title: IVH

city: New Haven

state: Connecticut

address: 333 Cedar St

institute: Yale University Department of Neurosurgery

data_processing: The demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger.

extract_protocol:
Animals were anesthetized with Ketamine/Xylazine and transcardially perfused with ice cold TBS before brain removal. Choroid plexi from bilateral lateral ventricles were microdissected in ice cold HBSS with 30uM Actinomycin D (ActD, Sigma, cat#A1410 ) and digested at 37oC for 20 min with Collagenases-I and -IV (10 U/mL, 400 U/mL final, Worthington, Cat# LS004194, and LS004184) and DNase I (30 U/mL, Roche, cat# 04716728001) and ActD (3uM). For Flow sorting, the cell suspension was blocked with CD16-CD32 antibodies (1:100, biolegend, cat#101302) and stained 30 min at 4oC with anti-rat CD45-PE/cy7 (1:100, biolegend, cat#202207) to and DAPI (50ug/mL). Cells were subsequently washed in FACS staining buffer (0.5% BSA, 2mM EDTA in PBS without Calcium/Magnesium) and centrifuged at 350 rcf for 5 minutes. Cells were resuspended in 300ul of FACS buffer and sorted by CD45 positivity on a BD ARIA instrument. CD45 positive and CD45 negative cells were collected in 0.4% BSA/PBS and 3uM ActD and sent for 10X 3prime library preparation and sequencing at Yale Center for Genome Analysis
Sequencing libraries were loaded on an Illumina HiSeq4000 flow cell with sequencing settings following the recommendations of 10x Genomics (read 1: 26 cycles; read 2: 98 cycles; index i7: eight cycles; index i5: no cycles; 2.1 pM loading concentration). The Cell Ranger pipeline was designed to perform sample demultiplexing and to generate FASTQ files for read 1, read 2 and the i7 sample index. Read 2, containing the cDNA, was mapped to the reference genome (mouse mm10) using STAR

tag: treatment

value: IVH-Treated


title: LPS

status: Public on Feb 17 2023

type: SRA

first: Kristopher

last: Kahle

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Rattus norvegicus

source_name: choroid plexus (ChP)

treatment_protocol: LPS/IVH 48 hhs ICV

value: LPS-Treated


title: MCF7, EPZ RNA-seq, rep3

city: Hong Kong

first: Jason

last: Wong

address: L1-51, 21 Sassoon Road

department: School of Biomedical Sciences

country: China

institute: The University of Hong Kong

data_processing:
For RNA-seq, raw reads were mapped to the human genome (hg38) using STAR aligner (version 2.7.10a).
Read counts were computed by featureCounts (version 2.0.1) based on canonical genes defined in GENCODE (version 39)
Assembly: hg38
Supplementary files format and content: RNA-Seq expression matrix (txt)

organism: Homo sapiens

extract_protocol:
Total RNA was extracted using FastPure Cell/Tissue Total RNA Isolation Mini Kit (Vazyme). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was prepared by end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: cell line

tag: cell type

value: Human breast cancer cell

value: EPZ


title: MCF7, EPZ RNA-seq, rep2


title: Control

value: Untreated


title: h1ddm1.f6.bsseq

city: Norwich

first: David

middle: B.

last: Lyons

state: Norfolk

address: Colney Lane

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: genomic

data_processing:
Bisulfite libraries were mapped to the genome following adaptor trimming with trim_galore (https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md) using BSMAP (Xi and Li 2009) using default settings for all analyses, except single-read analyses, for which we used Bismark (Kruger and Andrews 2011).
BSMAP output was converted to per-base methylation scores with BSMAP's methratio.py script using the -r setting to remove PCR duplicates.
Methratio.py output was converted to GFF and further processed and analysed using commands and workflows outlined in https://github.com/dblyons/modeling_h1ddm1/
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-seperated methratio.py output: chromosome, position, strand, cytosine context, ratio eff_CT_count, C_count, CT_count, rev_G_count, rev_GA_count, CI_lower, CI_upper.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: rosette leaf

growth_protocol: Arabidopsis were sown to soil, stratified for 4 days at 4degC and transferred to controlled environment chambers where they were grown in 16h light / 8hr dark at 20deg C.

extract_protocol:
DNA was isolated by pulverizing ~0.5 g of flash frozen rosette leaves of 4 week post-germination plants.  ~100 mg of resulting powder was used to extract genomic DNA (gDNA) with the DNeasy plant mini kit (Qiagen cat. no. 69104) per manufacturer's instructions. gDNA was subsequently sonicated with the Bioruptor Pico (Diagenode) to ~250 bp median fragment length using 10 cycles of 30 seconds on and off.  Agencourt Ampure beads (referred to as “beads” henceforth, cat. no. A63881) were then used at 2X volume to purify the sheared DNA.
Following ligation of methylated Truseq sequencing adapters (Illumina) to sheared DNA, bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Qiagen Epitect Kit, cat. no. 59104) except without using carrier RNA.  DNA was purified twice with 1.2X beads and converted a second time to ensure complete bisulfite conversion of unmethylated cytosine. Libraries were constructed using NEBnext kits (NEB cat. no. E7645) or Nugen/Tecan Ovation Ultralow (cat. no. 0344NB-08) following the manufacturer's instructions.   NEB next indexing primers (cat. no. E7335S) were used for generating multiplexed libraries during PCR amplification of libraries.

tag: ecotype

tag: tissue

value: rosette leaf


title: MCF7, EPZ RNA-seq, rep1


title: c30 cjPGCLCs, shallow WGBS, rep1

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

data_processing:
Raw fastq files were demultiplexed by bcl2fastq2 (v2.20). Barcode and index were trimmed by Trim Galore (v0.6.5) trim_galore --quality 30 --phred33 --illumina --stringency 1 --cores 4 -e 0.1 --fastqc --clip_R1 10 --three_prime_clip_r1 10 --length 20, then the trimmed fastq files were mapped to calJac4 from USCS using Bismark (v 0.22.3) using bismark --parallel 4 --genome_folder $REF --non_directional --score_min L,0,-0.6. CpG methylation was extracted and analyzed using methylKit (v1.22.0). Covered CpG loci were included in analysis. The genome was tiled by 2kb windows, then DNA methylation levels were summarized by methyKit (v1.22.0). Data was visualized by R (v4.1.0).
Assembly: calJac4
Supplementary files format and content: *_CpG.txt: Tab-delimited text files include CpG DNA methylation for each sample.

organism: Callithrix jacchus

source_name: cjPGCLCs

extract_protocol:
Cells were collected and lysed in 50 mM Tris (pH 8.0), 10 mM EDTA, 0.5% SDS, 100µg/ml Proteinase K. Then crude DNA was used to build methylation sequencing library according to the protocol of Pico Methyl-Seq Library Prep Kit (Zymo, #D5455). Then libraries were sequenced on Illumina HiSeq 2000.
Pico Methyl-Seq Library Prep Kit.

treatment_protocol: To collect cjiPSCs for methylation sequencing, colonies were picked up under microscope then collected into a 1.5ml tube for lysis. PGCLCs aggregates were digested using 400ul 0.25% Trypsin for 15mins, then 100ul FBS was used to stop digestion and pipette well to obtain a single cell suspension. The dissociated cells were stained with APC-conjugated anti-human PDPN, BV421-conjugated anti-human/mouse CD49f (INTEGRINα6), then PDPN+ fraction was sorted for methylation sequencing.

value: cjPGCLCs

value: extension culture


title: h1ddm1.f4.bsseq


title: c30 cjPGCLCs, shallow WGBS, rep2


title: d4 cjPGCLCs, shallow WGBS, rep2


title: iPSC YAP-/- 1_MESO (RNA-seq)

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: iPSC 102 #20 MESO

data_processing:
Quality Control: FastQC
Trimming adaptor and low quality seqs: Trimmomatic
Alignment: Star-aligner
Read counting: FeatureCount
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: iPSC

growth_protocol: The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec GmbH, Bergisch Gladbach, Germany). EBs were generated with a micro-contact printing (µCP) approach published in (). Multilineage differentiation of EBs was performed with differentiation induction medium (EB-medium) containing Knockout DMEM (Gibco, Carlsbad, USA), 20 % v/v FCS (Lonza, Basel, Switzerland), 2 mM L-Glutamine, 1x Non-Essential amino acids, 100 nM b-Mercaptoethanol, and 100 U/mL Penicillin/Streptomycin solution. EBs were differentiated in ultra-low attachment plates (Corning, New York, USA) for 5 days.

