=true. Sequencing saturation was examined with Qualimap (version 2.2.2)(García-Alcalde et al., 2012).
Two replicates of SpyCLIP samples were merged together for PURECLIP (version 1.2.0)(Krakau et al., 2017) analysis with -ld -nt 16 -dm 80.
Genome_build: hg38
Supplementary_files_format_and_content: Narrowpeak file of crosslink regions identifed by PURECLIP.

growth_protocol: SpyCLIP was perform according to previous study (Zhao et al., 2019) with several modifications. Briefly, HEY cell lines transfected with dox-inducible SpyTag-FLAG-BUD31 expression lentivirus were induced with doxycycline for 72 h before harvest.

extract_protocol:
RNA was purified and concentrated with Spin Column RNA Cleanup & Concentration Kit (Sangon).
Sequencing library was constructed with NEBNext Ultra RNA Library Prep Kit for Illumina.
High-throughput sequencing of SpyCLIP libraries was performed on the HiSeq 2500 with PE150 sequencing strategy (Novogene).

treatment_protocol: Cells were crosslinked and irradiated at 400 mJ/cm2 in a UV Crosslinker (UVP, CL-1000).  Cell nucleus was isolated with Nucleoprotein Extraction Kit (Sangon) before lysis. Turbo DNase (2 U /μl, Invitrogen, AM2238) and 1:200 diluted RNase I (100 U/μl, Invitrogen, AM2295) were used to remove DNA and fragment RNA. The mixed lysate was incubated with anti-FLAG magnetic beads (MBL, M185-11) at 25 °C for 40 min. After remove RNA binding protein from FLAG beads with phosphoserine phosphatase, the mixture was incubated with pre-washed fresh SpyCatcher beads at 25 °C for 1 hour. Stringent washes were conducted according to instruction and digested the beads with proteinase K (Roche, 3115828001).

tag: cell line

value: HEY

value: serous ovarian cancer cell line

value: Spy


title: CNT-D0-2

tag: genotype


title: SLO_HDB_naive_IGHCM

value: Secondary Lymphoid organ

value: naive

value: IGM


title: Itgb1-WT-Transitional B cells - DMSO-150

description: Gene expression profile of Itgb1-wt transitional B cells cultured on OP9-Dll1 cells and treatedd with DMSO -Rep2

value: Spleen

value: Transitional B cells cultured on OP9-Dll1 stromal cells


title: Itgb1-KO-Transitional B cells - DMSO-156

description: Gene expression profile of Itgb1-ko transitional B cells cultured on OP9-Dll1 cells and treatedd with DMSO -Rep1

value: Itgb1fl/fl Cd21Cre


title: SLO_HDC_CB_IGHC

value: centroblasts


title: CHLA-266_KD_3

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

institute: Universitätsklinikum des Saarlandes

data_processing:
Fastq files were imported into Partek Flow (Partek Incorporated, Missouri, USA).
Quality analysis and quality control were performed on all reads to assess read quality and to determine the amount of trimming required (both ends: 13 bases 5´and 1 base 3´).
trimmed reads using STAR v2.4.1d aligner and were further aligned against the Mmu10 genome using the STAR v2.4.1d aligner. Unaligned reads were further processed using Bowtie 2 v2.2.5 aligner.
Aligned reads were combined before quantifying the expression against the ENSEMBL (release 95) database by the Partek Expectation-Maximization algorithm using the counts per million normalization.
Genes with missing values and with a mean expression less than one were filtered out
Genome_build: HG38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was isolated using Qiagen kit
500 ng total RNA was processed using the TruSeq RNA Sample Preparation v2 Kit (low-throughput protocol; Illumina, San Diego, USA) to prepare the barcoded libraries.
Libraries were validated and quantified using DNA 1000 and high-sensitivity chips on a Bioanalyzer (Agilent, Böblingen, Germany); 7.5 pM denatured libraries were used as input into cBot (Illumina), followed by deep sequencing using HiSeq 2500 (Illumina) for 101 cycles, with an additional seven cycles for index reading.