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany).
Library preparation was carried out using QuantSeq 3´-mRNA (Lexgon) according to the manufacturer's instructions. Sequencing was done using NovaSeq 6000 sequencer (Ilumina). Library preparation and sequencing was carried out by Life&Brain (Bonn, Germany).

tag: genotype

value: YAP-/-

value: iPSC

tag: gender

value: female

tag: differentiation timepoint

tag: sample group

value: mesoderm


title: MCF7, DMSO RNA-seq, rep3

value: DMSO


title: h1ddm1drm2.f4_2.bsseq


title: d4 cjPGCLCs, shallow WGBS, rep1


title: MCF7, DMSO RNA-seq, rep2


title: OF/IWR1 cjiPSC, shallow WGBS, rep2

description: ipscs

source_name: cjiPSCs

value: cjiPSCs

value: on feeder, IWR1


title: h1ddm1drm2.f5_1.bsseq


title: MCF7, DMSO RNA-seq, rep1


title: h1ddm1drm2.f4_1.bsseq


title: h1ddm1.f8.bsseq


title: MCF7, EPZ Input_2, rep2

data_processing:
For ChIP-seq, raw reads were mapped to the human genome (hg38) using bwa (version 0.7.1).
bigWig files were generated by deepTools (version 3.5.1).
Assembly: hg38
Supplementary files format and content: bigWig ChIP-seq signal

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated to ~200 bp fragment using a probe sonicator.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

tag: chip antibody


title: h1ddm1drm2.f3_2.bsseq


title: OF/IWR1 cjiPSC, shallow WGBS, rep1

description: ipscs


title: h1ddm1cmt3.f4_3.bsseq


title: Co-culture, Pitavastatin 10µM

type: RNA

city: Uppsala

first: Tove

middle: Kristina

last: Selvin

address: Akademiska sjukhuset

department: Medical Sciences

country: Sweden

institute: Uppsala University

description: Gene expression data from HCT116-GFP co-cultured with PBMCs cells at a 1:4 ratio, treated with Pitavastatin 10µM for24h

hyb_protocol: GeneChip ST Arrays (Clariom_S_Human) were hybridized for 16 hours in a 45◦C incubator, rotated at 60 rpm, then washed and stained using the GeneChip TM Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip TM Scanner 3000 7G.

data_processing: Data normalization and data analysis was performed using the Transcriptome Analysis Console, version 4.0.2.15, provided by Thermo Fisher. The raw data was normalized using the Robust Multi-Array Average method (Summarization Method: Gene Level - RMA).

label: biotin

source_name: HCT116-GFP and peripheral blood mononuclear cells, treated with Pitavastatin 10µM for24h

label_protocol: 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip TM WT PLUS Reagent Kit manual Target Preparation for GeneChip TM Whole Transcript (WT) Expression Arrays User Guide (P/N 703174, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008 USA).

growth_protocol:
HCT116-GFP, obtained from AntiCancer Inc. (San Diego, CA, USA), were cultured in McCoy's 5A medium supplemented with 10% FBS, 2 mM L-glutamine, and Penicillin (100 U/mL)/ Streptomycin (100 μg/mL). PBMCs from anonymous, healthy donors were isolated by Histopaque-1077 density gradient centrifugation. On day 0, HCT116-GFP (1.5*10^5 cells/3mL/well) were seeded in 6-well Nunc plates.
On day 1, PBMCs (6*10^5 cells/3mL/well) stimulated with anti-CD3 (final concentration 100 ng/mL) and IL2 (final concentration 10 ng/mL) were seeded as monocultures or added to cancer cells precultured for 24 h at a 1:4 ratio.

extract_protocol: Total RNA was islolated using a RNeasy Mini Kit (Qiagen)

treatment_protocol: HCT116-GFP monocultures, PBMC monocultures, and co-cultures were treated with DMSO vehicle (0.1%) or pitavastatin (1µM or 10µM) for 24 h.

value: HCT116-GFP cells and PBMCs (co-culture)

tag: stimuli

value: anti-CD3 and IL-2

value: Pitavastatin 10µM


title: c30 cjPGCLC, rep1

data_processing:
Raw fastq files were demultiplexed by bcl2fastq2 (v2.20.0.422). Barcodes and adptors were removed by Trimmomatic (v0.32). Fastq files were mapped to the Callithrix jacchus (calJac4) reference genome by STAR (v 2.7.10a). The raw gene counts table was generated by featurecounts. DEGs were analyzed by edgeR (v3.36.0) with log2 fold change above 1, P-value < 0.05 and FDR < 0.05. RPKM (Reads Per Kilobase Million) was calculated in edgeR, gene length was obtained from UCSC table browser. Downstream Data analyses and visualization were performed by R (v4.1.0).
Assembly: calJac4
Supplementary files format and content: raw.counts_all.sample.csv: Comma-separated text files include raw count values for all Samples.
Supplementary files format and content: RPFK_all.sample.csv: Comma-separated text files include RPKM values for all Samples.

extract_protocol: CjiPSCs cultured in the presence or absence of feeders, in the presence or absence of IWR1, were collected. To minimize the contamination of feeder cells, >30 colonies of cjiPSCs cultured on feeder layer colonies were randomly picked up under inverted microscope and pooled before isolation of total RNA. Total RNA was extracted by RNeasy Plus Micro Kit (#74034, QIAGEN). RNA-seq libraries were made by SMRT-Seq HT plus kit (#R400748, Takara) by following the protocol. Briefly, total RNA was quantified by Qubit and RNA integrity was checked by Tapstation. Then 1 ng RNA was used for cDNA conversion following one-step first-strand cDNA synthesis and double-stranded cDNA amplification protocol. cDNA was purified by AMPxp beads, concentration was measued by Qubit, and quality was checked by Tapstation. Next, 2 ng cDNA was used for library construction. Libraries were dual indexed and pooled by equal molecular concentration. 100-base pair reads were sequenced on Illumina Hiseq 2000.

tag: Sex

value: male


title: h1ddm1cmt3.f4_2.bsseq


title: MCF7, DMSO Input_2, rep2

value: Human breast cancer cell


title: d6 cjPGCLCs, rep2


title: h1ddm1cmt2.f5_3.bsseq


title: PBMC monoculture, DMSO vehicle

description: Gene expression data from PBMCs, treated with DMSO vehicle for 24h

source_name: Peripheral blood mononuclear cells, treated with DMSO vehicle for 24h

value: PBMCs

value: DMSO vehicle


title: MCF7, DMSO Input_2, rep1


title: PBMC monoculture, Pitavastatin 10µM

description: Gene expression data from PBMCs, treated with Pitavastatin 10µM for24h

source_name: Peripheral blood mononuclear cells, treated with Pitavastatin 10µM for24h


title: h1ddm1cmt2.f5_2.bsseq

value: rosette leaf


title: d6 cjPGCLCs, rep1


title: Co-culture, DMSO vehicle

description: Gene expression data from HCT116-GFP co-cultured with PBMCs  at a 1:4 ratio, treated with DMSO vehicle for 24h

source_name: HCT116-GFP and peripheral blood mononuclear cells, treated with DMSO vehicle for 24h


title: RNA-Seq of Citrus Sinensis roots，pH 4.8,300 μM CuCl2 [P4.8CR-3]

city: FuZhou

first: Jiang

last: Zhang

state: FuJian

address: ShangXiaDian Street No.15

department: College of Resources and Environment

institute: Fujian Agriculture and Forestry University

data_processing:
Illumina NovaSeq 6000 software used for basecalling. default parameters
Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low-quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. default parameters
Use HISAT v2.1.0 to construct the index, and compare clean reads to the referenc genome. default parameters
Use featureCounts v1.6.2 /StringTie v1.3.4d to calculate the gene alignment and FPKM. default parameters
The screening criteria for DEGs were |log2 (fold change)| > 1 and False Discovery Rate (FDR) < 0.05 using DESeq2 v1.22.1
Assembly: C. sinensis
Supplementary files format and content: Excel files include FPKM values, chromosome name, start position,end position, and positive and negative chain information

organism: Citrus sinensis

source_name: roots

extract_protocol:
Equal frozen roots of four seedlings from four pots were pooled as one biological replicate. Twelve samples (four treatments × three biological replicates) were sent to Wuhan MetWare Biotechnology Co., Ltd. (Wuhan, Hubei, China) for RNA extraction.
A total amount of 1 ug RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®UltraTM RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer's recommendations.

treatment_protocol: Control with pH 4.8, low-pH with pH 3，and control with 0.5 μM CuCl2，300 μM CuCl2（Cu-toxicity）

tag: category

value: seedling

value: roots

value: 300 μM CuCl2 × pH 4.8

tag: biological replicates

value: P4.8CR-biol rep 3

tag: treatment time

value: 17 weeks


title: h1ddm1cmt2.f5_1.bsseq


title: h1ddm1cmt2.f4_3.bsseq


title: MCF7, EPZ Input_2, rep1

value: EPZ


title: MCF7, DMSO Menin ChIP-seq, rep2

value: anti-MEN1 (Bethyl Laboratories A300-115A)

value: DMSO


title: MCF7, EPZ Menin ChIP-seq, rep2


title: Co-culture, Pitavastatin 1µM

description: Gene expression data from HCT116-GFP co-cultured with PBMCs cells at a 1:4 ratio, treated with Pitavastatin 1µM for 24h

source_name: HCT116-GFP and peripheral blood mononuclear cells, treated with Pitavastatin 1µM for 24h

value: Pitavastatin 1µM


title: h1ddm1cmt2.f4_2.bsseq


title: HCT116-GFP monoculture, Pitavastatin 10µM

description: Gene expression data from HCT116-GFP, treated with Pitavastatin 10µM for 24h

source_name: Colorectal cancer cell line HCT116-GFP, treated with Pitavastatin 10µM for 24h

value: HCT116-GFP colorectal cancer cells


title: c30 cjPGCLC, rep2

value: cjiPSCs

value: extension culture


title: HCT116-GFP monoculture, Pitavastatin 1µM

description: Gene expression data from HCT116-GFP, treated with Pitavastatin 1µM for 24h

source_name: Colorectal cancer cell line HCT116-GFP, treated with Pitavastatin 1µM for 24h


title: HCT116-GFP monoculture, DMSO vehicle

description: Gene expression data from HCT116-GFP, treated with DMSO vehicle for 24h

source_name: Colorectal cancer cell line HCT116-GFP, treated with DMSO vehicle for 24h


title: RNA-Seq of Citrus Sinensis roots，pH 4.8,300 μM CuCl2 [P4.8CR-2]

value: P4.8CR-biol rep 2


title: d4 cjPGCLCs, rep1

value: male


title: d2 cjPGCLCs, rep2


title: RNA-Seq of Citrus Sinensis roots，pH 4.8,300 μM CuCl2 [P4.8CR-1]

value: P4.8CR-biol rep 1


title: MCF7, DMSO Menin ChIP-seq, rep1

value: Human breast cancer cell


title: MCF7, EPZ Input_1, rep2


title: RNA-Seq of Citrus Sinensis roots，pH 3,300 μM CuCl2 [P3CR-2]

value: 300 μM CuCl2 × pH 3

value: P3CR-biol rep 2


title: PBMC monoculture, Pitavastatin 1µM

description: Gene expression data from PBMCs, treated with Pitavastatin 1µM for 24h

source_name: Peripheral blood mononuclear cells, treated with Pitavastatin 1µM for 24h

value: PBMCs

value: anti-CD3 and IL-2


title: OF/IWR1 cjiPSCs, rep2

value: on feeder, IWR1


title: RNA-Seq of Citrus Sinensis roots，pH 3,300 μM CuCl2 [P3CR-3]

value: seedling

value: roots

value: P3CR-biol rep 3

value: 17 weeks


title: d4 cjPGCLCs, rep2


title: d2 cjPGCLCs, rep1


title: h1ddm1cmt2.f4_1.bsseq

value: rosette leaf


title: MCF7, EPZ Menin ChIP-seq, rep1

value: anti-MEN1 (Bethyl Laboratories A300-115A)

value: EPZ


title: h1ddm1cmt2.f3_2.bsseq


title: MCF7, EPZ Input_1, rep1


title: OF cjiPSCs, rep2

value: cjiPSCs

value: on feeder


title: MCF7, DMSO Input_1, rep2

value: DMSO


title: MCF7, DMSO Input_1, rep1


title: h1ddm1cmt2.f2_1.bsseq


title: h1ddm1cmt2.f3_1.bsseq


title: ddm1.f5_1.bsseq


title: RNA-Seq of Citrus Sinensis roots，pH 4.8,5 μM CuCl2 [P4.8R-2]

value: 0.5 μM CuCl2（control）× pH 4.8（control）

value: P4.8R-biol rep 2


title: RNA-Seq of Citrus Sinensis roots，pH 4.8,5 μM CuCl2 [P4.8R-3]

value: P4.8R-biol rep 3


title: RNA-Seq of Citrus Sinensis roots，pH 4.8,5 μM CuCl2 [P4.8R-1]

value: P4.8R-biol rep 1


title: MCF7, EPZ H3K79me2 ChIP-seq, rep1

value: Human breast cancer cell

value: anti-H3K79me2 (Abcam, ab3594)


title: RNA-Seq of Citrus Sinensis roots，pH 3,0.5 μM CuCl2 [P3R-3]

value: 0.5 μM CuCl2 × pH 3

value: P3R-biol rep 3


title: ddm1.f4_2.bsseq


title: FF/IWR1 cjiPSCs, rep2

value: male

value: feeder free, IWR1


title: MCF7, EPZ H3K79me2 ChIP-seq, rep2


title: MCF7, DMSO H3K79me2 ChIP-seq, rep2


title: ddm1.f4_1.bsseq


title: RNA-Seq of Citrus Sinensis roots，pH 3,300 μM CuCl2 [P3CR-1]

value: seedling

value: roots

value: 300 μM CuCl2 × pH 3

value: P3CR-biol rep 1

value: 17 weeks


title: OF/IWR1 cjiPSCs, rep1

value: cjiPSCs

value: on feeder, IWR1


title: FF cjiPSCs, rep2

value: feeder free


title: MCF7, DMSO H3K79me2 ChIP-seq, rep1

value: DMSO


title: RNA-Seq of Citrus Sinensis roots，pH 3,0.5 μM CuCl2 [P3R-1]

value: P3R-biol rep 1


title: RNA-Seq of Citrus Sinensis roots，pH 3,0.5 μM CuCl2 [P3R-2]

value: P3R-biol rep 2


title: ddm1.f2_1.bsseq

value: rosette leaf


title: ddm1.f3_1.bsseq


title: OF cjiPSCs, rep1

value: on feeder


title: FF/IWR1 cjiPSCs, rep1


title: WT, TGFb3, d56, rep4

status: Public on Feb 16 2023

city: St Louis

first: Amanda

last: Dicks

state: MO

address: 1 Brookings Dr

institute: Washington University in St. Louis

data_processing:
Basecalls and demultiplexing were performed with Illumina's bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5-p5
Isoform expression of know Ensembl transcripts were estimated with Salmon version 0.8.2
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeOC version 2.6.2
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: tab-delimited text files with gene counts, CPM, RPKM

source_name: hiPSC-derived chondrocytes

growth_protocol: hiPSCs were maintained in E8 Flex medium and differentiated into chondroprogenitors with a 50/50 mixture of IMDM and F12 supplemented with various growth factors driving step-wise mesodermal differentiation over 12 days

extract_protocol:
RNA was isolated using the Total RNA Purification Plus Kit, treated with Dnase, and cleaned (Norgen Biotek)
Libraries were preared according to manufacturer's protocol
RNA seq - Samples were indexed, pooled, and sequenced at a depth of 30 million reads per sample on an Illumina NovaSeq 6000

treatment_protocol:
Chondroprogenitors were differentiated into chondrocytes in DMEM with ascorbate, proline, and TGFb3 for 28 to 56 days
Day-28 chondrocytes were hypertrophically differentiated by replacing TGFb3 with BMP4 for 28 days

value: induced pluripotent stem cell

value: WT

value: TGFb3 for 56 days


title: FF cjiPSCs, rep1

value: male


title: T89I, TGFb3, d56, rep4

value: TRPV4-T89I mutation


title: WT, BMP4, d56, rep2

value: TGFb3 for 28 days, BMP4 for 28 days


title: WT, TGFb3, d56, rep2


title: WT, BMP4, d56, rep3


title: HFN mouse liver at ZT18, biological rep3

city: MEXICO CITY

first: LORENA

last: AGUILAR ARNAL

address: TERCER CIRCUITO EXTERIOR, CU

department: BIOLOGIA CELULAR Y FISIOLOGIA

country: Mexico

institute: INSTITUTO DE INVESTIGACIONES BIOMEDICAS- UNIVERSIDAD NACIONAL AUTONOMA DE MEXICO

description: ZT18, high fat diet, NAD+ treated at ZT11 #3

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on Clariom™ D assays, mouse arrays (Affymetrix  902514).

scan_protocol: The arrays were scanned in the GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console Software was used to obtain the .CEL intensity file.

data_processing: Normalized gene expression data (.CHP files) were obtained with the Transcriptome Analysis Console (TAC 4.0.1.36) software using default parameters.

organism: Mus musculus

label_protocol: The GeneChip™ WT Terminal Labeling Kit (Thermo Fisher Scientific) was used following manufacturer´s  prescribed protocols. Following fragmentation, the resulting fragmented cRNA was labeled using terminal deoxynucleotidyl transferase (TdT) in the presence of a proprietary biotinylated compound, GeneChip DNA Labeling Reagent.

growth_protocol: Animals housed in 12-hr L/D cycle, fed adlibitum

extract_protocol: 20 mg of tissue were homogenized (Benchmark Scientific, D1000 homogenizer) for 30 seconds with 0.5 ml of TRIzol (Invitrogen, Carlsbad, CA). Total RNA was extracted following manufacturer´s instructions. Total RNA was resuspended in 30 ul of RNase free water, and cleaned using the Qiagen RNeasy Mini purification kit (Redwood, CA), following the manufacturer’s protocol. Eluted RNA was quantified with a nano-drop spectrophotometer (Thermo Fisher Scientific, Wilmington, DE). The quality of the RNA was assessed on an Agilent Bioanalyzer 2100 (Santa Clara, CA).