title: Spy_re2

description: nuclear RNA


title: Marginal zone B cells - Itgb1KO - 891

description: Gene expression in ex vivo sorted marginal zone B cells - Itgb1KO

value: Marginal zone B cells (CD19+CD93-CD23-CD21+)


title: Itgb1-WT-Transitional B cells - DMSO-144

description: Gene expression profile of Itgb1-wt transitional B cells cultured on OP9-Dll1 cells and treatedd with DMSO -Rep1

value: Itgb1+/+ Cd21Cre


title: Input_re2

description: nuclear RNA


title: SLO_HDB_PB_IGHC

value: plasmablasts


title: CHLA-266_control_2

value: siCTRL


title: CHLA-266_KD_1


title: SLO_HDB_CC_IGHC

value: centrocytes

value: IGM and IGG and IGA


title: CHLA-266_KD_2


title: CHLA-266_control_1


title: Transitional B cells  - Itgb1KO - 891

description: Gene expression in ex vivo sorted transitional B cells  - Itgb1KO

value: Transitional B cells (CD19+CD93+)


title: SLO_HDB_CB_IGHC


title: SLO_HDA_naive_IGHC


title: SLO_HDA_memB_IGHC

value: memory B cells


title: Follicular B cells - Itgb1KO - 891

description: Gene expression in ex vivo sorted follicular B cells - Itgb1KO

value: Follicular B cells (CD19+CD93-CD23+CD21-)


title: BT-12_control_3


title: Input_re1

description: nuclear RNA

value: HEY

value: serous ovarian cancer cell line


title: SLO_HDA_PB_IGHC

value: Secondary Lymphoid organ


title: BT-12_control_2


title: BT-12_control_1


title: Marginal zone B cells - Itgb1KO - 890


title: SLO_HDA_CC_IGHC


title: OR3350_rep4 [RNA-Seq]

tag: gentoye

value: odIs131; egl-9 vs. egl-9 hif-1


title: BT-12_KD_2


title: BT-12_KD_1


title: OR3350_rep1 [RNA-Seq]


title: OR3350_rep3 [RNA-Seq]


title: E9H1_rep3


title: Transitional B cells  - Itgb1KO - 876

tag: tissue

value: Spleen


title: Follicular B cells - Itgb1KO - 890


title: E9H1_rep4


title: Follicular B cells - Itgb1KO - 876


title: E9_rep4


title: OR3350_rep2 [RNA-Seq]


title: E9_rep3


title: CRE_DH_cre_del.2

city: San Francisco

first: Benoit

last: Bruneau

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

data_processing:
Alignment by TopHat2
counts per gene tallied by featureCounts
EdgeR for differentially expressed genes
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts or normalized CPM values for each sample.

source_name: embryonic heart

extract_protocol:
Qiazol and miRNeasy micro kit
Ovation RNA-seq system V2 kit

value: embryonic heart

value: Tbx5 del/CreERT2

tag: timepoint


title: CRE_DH_cre_del.4


title: CRE_DH_cre_del.3


title: Hif1_rep4


title: Hif1_rep3


title: Marginal zone B cells - Itgb1WT - 903

description: Gene expression in ex vivo sorted marginal zone B cells - Itgb1WT


title: CRE_DH_cre_del.1


title: N2_rep4

value: wild-type


title: Transitional B cells  - Itgb1KO - 890

value: Itgb1fl/fl Cd21Cre


title: N2_rep3

value: Wild-type


title: SLO_HDA_CB_IGHC

value: centroblasts


title: Marginal zone B cells - Itgb1KO - 876

value: Marginal zone B cells (CD19+CD93-CD23-CD21+)


title: CRE_CH_cre_plus.4

value: Tbx5 CreERT2/+


title: SI, normal, replicate 3 [1724]

city: Chicago

first: Veronica

last: Locher

state: IL

institute: University of Chicago

data_processing:
FASTQ files from each multiplexed capture library were mapped to a custom reference containing GRCh19 using the cellranger (v2.0.0) (10X Genomics) count function. After demultiplexing cells into samples, Seurat (v3.1.5) was used to perform quality control filtering of cells.
Assembly: GRCh19
Supplementary files format and content: Cell Ranger Outputs for each sample