treatment_protocol: Livers were  rinsed in PBS and then rapidly frozen in liquid nitrogen. All samples stored at -80 until RNA preparation.

value: Liver

tag: strain

tag: diet

value: High Fat Diet + NAD+ treatment

tag: harvest timepoint


title: WT, TGFb3, d56, rep3

tag: cell line

tag: treatment


title: WT, TGFb3, d56, rep1

tag: cell type


title: WT, BMP4, d56, rep4


title: T89I, TGFb3, d56, rep2


title: T89I, TGFb3, d56, rep3


title: HF mouse liver at ZT18, biological rep3

description: ZT18, high fat diet #3

source_name: HF mouse liver at ZT18, biological rep3

tag: tissue

value: High Fat Diet


title: HF mouse liver at ZT6, biological rep2

description: ZT6, high fat diet #2

source_name: HF mouse liver at ZT6, biological rep2


title: HFN mouse liver at ZT18, biological rep1

description: ZT18, high fat diet, NAD+ treated at ZT11 #1


title: HF mouse liver at ZT6, biological rep3

description: ZT6, high fat diet #3

source_name: HF mouse liver at ZT6, biological rep3


title: HF mouse liver at ZT18, biological rep2

description: ZT18, high fat diet #2

source_name: HF mouse liver at ZT18, biological rep2


title: CD mouse liver at ZT6, biological rep2

description: ZT6, control diet #2

source_name: CD mouse liver at ZT6, biological rep2

value: Control Diet


title: HFN mouse liver at ZT18, biological rep2

description: ZT18, high fat diet, NAD+ treated at ZT11 #2


title: HFN mouse liver at ZT6, biological rep2

description: ZT6, high fat diet, NAD+ treated at ZT11 #2

source_name: HFN mouse liver at ZT6, biological rep2


title: CD mouse liver at ZT18, biological rep1

description: ZT18, control diet #1

source_name: CD mouse liver at ZT18, biological rep1


title: HFN mouse liver at ZT6, biological rep3

description: ZT6, high fat diet, NAD+ treated at ZT11 #3

source_name: HFN mouse liver at ZT6, biological rep3


title: HFN mouse liver at ZT6, biological rep1

description: ZT6, high fat diet, NAD+ treated at ZT11 #1

source_name: HFN mouse liver at ZT6, biological rep1


title: HF mouse liver at ZT18, biological rep1

description: ZT18, high fat diet #1

source_name: HF mouse liver at ZT18, biological rep1


title: CD mouse liver at ZT6, biological rep1

description: ZT6, control diet #1

source_name: CD mouse liver at ZT6, biological rep1


title: HF mouse liver at ZT6, biological rep1

description: ZT6, high fat diet #1

source_name: HF mouse liver at ZT6, biological rep1


title: WT, BMP4, d56, rep1

tag: genotype


title: T89I, TGFb3, d56, rep1


title: CD mouse liver at ZT6, biological rep3

description: ZT6, control diet #3

source_name: CD mouse liver at ZT6, biological rep3


title: T89I, BMP4, d56, rep3


title: CD mouse liver at ZT18, biological rep2

description: ZT18, control diet #2

source_name: CD mouse liver at ZT18, biological rep2


title: T89I, BMP4, d56, rep2


title: T89I, BMP4, d56, rep1


title: V620I, BMP4, d56, rep4

value: TRPV4-V620I mutation


title: V620I, TGFb3, d56, rep3


title: CD mouse liver at ZT18, biological rep3

description: ZT18, control diet #3

source_name: CD mouse liver at ZT18, biological rep3


title: V620I, TGFb3, d56, rep2


title: V620I, TGFb3, d56, rep1


title: V620I, BMP4, d56, rep3


title: V620I, BMP4, d56, rep2


title: WT, TGFb3, d28, rep1

value: TGFb3 for 28 days


title: WT, TGFb3, d28, rep2


title: T89I, TGFb3, d28, rep2


title: V620I, BMP4, d56, rep1


title: WT, TGFb3, d28, rep3


title: V620I, TGFb3, d28, rep3


title: T89I, TGFb3, d28, rep3


title: T89I, TGFb3, d28, rep1


title: V620I, TGFb3, d28, rep1


title: V620I, TGFb3, d28, rep2


title: E0771-LG shPTN3

city: Washington

first: Marcel

middle: O

last: Schmidt

state: DC

address: 3970 Reservoir Road, N.W.,  NRB #E311

department: Oncology

institute: Georgetown University

data_processing:
Illumina multiplex analysis -> fastq
hisat2 alignment -> BAM
featurecounts -> DE table
Rsubread/limma, EdgeR
Assembly: mm10 (GRCm38)
Supplementary files format and content: all_dep_ctrl_noNA.csv: Comma-delimited text file includes CPM values for each Sample. Rsubread/limma, EdgeR.

source_name: breast cancer cell line

growth_protocol: Cells were grown in DMEM +10% FBS +1% PS.

extract_protocol:
Breast tumors or cell lines were removed or collected, preserved in -80C, and total RNA was harvested using the RNeasy kit (Qiagen). Sequencing results (fastq files) were provided by Novogene (Sacramento, CA) using Illumina Hiseq.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 3B10 was treated at 15mg/kg twice weekly.

tag: ptn kd

value: yes


title: E0771-LG shPTN1


title: E0771-LG shPTN2


title: E077-LG plko3

value: no


title: E077-LG plko2


title: E0771 shPTN3


title: E0771 shPTN1


title: BT474.D.hand.24hr.rep2

city: Los Angeles

first: Peyton

middle: J

last: Tebon

state: CA

address: 615 Charles E Young Dr S

department: Orthopaedic Surgery

institute: UCLA

data_processing:
pipeline-align-RNA v6.2.2 The align-RNA Nextflow pipeline allows users to align RNA-seq reads using STAR and HISAT2 for single and paired-end reads.
pipeline-quantitate-RNA v2.0.0 The quantitate-RNA pipeline quantitates RNA at the gene and transcript isoform level.
pipeline-quantitate-SpliceIsoform v2.0.5 This pipeline quantitates the relative usage of splice isoforms using aligned RNA-Seq data as input.
pipeline-call-RNAEditingSite v5.6.0 RNA editing events are called with REDItools2 by comparing DNA-seq (WGS) BAMs and RNA-Seq BAMs.
pipeline-call-FusionTranscript This nextflow pipeline detects the gene fusion events from the given RNA-seq data.
Assembly: Human NCBI genome build 36
Supplementary files format and content: tab-delimited of raw counts, TPM, normalized spliceisoforms, editing sits and fusion transcripts

source_name: Mammary gland, ductal carcinoma

growth_protocol: Cells were harvested from 2D culture in petri dishes (BT474 passage 5, MCF7 passage 2) and suspended in a cold solution of 3:4 Mammocult medium:Matrigel. Samples denoted "hand"  were plated as maxi-rings according the protocol outlined by Nguyen & Soragni (STAR Protocols, 2020). Samples marked "print" were incubated at 18C for 30 minutes prior to extrusion through a 25G needle with 15kPa using a Cellink BioX bioprinter. Cells were grown in 3D for 1, 24, or 72 hours at 37C, 5% CO2 in Mammocult medium. Medium was exchanged after 48 hours for samples culutred for 72 hours.

extract_protocol:
We added 1mL of 5mg/mL Dispase to each ring and incubated for 20 minutes at 37C. After the matrix was digested, cells were collected in media and spun at 1500xg for 5 minutes. The supernatant was aspirated and 45mL of cold PBS was added gently to the tube. We spun the tube at 2000xg for 5 minutes, and the supernatant was aspirated. The cell pellets were frozen quickly by placing tubes at -80C.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit (Cat.KK8420). The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand.  cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina NovaSeq 6000 for PE 2x150 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