source_name: Small Intestine

extract_protocol:
Single cells were captured by droplet-based microfluidics, lysed
sequencing libraries prepared in a single bulk reaction following the 10X Genomics protocol

treatment_protocol: Briefly, the SI was dissected, washed, and cut into 1 cm fragments. Mucus from the SI was removed by DTT washes and the SI epithelial layer was removed by EDTA washes. The SI was digested in collagenase IV (Life Technologies) and DNase (Roche), filtered, and lymphocytes isolated by 20/40/80 Percoll (GE Healthcare) gradient centrifugation. PLZF+CD4+ TCR-β+ T cells were sorted on proxy surface markers

value: Small Intestine

value: PLZF+CD4+ T cells

value: second trimester


title: SI, normal, replicate 2 [1722]


title: CRE_CH_cre_plus.2


title: SI, normal, replicate 1 [1721]


title: SI, PLZF+, 1725, PMA/iono stim

data_processing:
The reads from the Illumina HiSeq sequencer in fastq format were verified for quality control using the fastqc software package. Reads were aligned to the human genome (hg38) and read counts aggregated by gene using the Ensembl GRCh38.78 annotation using STAR (52).
Assembly: hg38
Supplementary files format and content: count txt file

source_name: Small Intestine Lamina Propria

growth_protocol: Briefly, the SI was dissected, washed, and cut into 1 cm fragments. Mucus from the SI was removed by DTT washes and the SI epithelial layer was removed by EDTA washes. The SI was digested in collagenase IV (Life Technologies) and DNase (Roche), filtered, and lymphocytes isolated by 20/40/80 Percoll (GE Healthcare) gradient centrifugation. PLZF+CD4+ TCR-β+ T cells were sorted on proxy surface markers.

extract_protocol:
RNA was extracted and purified with the Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific).
mRNA libraries were constructed using the Nugen/Nextera XT Library Prep Kit (Illumina), and 3 samples (3 donors) were sequenced on an Illumina HiSeq 4000 by the Functional Genomics Core Facility at UCSF.

treatment_protocol: Half the sorted cells were stimulated with 50 ng/ml PMA (Santa Cruz Biotechnology Inc.) and 5μg/ml Ionomycin (Sigma-Aldrich) for 3 hours at 37°C in 4% O2, the remaining cells were left unstimulated.

value: Small Intestine Lamina Propria

value: PMA/ionomycin stimulation


title: Follicular B cells - Itgb1WT - 903

description: Gene expression in ex vivo sorted follicular B cells - Itgb1WT

value: Follicular B cells (CD19+CD93-CD23+CD21-)

value: Itgb1+/+ Cd21Cre


title: Marginal zone B cells - Itgb1WT - 898


title: SI, PLZF+, 1725, rest


title: SI, PLZF+, 1719, PMA/iono stim


title: SI, PLZF+, 1724, rest


title: Transitional B cells  - Itgb1WT - 898

description: Gene expression in ex vivo sorted transitional B cells  - Itgb1WT

value: Transitional B cells (CD19+CD93+)


title: CRE_CH_cre_plus.1


title: CRE_BH_del_plus.3

value: Tbx5 del/+


title: SI, PLZF+, 1716, PMA/iono stim


title: SI, PLZF+, 1719, rest


title: CRE_BH_del_plus.4

value: embryonic heart


title: Transitional B cells  - Itgb1WT - 903

value: Spleen


title: Follicular B cells - Itgb1WT - 898


title: Marginal zone B cells - Itgb1WT - 872


title: SI, PLZF+, 1716, rest


title: HEY_shBUD31_2

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were filtered to obtain clean reads after removal of reads containing adapter and at low quality
High-quality reads were mapped to the human reference genome hg38 using HISAT2 software
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: hg38
Supplementary_files_format_and_content: Gene FPKM of all the samples was provided as a compressed tar.gz file.

extract_protocol:
Total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEY

value: serous ovarian cancer cell line

tag: transfection


title: Transitional B cells  - Itgb1WT - 872


title: Follicular B cells - Itgb1WT - 872


title: HEY_shBUD31_3


title: CRE_BH_del_plus.2


title: HEY_shBUD31_1


title: CRE_BH_del_plus.1


title: HEY_shNC_3

value: shNC


title: CRE_CH_cre_plus.3


title: SI, PLZF+, 1717, rest


title: HEY_shNC_2


title: CRE_AH_WT.4

value: wildtype


title: ChIP-seq_β-actin KO-NLS-beta-actin_3

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

address: Saadiyat Campus, Abu Dhabi

institute: New York University Abu Dhabi

data_processing:
Raw reads quality trimmed using trim-galore with default settings and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2
RPKM normalized bamCoverage files for two replicates of each condition were averaged and blacklisted regions were removed using deeptools2
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig files containing RPKM normalized ChIP-Seq signal for each sample and bigwig files of averaged replicates of each condition

source_name: Mouse Embronic Fibroblast

growth_protocol: Cells were maintained and cultured with Dulbecco’s modified Eagle medium (DMEM) with high glucose, 10% fetal bovine serum (FBS) and 100 U/mL penicillin and 100 μg/mL streptomycin, in a humidified incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells were crosslinked  using 1% formaldehyde (Sigma Cat. No. F8775) for 10 min followed by quenching with 0.125 M Glycine for 5 min and lysis with lysis buffer 1-LB1-(50 mM Hepes KOH pH 7.5, 10 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100). Nuclei were pelleted, collected and washed using lysis buffer 2-LB2- (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). This was followed by lysis using lysis buffer 3 LB3 (10 mM Tris-HCl pH 8; 100 mM NaCl, 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate, 0.5% N-laurylsarcosine). Chromatin was sheared using Qsonica Sonicator (4 cycles of 3 min at 70 % Amplitude), and then checked on 0.8% agarose gel. 100 μg of fragmented chromatin was mixed with 5 μg of H3K27ac-Anti-Histone H3 (acetyl K27) antibody-ChIP Grade (ab4729) - abcam). The protein-antibody immunocomplexes were recovered by the Pierce Protein A/G Magnetic Beads (Thermo-Scientific). Beads and attached immunocomplexes were washed twice using Low salt wash buffer (LS) (0.1% SDS; 2 mM EDTA, 1% Triton X-100, 20 mM Tris-HCl pH 8, 150 mM NaCl), and High Salt (HS) wash buffer (0.1% SDS, 2 mM EDTA, 1% Triton X-100, 20 mM Tris-HCl pH 8, 500 mM NaCl), respectively. The beads were resuspended in elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS). De-crosslinking was achieved by adding 8 µL 5 M NaCl and incubating at 65 °C overnight. RNase A (1 µL 10 mg/mL) was added for a 30 min incubation at 37 °C. Then, 4 µL 0.5 M EDTA, 8 µL 1 M Tris-HCl, and 1 µL 20 mg/mL proteinase K (0.2 mg/mL) were added for a 2-hour incubation at 42 °C to digest the chromatin. DNA was purified by QIAquick PCR purification kit (Qiagen, Germantown, MD, USA) for qPCR analysis and sequencing. Library preparation and sequencing was performed by Novogene Co., Ltd using standard illumina protocols.
Library preperation and sequencing was performed by Novogene. Co Ltd using standard illumina protocols

value: BALB/c

value: 10.5 day old embryos

value: Beta-actin KO-NLS

tag: chip antibody


title: T cells_KPC-SubQ_Ant08+PD1-3

city: Atlanta

first: Edmund K.