value: breast cancer

tag: time point


title: BT474.E.print.72hr.rep2


title: E0771 shPTN2


title: MCF7.E.print.72hr.rep2

source_name: Mammary gland, adenocarcinoma


title: BT474.A.print.1hr.rep2


title: MCF7.F.hand.72hr.rep2


title: BT474.C.print.24hr.rep2


title: MCF7.C.print.24hr.rep2


title: E0771 plko3


title: MCF7.B.hand.1.hr.rep2


title: MCF7.A.print.1hr.rep2


title: E0771 plko2


title: BT474.F.hand.72hr.rep2


title: BT474.F.hand.72hr.rep1


title: PyMT 3B10 3

source_name: breast mammary tumor

tag: breast cancer model

value: MMTV-PyMT

value: FVB/N

tag: antibody treatment


title: E0771 plko1


title: PyMT 3B10 2


title: BT474.B.hand.1hr.rep2


title: BT474.E.print.72hr.rep1


title: PyMT 3B10 1


title: E077-LG plko1


title: BT474.C.print.24hr.rep1


title: BT474.B.hand.1hr.rep1


title: PyMT C44 3


title: BT474.A.print.1hr.rep1


title: MCF7.F.hand.72hr.rep1


title: 4T1 3B10 2

value: BALB/c


title: MCF7.D.hand.24hr.rep2


title: 4T1 C44 3


title: PyMT C44 2


title: BT474.D.hand.24hr.rep1


title: HeLa siEIF4A3 Input rep2

city: Chicago

first: Philip

middle: Cody

last: He

state: IL

address: 929 E 57th Street

institute: University of Chicago

data_processing:
Low quality reads were filtered using ‘fastq_quality_filter’, and adapter were clipped using ‘fastx_clipper’, then adapter-free were collapsed to remove PCR duplicates by using ‘fastx_collapser’ and finally reads longer than 15 nt were retained for further analysis (http://hannonlab.cshl.edu/fastx_toolkit/). Reads from rRNA were removed.
The preprocessed reads were mapped to hg38 using bowtie with ‘-v 3 -m 10 -k 1 –best –strata’ parameters.
Genome_build: hg38
Supplementary_files_format_and_content: text files include read counts for each Sample

source_name: Uterus

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
After irradiation, cells were harvested with a scraper, transferred to a microtube, pelleted at 4000 rpm for 3 min at 4°C, and then lysed in lysis buffer (150 mM NaCl, 0.5% NP-40, 50 mM Tris-HCl (pH 7.5), 2 mM EDTA) with cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail and SUPERase In at 4°C for 1 hour. Subsequently, the lysis mixture was centrifuged at 17,000 g at 4°C for 30 min and the supernatant was carefully collected. The samples were then treated with RNase T1 (1 u/µL) at RT for 15 min and centrifuged to collect the supernatant, 10% of which was saved as input. Then YTHDF2 antibody-conjugated protein G beads prepared by incubating antibody and beads at 4°C for 6 hours were added into the samples and incubate overnight. After beads washing, 10 u/µl RNase T1 was added and incubated at RT for 8 minutes. After incubation, the beads were extensively washed and then resuspended in 50 µL of SDS-PAGE loading buffer and heated at 95°C for 5 min. The RNA was finally extracted by cutting and recovering the band of YTHDF2-RNA complex from the SDS-PAGE gel. Before library preparation, end-repair by PNK and ATP was performed for the input and IP RNAs. The
Library was prepared by NEBNext® Small RNA Library Prep kit following manufacturer's protocols.

treatment_protocol: Irradiated twice with 400 mJ/cm2 at 254 nm in Stratalinker on ice.

value: Uterus

value: HeLa

value: epithelial cell

value: EIF4A3 knockdown

value: UV 254 nm crosslink


title: Single cell RNA-seq (scRNA-seq) of 48h GCBC cultures

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

data_processing:
The 10x raw data from each sample were demultiplexed and FASTQ files were generated using the “mkfastq” Cell Ranger pipeline (v5.0.0, 10X Genomics).
Cell Ranger “count” was used to align reads to the mm10 reference genome, and mRNA transcript, and HTO unique molecular identifier (UMI) quantification tables were generated.
The raw barcode matrix files generated from the Cell Ranger pipeline were further utilized for downstream analysis using the Seurat package (v4.0.0) in R (v3.4.3).
Genome_build: Mus musculus reference genome (mm10).
Supplementary_files_format_and_content: Raw count output file from Cellranger.

source_name: Stimulated GCBC from spleen

extract_protocol:
RNA was isolated using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takata Cat# 634894).
Single Cell RNA-Seq

treatment_protocol: GCBC were purified from B1-8i mice at day 14 post NP-CGG immunization and stimulated with IL-21 + anti-CD40, NP-Ficoll + anti-CD40 and IL-21 + NP-Ficoll + anti-CD40 for 48 hours, as described in cell preparation and stimulation. After 48 hours, cells were washed and exposed to 2.4G2 antibody to block Fc receptors. 1x10^6 live cells of each stimulation condition (7AAD-) were sorted individually using a BD FACS ARIAII. Cells were counted and combined at equal ratios post-sort. 24x10^3 pooled cells were subjected to 10x Genomics run.

value: B1-8i mice

value: Spleen

value: GCBC cell


title: MCF7.A.print.1hr.rep1


title: PyMT C44 1


title: 4T1 3B10 3


title: MCF7.D.hand.24hr.rep1


title: MCF7.C.print.24hr.rep1


title: 4T1 3B10 1


title: HeLa siEIF4A3 IGF2BPs-CLIP rep2


title: HeLa siEIF4A3 YTHDF2-CLIP rep2


title: HeLa siControl YTHDF2-CLIP rep2

value: control knockdown


title: HeLa siEIF4A3 Input rep1


title: MCF7.B.hand.1.hr.rep1


title: HeLa siEIF4A3 YTHDF2-CLIP rep1


title: HeLa siControl Input rep1


title: HeLa siControl  IGF2BPs-CLIP rep1


title: 4T1 C44 1


title: HeLa siControl YTHDF2-CLIP rep1


title: HeLa siControl Input rep2


title: HeLa siControl Input for RiboLace  rep2

data_processing:
Raw reads were trimmed by Cutadapt to remove low-quality bases and adapters then aligned to the human genome (hg38) using STAR.
Genome_build: hg38
Supplementary_files_format_and_content: text files include read counts for each Sample

molecule: polyA RNA

extract_protocol:
RNA samples are extracted by RIBOLACE Ribosome Profiling All-In-One Set following manufacturer's protocols.
Library was prepared by Illumina stranded mRNA library kit following manufacturer's protocols.

value: 10 ug/mL of cycloheximide (CHX) for 5 min at 37°C


title: HeLa siControl Input for RiboLace rep1


title: Hippocampus_Control_rep7

city: Sao Paulo

first: Camila

last: Nascimento

state: Sao Paulo

address: Rua Dr. Ovídio Pires de Campos, 785

department: Psychiatry

country: Brazil

institute: University of Sao Paulo

description: Gene expression of hippocampus of control

hyb_protocol: 1.5 ug of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3 per ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray (G4851C) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan settings for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software v11.5.1.1 (Agilent) using default parameters and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.).

source_name: Control, Hippocampus, replicate 1

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent Technologies, EUA) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were determined on the NanoVue spectrophotometer (GE Health Care, USA).

extract_protocol: Total RNA was extracted using the QIAsymphony RNA Kit (Qiagen Inc., Düsseldorf, Germany). The RNA quality and RNA integrity number (RIN) were assessed by automated electrophoresis using the Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara,CA). Samples with RIN ≥6.2 were employed.

treatment_protocol: We dissected 30mg of the snap frozen hippocampus and homogenized the tissue.

value: Brain

value: female

tag: age


title: Hippocampus_Control_rep9

tag: Sex


title: Hippocampus_Control_rep8


title: Hippocampus_Control_rep6


title: Hippocampus_Control_rep11


title: Hippocampus_Control_rep2


title: MCF7.E.print.72hr.rep1


title: HeLa siControl  IGF2BPs-CLIP rep2


title: Hippocampus_Control_rep1


title: Hippocampus_Control_rep10

value: male


title: Hippocampus_BipolarDisorder_rep10

description: Gene expression of hippocampus of bipolar disorder

source_name: Bipolar Disorder, Hippocampus, replicate 1


title: 4T1 C44 2


title: HeLa siEIF4A3 IGF2BPs-CLIP rep1


title: HeLa siEIF4A3 RiboLace rep1


title: HeLa siEIF4A3 Input for RiboLace  rep2


title: U87 siEIF4A3 Input rep2

data_processing:
Raw reads were trimmed with Trimmomatic-0.39
Trimmed reads were aligned to human genome and transcriptome (hg38) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters.
Mapped reads were separated by strands with samtools (version 1.9)
Genome_build: hg38
Supplementary_files_format_and_content: text files include read counts for each Sample

extract_protocol:
Total RNA was purified by TRIzol reagent. mRNA was isolated by Dynabeads™ mRNA DIRECT™ Purification Kit following manufacturer's protocols.
Library was prepared by Illumina stranded mRNA library kit following manufacturer's protocols.


title: HeLa siEIF4A3 RiboLace rep2


title: HeLa siEIF4A3 Input for RiboLace  rep1


title: Hippocampus_Control_rep4


title: Hippocampus_Control_rep5


title: U87 siControl m6A-IP rep1


title: U87 siEIF4A3 Input rep1


title: HeLa siControl RiboLace rep2


title: Hippocampus_BipolarDisorder_rep6


title: HeLa siControl RiboLace rep1


title: Hippocampus_Control_rep3


title: Hippocampus_BipolarDisorder_rep11


title: U87 siEIF4A3 m6A-IP rep2


title: U87 siControl m6A-IP rep2


title: Hippocampus_BipolarDisorder_rep2


title: Hippocampus_BipolarDisorder_rep3


title: ATHB8-GFP_24h_uninduced_rep3

city: tokyo

first: Kyoko

last: Ohashi-Ito

address: 7-3-1 hongo bunkyo-ku

department: biological sciences

country: Japan

institute: the university of tokyo

description: Estrogen-inducible ATHB8-GFP transformed cells treated without estrogen for 24h