last: Waller

state: Georgia

address: 1365 Clifton Rd Building C

department: Hematology and Medical Oncology

institute: Emory University School of Medicine

description: synthetic immune repertoire and primer amplification

data_processing:
Sequencing of TCR-β CDR3 V and J sequences performed by Adaptive Biotechnologies (Seattle, WA).
Raw Immunosequencing data (n=16) was assessed for QC, imported and analyzed using immunoSEQ Analyzer - Adaptive Biotechnologies.
Supplementary files format and content: shared clones in each treatment group
Library strategy: TCR-seq

source_name: T cells_KPC-SubQ_Ant08+PD1-3

extract_protocol: Singlet cell suspensions of tumors were subjected to magnetic T cell isolation using EasySepTM Mouse CD90.2 Positive Selection kit II from STEMCELL technologies (Vancouver, Canada). Purity of T cells following isolation was 80-85%. Qiagen RNeasy Micro kit was used to extract RNA, and quantity and quality was assessed using the Nanodrop and Agilent 2100. RNA analyzed using the nCounter Metabolic Pathways Panel (Nanostring Technologies, Seattle, WA)

treatment_protocol: For the subcutaneous model, 5x105 KPC-Luc cells were injected subcutaneously near the right flank of female C57BL/6 mice. 6-7 days after tumor implantation mice were randomized into 4 treatment groups and treatedwith VIP-R antagonist and/or anti-PD-1. While scram+IgG control mice received scrambled peptide and isotype IgG, the VIP-R antagonist, anti-PD-1 and VIP-R antagonist and anti-PD-1 groups received VIP-R antagonist and IgG; scrambled peptide and anti-PD-1; and VIP-R antagonist and anti-PD-1, respectively. The treatment regimen involved administering 10μg of scrambled or VIP-R antagonist: ANT008, subcutaneously every day and 200μg of IgG or anti-PD-1 intraperitoneally once every three days, for a total of 10 days.

value: T cells

tag: Sex

value: Female


title: HEY_shNC_1


title: T cells_KPC-SubQ_Ant08+PD1-4

source_name: T cells_KPC-SubQ_Ant08+PD1-4


title: ChIP-seq_β-actin KO-NLS-beta-actin_2

tag: developmental stage


title: CRE_AH_WT.3


title: T cells_KPC-SubQ_PD1-4

source_name: T cells_KPC-SubQ_PD1-4

tag: cell type


title: T cells_KPC-SubQ_Ant08+PD1-1

source_name: T cells_KPC-SubQ_Ant08+PD1-1


title: CRE_AH_WT.1


title: T cells_KPC-SubQ_Ant08+PD1-2

source_name: T cells_KPC-SubQ_Ant08+PD1-2


title: ATAC-seq_β-actin KO-NLS-beta-actin_2

data_processing:
Raw reads quality trimmed using trim-galore with default settings and assessed with fastqc
Surviving paired reads were then aligned against the mouse reference genome mm10 using bwa-mem
Resulting BAM alignments were then processed through PICARD tools (http://broadinstitute.github.io/picard), to clean, sort and deduplicate (PCR and Optical duplicates).
RPKM normalized bamCoverage files were produced using deeptools2 for replicate-merged bams of each conditions
Assembly: GRCm38 (mm10)
Supplementary files format and content: bigwig files containing RPKM normalized ATAC signal for merged replicates of each condition

extract_protocol:
Samples were shipped in frozen medium on dry ice to Novogene (Beijing, China). All subsequent processing was performed by Novagene using standard DNA extraction and library preperation protocols.All processing was performed by Novagene (Beijing, China). Cell nuclei were isolated, mixed with Tn5 Transposase with two adapters and tagmentation was performed for 30 minutes at 37⁰C. The fragmented DNA was purified and amplified with limited PCR cycle using index primers. Llibraries were prepared according to recommended Illumina NovaSeq6000 protocols.
Library preperation and sequencing was performed by Novogene. Co Ltd using standard illumina protocols


title: T cells_KPC-SubQ_PD1-2

source_name: T cells_KPC-SubQ_PD1-2


title: CRE_AH_WT.2


title: T cells_KPC-SubQ_Ant08-4

source_name: T cells_KPC-SubQ_Ant08-4


title: T cells_KPC-SubQ_PD1-1

source_name: T cells_KPC-SubQ_PD1-1


title: ATAC-seq_β-actin KO-NLS-beta-actin_1


title: LQ004_D6_UT

city: New York

first: Kam

last: Leong

state: NY

address: 3600 Broadway, RM450C

department: Biomedical Engineering

institute: Columbia University

description: Chromium 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: GRCm38
Supplementary files format and content: Expression matrix of each sample.
Supplementary files format and content: For each sample, "features.tsv.gz" corresponded to gene names. "barcodes.tsv.gz" corresponded to cell barcodes. "matrix.mtx.gz" was the expression counts in sparce matrix.