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

source_name: ATHB8 culture cell, 24h

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix)

growth_protocol: Cell suspension was cultured on a rotary shaker at 124 rpm at 23°C in the dark.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN)

treatment_protocol: Cultured cells were treated with/without 5 μM estrogen for 24h

value: culture cell, Alex

value: treated without estrogen


title: Hippocampus_BipolarDisorder_rep8


title: Hippocampus_BipolarDisorder_rep7


title: Hippocampus_BipolarDisorder_rep9


title: Hippocampus_BipolarDisorder_rep5


title: U87 siControl Input rep2


title: Hippocampus_BipolarDisorder_rep4


title: U87 siEIF4A3 m6A-IP rep1


title: U87 siControl Input rep1


title: HepG2 siUPF1 3h rep2

data_processing:
Raw reads were trimmed by Trimmomatic-0.39 to remove low-quality bases and adapters,
Reads were aligned to the human genome (hg38), together with ERCC RNA spike-in control (Thermo Fisher Scientific) using HISAT2 (version 2.1.0) with ‘--rna-strandness RF -k 5’ parameters.
Genome_build: hg38
Supplementary_files_format_and_content: text files include read counts for each Sample

source_name: Liver

growth_protocol: HeLa or HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

value: Liver

value: epithelial-like

value: UPF1 knockdown

value: actinomycin D treatment 0 hour


title: TALL-104, control, DMSO 24 hour treatment, biological replicate 3

city: Providence

first: Kelsey

middle: Elizabeth

last: Huntington

state: RI

address: 70 Ship Street, Campus Box G-E5

department: Pathology and Laboratory Medicine

institute: Brown University

description: Gene expression data from a human CD8+ T cell line

hyb_protocol: Following biotinylation, 5.15 μg of cDNA were hybridized for 17 hr at 45C on GeneChip Array. GeneChips were washed and stained using Protocol FS450_0001 on the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Applied Biosystems Transcriptomic Analysis Console (TAC) software version 4.0 (RRID:SCR_016519) was used to calculate fold-changes in gene expression relative to the control samples. Values were considered statistically significant for p values <0.05. The TAC 4.0.2 user guide was used (Publication # 703150, Revision 8).

source_name: TALL-104 human cell line

label_protocol: GeneChip™ Human Transcriptome Array 2.0 assays were conducted according to manufacturer instructions in two batches using randomized samples to limit batch effects (Cat# 902162, Applied Biosystems, Waltham, MA, USA). We started with 50 ng total RNA. 15 μg of in vitro transcribed cRNA was used to make the second cycle cDNA. We then took 5.5 μg of second cycle sscDNA into fragmentation. Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 5.15 μg total sscDNA (GeneChip WT PLUS Reagent Kit protocol, Affymetrix, Part# 703174, revision 1).

growth_protocol: Human CRC cells HCT-116 (RRID:CVCL_0291), HT-29 (RRID:CVCL_0320), and KM12C (RRID:CVCL_9547) were used in this study. HCT-116 and HT-29 cells were cultured in McCoy’s 5A (modified) Medium supplemented with 10% FBS and 1% Penicillin-Streptomycin. KM12C cells were cultured in Eagle's Minimal Essential Medium supplemented with 10% FBS and 1% Penicillin-Streptomycin.  Human immune cells NK-92 (RRID:CVCL_2142) and TALL-104 (RRID:CVCL_2771) were also used in this study. NK-92 cells were cultured in Alpha Minimum Essential medium supplemented with 2 mM L-glutamine, 1.5 g/L sodium bicarbonate, 0.2 mM inositol, 0.1 mM 2-mercaptoethanol, 0.02 mM folic acid, 12.5% horse serum, and 12.5% FBS. TALL-104 cells were cultured in RPMI-1640 containing 20% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin. Recombinant human IL-2 (Miltenyi cat# 130-097744) with a final concentration of 100 units/mL was added all immune cell culture media. All cell lines were incubated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: RNA was isolated from cell pellets in batches of 6 using an RNeasy plus Mini Kit (Cat # 74134, Qiagen, Hilden, Germany) according to manufacturer instructions. Acceptable RNA concentration and quality were verified with Nanodrop and Bioanalyzer measurements.

treatment_protocol: A total of 0.5E6 tumor cells (HCT-116, HT-29, KM12C) were plated in a 6-well plate and allowed to adhere overnight before 24-hour treatment with 1 μM elraglusib or DMSO (no treatment [NT] vehicle only control).  1E6 immune cells (NK92, TALL-104) were plated and treated with 1 μM elraglusib or DMSO (no treatment [NT] vehicle only control) for 24 hours. Samples were prepared in triplicate.

value: CD8+ T

value: DMSO 24 hour treatment


title: Hippocampus_BipolarDisorder_rep1


title: ATHB8-GFP_24h_induced_rep3

description: Estrogen-inducible ATHB8-GFP transformed cells treated with estrogen for 24h

value: treated with estrogen


title: ATHB8-GFP_24h_uninduced_rep2

value: Estrogen-inducible ATHB8-GFP transformed cells


title: HepG2 siControl 0h rep1


title: HepG2 siUPF1 6h rep2

value: actinomycin D treatment 6 hour


title: HepG2 siUPF1 6h rep1


title: TALL-104, control, DMSO 24 hour treatment, biological replicate 2


title: HeLa siControl 6h rep2

value: Uterus

value: HeLa

value: epithelial cell


title: HepG2 siControl 6h rep1

value: control knockdown

value: actinomycin D treatment 3 hour


title: HepG2 siUPF1 0h rep2


title: TALL-104, 9-ING-41 24 hour treatment, biological replicate 1

value: 9-ING-41 24 hour treatment


title: NK-92, control, DMSO 24 hour treatment, biological replicate 3

description: Gene expression data from a human natural killer cell line

source_name: NK-92 human cell line

value: natural killer


title: HepG2 siUPF1 3h rep1


title: HepG2 siControl 3h rep2


title: ATHB8-GFP_24h_uninduced_rep1

value: culture cell, Alex

value: treated without estrogen


title: HepG2 siControl 6h rep2

value: Liver

value: epithelial-like


title: TALL-104, control, DMSO 24 hour treatment, biological replicate 1


title: TALL-104, 9-ING-41 24 hour treatment, biological replicate 3


title: HepG2 siControl 3h rep1


title: HeLa siEIF4A3 0h rep2

value: EIF4A3 knockdown

value: actinomycin D treatment 0 hour


title: HepG2 siUPF1 0h rep1

value: UPF1 knockdown


title: ATHB8-GFP_24h_induced_rep2

value: treated with estrogen


title: TALL-104, 9-ING-41 24 hour treatment, biological replicate 2

value: CD8+ T


title: sample 7

city: Wuhan

first: Yuehan

last: Li

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

source_name: Extracellular vesicles from Fallopian tube

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.


title: sample 8

value: Extracellular vesicles from Fallopian tube


title: HeLa siEIF4A3 3h rep2

value: Uterus


title: HeLa siControl 0h rep2

value: HeLa


title: sample 4


title: HepG2 siControl 0h rep2


title: HeLa siEIF4A3 6h rep2

value: epithelial cell

value: actinomycin D treatment 6 hour


title: sample 3


title: sample 6


title: HeLa siControl 3h rep2

value: control knockdown

value: actinomycin D treatment 3 hour


title: HeLa siControl 6h rep1


title: sample 2


title: HeLa siEIF4A3 3h rep1


title: NK-92, 9-ING-41 24 hour treatment, biological replicate 3

value: natural killer

value: 9-ING-41 24 hour treatment


title: sample 1


title: NK-92, control, DMSO 24 hour treatment, biological replicate 2

value: DMSO 24 hour treatment


title: NK-92, 9-ING-41 24 hour treatment, biological replicate 2


title: ATHB8-GFP_24h_induced_rep1

value: culture cell, Alex

value: Estrogen-inducible ATHB8-GFP transformed cells


title: HeLa siEIF4A3 6h rep1

value: EIF4A3 knockdown


title: HeLa siControl 3h rep1


title: NK-92, control, DMSO 24 hour treatment, biological replicate 1


title: HeLa siEIF4A3 0h rep1

value: actinomycin D treatment 0 hour


title: WRO-Vemr6-Vem2uM-2

city: Houston

first: Irene

middle: M

last: Min

state: TX

address: 6565 Fannin Street

department: Radiology

institute: Houston Methodist Research Institute

description: expression.WRO.xls

data_processing:
Illumina bcl2fastq v1.8.4 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file,  normalized expression

source_name: WRO cell line

growth_protocol: The 8505C cell line was obtained from DSMZ (#ACC 219), and the WRO cell line was generously provided by Dr. Juillard’s laboratory at UCLA. Two human immortalized undifferentiated BRAFV600E mutant thyroid carcinoma cell lines (8505C, WRO), and their respective vemurafenib-resistant clones (8505C-Res-1, WRO-Res-6) were grown at 37°C under 5% CO2. All cell lines were grown in RPMI-1640 media supplemented with L-glutamine, 10% fetal bovine serum (FBS) and antibiotic and antimycotic solution (ThermoFisher). For vemurafenib-resistant clones additionally contained 1 µM vemurafenib (Selleck Chemicals, #S1267). Cell lines were maintained from cryopreserved stocks made at low passage numbers and all cells used in experiments were of a passage number <30. Cell lines were authenticated using the STR typing service (ATCC).