growth_protocol: 3T3-L1 cells were cultured in high glucose DMEM supplemented with 10% calf serum (CS, Gemini Bio-Products 100-506), and 1× Pen Strep (Thermo Fisher). Cells were differentiated in the standard adipogenic cocktail after reaching confluence for 2 days. The cocktail contains DMEM, 10% FBS (heat-inactivated, Corning 35-011-CV), 1 μM dexamethasone (DEX), 10 μg/mL insulin and 0.5 mM 3-isobutyl-1-methylxanthine (IBMX). After induction for two days, cells were maintained in a complete medium containing 2.5 μg/mL insulin until fully differentiated.

extract_protocol:
Cells were gently dissociated into single cells with trypsin enzymatic digestion.
Library was performed according to the manufacter’s instructions (Chromium single cell 3’ v2 protocol, 10x Genomics).

treatment_protocol: P-G3 polymers (10 μg/mL) were added to the medium since the induction of differentiation Day 0, and cells were harvested at indicated times for analyses.

value: Immature adipocytes, adipocytes,lipogenic adipocyte

tag: time

tag: adipogenic differentiation_treatment

value: Yes

tag: polymer treatment

value: Untreated


title: LQ005_D6_PG3

description: Chromium 10x Genomics


title: Dbif_ChIP_input

city: Acton

first: Rippei

last: Hayashi

address: 131 Garran Road

institute: The Australian National University

description: chromatin from Drosophila bifasciata ovaries fixed by formaldehyde

data_processing:
genome_build: UCBerk_Dbif_1.0/GCA_009664405.1
R1 reads were trimmed of the adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting.  The trimmed reads were then mapped against the genome using bowtie 1.2.3, allowing up to three mismatches.  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of reads that are uniquely mapping to the genome

organism: Drosophila bifasciata

source_name: ovaries

extract_protocol:
Ovaries were dissected from 3 -7 days old female flies.   Ovaries were fixed with PBS containing 2% para-formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using BioRuptor (ten cycles of 30sec/30sec ON/OFF).
IP and 5% of input DNA were End-repaired (NEB) and ligated to the NEBNext adapter for Illumina (NEB, E7337A). The libraries were amplified by the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers.  Post amplification libraries were size selected at 200-500bp in length in a low-melt Agarose gel.

value: ovaries

value: female

tag: stain

value: Jozankei, Hokaidou

value: wild type

tag: age

value: 2 - 7 days old

tag: condition

value: standard food


title: T cells_KPC-SubQ_Ant08-3

source_name: T cells_KPC-SubQ_Ant08-3

tag: strain


title: Dbif_ChIP_polII-CTD

value: RNA Polymerase II CTD (gift from Hiroshi Kimura, PMID:25252976)


title: T cells_KPC-SubQ_Ant08-2

source_name: T cells_KPC-SubQ_Ant08-2


title: Dbif_ovary_polyA

description: polyA selected RNA from Drosophila eugracilis ovaries

data_processing:
genome_build:  UCBerk_Dbif_1.0/GCA_009664405.1
We used both R1 and R2 reads from the standard RNA-seq, and only the R1 reads from the Quantseq 3' mRNA-seq for the mapping and analyses.   Reads were trimmed of the adapters 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' and 'AGATCGGAAGAGCGTCGTGTAGGGAAAGA' at the 3' ends of R1 and R2 reads, respectively, using fastx_clipper (fastx_toolkit, Hannon Lab) with the default setting.  Trimmed reads were mapped against the genome using STAR 2.7.3a, allowing up to three mismatches.  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of reads that are uniquely mapping to the genome

extract_protocol:
Ovaries were dissected from 3 -7 days old female flies. Total RNA was extracted from ovaries using TRIZOL. Oligo-dT magnetic beads (NEB) was used to purify polyA+ RNA.  PolyA+ RNA was used to make standard RNA-seq libraries while the total RNA was used to make a Quant-seq mRNA 3' end sequencing library.
The RNA-seq library was made using NEB Ultra II Directional RNA library prep kit (NEB), while the mRNA 3' end-seq library was made using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen).  For both library constructions, we used the Kapa LongRange DNA polymerase (Sigma) with TruSeq compatible primers to amplify the libraries.