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq RNA-Seq kit. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 1x51 end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Duplicates of the following RNA samples were processed for RNA-sequencing analysis:  Parental 8505C treated with 2 µM vemurafenib or 0.1% DMSO, 8505C-Res-1 treated with 2 µM vemurafenib or 0.1% DMSO, Parental WRO treated with 2 µM vemurafenib or 0.1% DMSO, and WRO-Res-6 treated with 2 µM vemurafenib or 0.1% DMSO. All treatment was for 24 hours.

value: WRO

tag: parental or vem-resistant clone

value: vemurafenib-resistant clone Vem-R6

tag: replicates

value: replicate 2

value: 2 uM of vemurafenib (PLX4032), 24 hours


title: KM12C, control, DMSO 24 hour treatment, biological replicate 3

description: Gene expression data from a human colorectal cancer cell line

source_name: KM12C human cell line

value: colorectal cancer


title: U87_E21K_72_2

city: Beijing

first: He

middle: Meng

last: Jiao

state: Beijing

address: No.20 Dongda Street

institute: Academy of Military Medical Sciences

description: 72 hpi

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size(RPKM) were calculated using a protocol from Chepelev et al.,Nucleic Acids Research, 2009. In short,exons from all isoforms.
Assembly: mm8
Supplementary files format and content: table-delimited text files inclide RPKM values for each Sample ......

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

value: tumor cells

value: E21K infected


title: U87_E21K_72_3

description: 72 hpi


title: WRO-Vemr6-Vem2uM-1

description: expression.WRO.xls

value: replicate 1


title: WRO-Vemr6-UT-2

description: expression.WRO.xls

value: 0.1% DMSO as diluent control, 24 hours


title: NK-92, 9-ING-41 24 hour treatment, biological replicate 1


title: U87_WT_72_3

description: 72 hpi

value: WT infected


title: WRO-Vemr6-UT-1

description: expression.WRO.xls


title: U87_WT_72_2

description: 72 hpi


title: U87_E21K_72_1

description: 72 hpi


title: KM12C, control, DMSO 24 hour treatment, biological replicate 2


title: HeLa siControl 0h rep1

value: Uterus

value: HeLa

value: epithelial cell

value: control knockdown


title: KM12C, control, DMSO 24 hour treatment, biological replicate 1

value: DMSO 24 hour treatment


title: U87_WT_72_1

description: 72 hpi


title: WRO-Par-Vem2uM-2

description: expression.WRO.xls

value: parental, unselected


title: KV_H1_20191114

city: Baltimore

first: Suvarna

last: Nadendla

state: MD

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description: Total RNAs extracted from PMNs from this donor D31 were of lower quality (lower RNA integrity [RIN] values), affecting overall RNA-seq data quality

data_processing:
Streptococcus pnemoniae : Sequence reads were trimmed for adaptor sequence and mapped to the EF3030 using bowtie v1.0 with parameters -mode=v --num_mismatches=2 --file-type=fastq --seedlen=28 --minins=0 --maxins=600 --library-type=fr  --args='--sam' --v --gzip
Homo sapiens: Sequenced reads were trimmedfor adaptor sequence and mapped to the 2018 GRCh38 Human genome assembly using HISAT v2.0 with parameters -mismatch-penalties=6,2 --softclip-penalties=2,1 --read-gap-penalties=5,3 --ref-gap-penalties=5,3 --min-intronlen=20 --max-intronlen=500000 --score-min=L,0,-0.2 --pen-cansplice=0 --num-threads=1 --pen-noncansplice=12 --pen-canintronlen=G,-8,1 --pen-noncanintronlen=G,-8,1 --rna-strandness=RF --dta-cufflinks=1 --num-alignments=5 --minins=0 --maxins=600 --no-unal=1 --args='' --v
Streptococcus pneumoniae: Transcripts Per Million values for gene features were calculated as described in D'Mello et al. Proceedings of the National Academy of Sciences of the United States of America vol. 117,52 (2020): 33507-33518. doi:10.1073/pnas.2010428117
Homo sapiens: Transcripts Per Million values for exon features were calculated as described in D'Mello et al. Proceedings of the National Academy of Sciences of the United States of America vol. 117,52 (2020): 33507-33518. doi:10.1073/pnas.2010428117
Assembly: Streptococcus pnemoniae:EF3030 accession NZ_CP035897.1 ;  Human: 2018 GRCh38 Human genome assembly GCA_000001405.15

source_name: Deep sequencing of cDNA from Streptococcus pneumoniae EF3030 bacteria and normalized human broncial epithelial cells (nHBEC), alone, together, and after coincubation with Influenza A virus pH1N1.

growth_protocol: Primary human bronchial epithelial cells were obtained from human lung tissue through the tissue donation program by the International Institute for the Advancement of Medicine . Cells were harvested from the human tracheobronchial tissues and plated onto collagen-coated 100-mm plates (Biocoat; Becton Dickinson), in BEGM medium to ~80% confluency, followed by passaging onto 6.5-mm Transwell inserts (0.4-μm pore size) with FNC coating (0407, AthenaES) and differentiated at an Air-Liquid Interface (ALI) using Lonza tissue culture reagents. Differentiation was further enhanced by adding 10 nM recombinant human neuregulin-1α/epidermal growth factor-like domain of heregulin-α (296-HR-050, R&D Systems) to the basolateral ALI media . Cells were incubated for approximately two weeks until appearance of ciliated cells and mucus production was seen.

extract_protocol:
On the day of RNA isolation, transwell samples were thawed and the membranes cut out using a scalpel. RNAprotect and isolated membranes were centrifuged at 10,000 rpm, to pellet the membrane and any dislodged cells, and the supernatant discarded. Pellets were then incubated in 100 μL of lysis buffer (10 μL of mutanolysin, 20 μL of proteinase K, 30 μL of lysozyme, 40 μL of TE buffer) for 10 minutes. Followed by mechanical disruption in 600 μL RLT buffer (RNeasy Mini Kit, Qiagen) containing 1% ß-mercaptoethanol, using a motorized pestle for 30 seconds. RNA was then captured on the RNeasy Mini Kit columns with DNase treatment on column (Qiagen protocol).
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following culture of differentiated human bronchial epithelial cells on transwells, cells were infected with pH1N1 or mock infected (no pH1N1 controls) for 72 h (~50% of cells infected with IAV). pH1N1 infected cells were then exposed to 1000 CFUs of Streptococcus pneumoniae strain EF3030 for 6 h. For pneumococcal EF3030 control samples, ~50,000 CFUs of EF3030 were cultured in ALI media for 6 hours. 1ml of RNA protect was then added to all transwells and then stored in 5ml of RNAprotect Bacteria Reagent in 50 ml falcon tubes at -80C.

tag: treatment condition

value: Co-culture

tag: human cell type

value: nHBEC

tag: incubation time


title: KV_H4_20200130


title: KM12C, 9-ING-41 24 hour treatment, biological replicate 3

value: 9-ING-41 24 hour treatment


title: KV_H3_20200130


title: U87_PBS_72_3

description: 72 hpi

value: mock


title: U87_PBS_72_2

description: 72 hpi


title: U87_PBS_72_1

description: 72 hpi


title: WRO-Par-Vem2uM-1

description: expression.WRO.xls

value: WRO

value: 2 uM of vemurafenib (PLX4032), 24 hours


title: 2269-RELAK5R

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

country: France

institute: Institut Curie

data_processing:
For transcriptional response to cGAMP, the data was aligned to the hg19 genome (ENSEMBL annotation v.74) using STAR (v 2.6.1) after trimming with TrimGalore (v 0.6.2). Additional quality control was done with picard (v.2.18.15), RSeQC (v.2.6.4) and preseq (v.2.0.3). Read counts were generated with STAR. We filter the count matrix to only keep genes that have in at least one sample a TPM value of 1. TPM values were calculated with exonic gene lengths.
For RELA vs RELAK5R transcriptional response, analysis of sequencing data quality, reads repartition (e.g., for potential ribosomal contamination), inner distance size estimation, genebody coverage, strand-specificity of library were performed using FastQC v0.11.2, Picard-Tools v1.119, Samtools v1.0, and RSeQC v2.3.9. Reads were mapped using STAR v2.7.5a on the human hg38 genome assembly and read count was performed using featureCount from SubRead v1.5.0. Gene expression was estimated as described previously using Human FAST DB v2022_1 annotations. Only genes expressed in at least one of the two compared conditions were analyzed further. Genes were considered as expressed if their FPKM value was greater than FPKM of 96% of the intergenic regions (background).
Assembly: hg19/hg38
Supplementary files format and content: GSE182647_tablecounts_raw.csv.gz: raw counts for samples regarding transcriptional response to cGAMP
Supplementary files format and content: GSE182647_tablecounts_tpm.csv.gz: TPM normalized expression levels for samples regarding transcriptional response to cGAMP
Supplementary files format and content: deseq2_normalized_expression_with_annotations.txt: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2022_1 were also provide

source_name: blood

growth_protocol: PBMCs were isolated from blood donated on the same day. Isolated PBMCs were stored overnight in DC media at 4C. The following moorning, CD4+ T cells were isolated by negative selection, TCR was subsequently activated using Dynabeads at a ratio of 1:5 and cultured in Xvivo + recombinant human IL-2 (100 U/ml) for 3 days.