title: T cells_KPC-SubQ_Ant08-1

source_name: T cells_KPC-SubQ_Ant08-1


title: T cells_KPC-SubQ_Control-4

source_name: T cells_KPC-SubQ_Control-4


title: LQ003_D3_PG3

description: Chromium 10x Genomics

tag: cell line

value: Immature adipocytes, adipocytes


title: T cells_KPC-SubQ_Control-2

source_name: T cells_KPC-SubQ_Control-2


title: T cells_KPC-SubQ_Control-3

source_name: T cells_KPC-SubQ_Control-3


title: ChIP-seq_β-actin KO-NLS-beta-actin_1

state: Abu Dhabi

tag: genotype


title: Dbif_embryo_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila bifasciata embryos

data_processing:
genome_build:UCBerk_Dbif_1.0/GCA_009664405.1
Reads in the fastq files were adapter 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' clipped using fastx_clipper (fastx_toolkit, Hannon Lab) using the default setting.  The first and the last four bases were trimmed (both adapters contain four random nucleotides at their respective termini) and reads of >17nt and <41nt were kept for the analyses.  Trimmed reads were mapped with bowtie v1.2.3 to the respective genomic sequences (allowing up to one mismatch) or transposon reference sequences (allowing up to three mismatches).  The sam file was further processed to the bam file, then to the bed file, the bedgraph file, and finally to the bigWig file, using samtools/1.10, bedtools/2.28.0, and kent-ucsc tools.
Supplementary files format and content: *.tile-coverage.txt: counts of piRNA (>22nt & <41nt) reads that uniquely mapped to the genomic 0.5kb tiles (allowing up to one mismatch), normalised to one million genome unique mappers
Supplementary files format and content: *.TE-mapping.txt: counts of piRNA (>22nt & <41nt) reads that mapped to the transposon reference sequences (allowing up to three mismatches, --all --best --strata option in bowtie), normalised to one million all genome mappers
Supplementary files format and content: *.genome-unique-mappers.bed: bed file of piRNA reads (>22nt and <41nt) that are uniquely mapping to the genome

source_name: embryos

extract_protocol:
Either ovaries or embryos were collected for the RNA extraction.  Ovaries were dissected from 3 -7 days old female flies. Embryos were collected between zero to two hours after fertilisation. Embryos were further dechorionated by 20% bleach and further rinsed by water.  Total RNA was extracted from ovaries/embryos using TRIZOL.
For oxidised small RNA libraries: Small RNAs were first size-selected by 12% w/v UREA-PAGE, and oxidised using sodium periodate.  For non-oxidised small RNA libraries: 2S rRNA was first removed from the total RNA using a biotinylated DNA ligo 'TACAACCCTCAACCATATGTAGTCCAAGCA'. 2S-rRNA-depleted total RNA was then size-selected by 12% w/v UREA-PAGE to yield the pool of small RNA.  The oxidised or unoxidised small RNAs were further size-selected by PAGE before 3' and 5' adapters were ligated.  The first strand cDNA synthesis was performed using SuperScript II (Thermo Fisher) and the library was amplified using KAPA LongRange DNA polymerase (Sigma) with TruSeq compatible primers.

value: embryos

value: pooled male and female

value: 0 - 2 hr post-fertlisation

tag: treatment

value: unoxidised


title: Dbif_ovary_oxidised_sRNA

description: oxidised small RNAs (18-40nt) from Drosophila bifasciata ovaries

tag: tissue

value: oxidised


title: T cells_KPC-SubQ_PD1-3

source_name: T cells_KPC-SubQ_PD1-3

value: T cells

value: Female