extract_protocol:
RNA was extracted using macherey-nagel DNA, RNA and protein purification kit as per manufacturer's instructions.
RNA libraries were prepared using standard Illumina protocol with TruSeq stranded mRNA kit.

treatment_protocol: For the transcriptional response to cGAMP, 3 days post TCR stimulation, CD4+ T cells were stimulated with cGAMP (6ug/ml) delivered by digitonin mediated membrane permeabilization. For RELA vs RELAK5R transcriptional response, CD4+ T cells were transduced with either pTRIP-SFFV-GFP or pTRIP-SFFV-GFP-RELA or pTRIP-SFFV-GFP-RELA K5R and RNA was isolated 4 days post-transduction.

value: blood

value: activated CD4+T cells

value: untreated


title: 2269-RELA


title: 2269-GFP


title: KM12C, 9-ING-41 24 hour treatment, biological replicate 2

value: colorectal cancer


title: WRO-Par-UT-2

description: expression.WRO.xls

value: replicate 2

value: 0.1% DMSO as diluent control, 24 hours


title: 2266-RELAK5R


title: HT-29, control, DMSO 24 hour treatment, biological replicate 3

source_name: HT-29 human cell line


title: KM12C, 9-ING-41 24 hour treatment, biological replicate 1


title: WRO-Par-UT-1

description: expression.WRO.xls

value: replicate 1


title: sample 5

value: Extracellular vesicles from Fallopian tube


title: 2266-RELA


title: 8505C-Vemr1-Vem2uM-2

source_name: 8505C cell line

value: vemurafenib-resistant clone Vem-R1


title: 2266-GFP


title: 2265-RELA


title: 8505C-Vemr1-Vem2uM-1


title: 2265-RELAK5R


title: 2261-RELAK5R


title: 2261-RELA


title: 8505C-Vemr1-UT-1


title: 2261-GFP


title: 8505C-Vemr1-UT-2


title: 8505C-Par-Vem2uM-2


title: 8505C-Par-UT-2


title: HT-29, control, DMSO 24 hour treatment, biological replicate 1

value: DMSO 24 hour treatment


title: C30

city: Zhuzhou

first: Guo

last: Yuan

address: No. 116, Changjiang South Road, Tianyuan District

institute: Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4) .
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set，then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05. To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expressed gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count for each Sample

source_name: lung tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the atterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: lung tissue

value: Control


title: C29


title: C27


title: C24

value: Bleomycin


title: ALD2_1226_scGEX

city: Kiel

first: Elisa

last: Rosati

address: Rosalind-Franklin Strasse 12

department: Institute of Clinical Molecular Biology

institute: University of Kiel

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The preprocessing of the single cell RNA-data was performed with the 10x Genomics’ Cell Ranger software v6.0.0 using the reference GRCh38 v3.0.0 for the mappings.
Single-cell T-cell receptor repertoire clonotype tables were generated using the VDJ command of the Cellranger software v6.0.0 from 10xGenomics and using the reference GRCh38 version 5.0.0.
Assembly: h38
Supplementary files format and content: 2x sparse gene expression matrix (.h5)
Supplementary files format and content: 2x TCR contig file table (.csv)

source_name: Blood

extract_protocol:
Cells were sorted via FACS. Cells were centrifuged for 10 min at 400xg, the supernatant was carefully removed leaving 20 µL for loading on a Chromium Chip K (10x Genomics) according to the manufacturer’s instructions for processing with the Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v2.
gene expression libraries were prepared with the Next GEM Single Cell 5′ Library and Gel Bead Kit v2. TCR single-cell libraries were subsequently prepared with the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell. Libraries were sequenced on Illumina NovaSeq 6000 machine with 2x100 bp for gene expression, aiming for 50,000 reads per cell for gene expression and 5000 reads per cell for TCR libraries.

value: Blood

value: T cell, CD154+

tag: diagnosis

value: ALD


title: ALD2_1226_scTCR

description: 10x Genomics

data_processing:
The preprocessing of the single cell RNA-data was performed with the 10x Genomics’ Cell Ranger software v6.0.0 using the reference GRCh38 v3.0.0 for the mappings.
Single-cell T-cell receptor repertoire clonotype tables were generated using the VDJ command of the Cellranger software v6.0.0 from 10xGenomics and using the reference GRCh38 version 5.0.0.
Assembly: h38
Supplementary files format and content: 2x sparse gene expression matrix (.h5)
Supplementary files format and content: 2x TCR contig file table (.csv)
Library strategy: scTCR-seq


title: 2265-GFP


title: 8505C-Par-UT-1

tag: cell line

value: parental, unselected


title: C11

tag: treatment


title: C23


title: D4 -CD4T -CGAMP

data_processing:
The data was aligned to the hg19 genome (ENSEMBL annotation v.74) using STAR (v 2.6.1) after trimming with TrimGalore (v 0.6.2)
Additional quality control was done with picard (v.2.18.15), RSeQC (v.2.6.4) and preseq (v.2.0.3)
Read counts were generated with STAR. We filter the count matrix to only keep genes that have in at least one sample a TPM value of 1. TPM values were calculated with exonic gene lengths.
Differential expression analysis was done using DESeq2 (v 1.26.0)
Pathway analysis was done using clusterProfilter (v 3.14.3)
Transcription factor analysis was done with HOMER
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated file of raw counts from STAR
Supplementary_files_format_and_content: Comma-separated file of normalized TPM counts

source_name: activated CD4+T cells

growth_protocol: PBMCS were isolated from blood donated on the same day. Isolated PBMCS were stored overnight in DC media at 4C. The following moorning, CD4+T cells were isolated by negtive selection, TCR was subsequently activated using dynabeads at a ratio of 1:5 and cultured in Xvivo +rhuIL2 (100U/m) for 3 days.

extract_protocol:
RNA was extracted using macherey-nagel DNA, RNA and protein purification kit as per manufacturer's instructions
RNA libraries were prepared using standard Illumina protocol with TruSeq stranded mRNA kit

treatment_protocol: 3 days post TCR stimulation, CD4+T cells were stimulated with cGAMP (6ug/ml) delivered by digitonin mediated membrane permeabilization and TSA 100nM for 6 hrs . Cell pellets were stored at -80C for RNA extraction

tag: agent

value: cGAMP

tag: donor


title: C5

tag: tissue

value: Donepezil


title: 8505C-Par-Vem2uM-1

value: 2 uM of vemurafenib (PLX4032), 24 hours


title: VFP+ CD69+ spleen CD4 T cells, IL-21 positive [S3plus]

city: Hershey

first: Aron

last: Lukacher

address: 500 University Dr.

department: Microbiology & Immunology

institute: Penn State College of Medicine

description: CD69+ CD4 T cells from the spleens of Mouse Polyomvirus-infected mice at 15 dpi were sorted to purity (enriched >94% based on post-sort analysis) using a BD FACSAria II (BD Biosciences, San Diego, CA).

data_processing:
The STAR Aligner v2.5 (github.com/alexdobin/STAR) with two-pass method
Raw sequence reads were trimmed for adaptor sequence/read quality was checked with FastQC
Trimmed sequence reads  were aligned to mouse genome GRCm38.96.
The gene expression  profiles were quantified using Bioconductor R package of DESeq2 version 1.26 to get the reads per kilobase of transcript per million mapped reads (RPKM)
Assembly: mm10 (GRCm38.96)
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: Spleen

extract_protocol:
RNA was extracted using Trizol reagent (Ambion Life Technologies, Austin, TX).
mRNA was obtained from total RNA after depletion of rRNA using RiboGone-Mammalian Kit (Takara Bio Inc., Liaoning, China) and then purified using the AMPure PCR Purification Kit (Beckman Coulter, Indianapolis, IN). cDNA libraries were subsequently prepared using the SMARTer Stranded RNA-seq Kit (Takara Bio Inc., Liaoning, China).

value: Spleen

tag: cell type

value: VFP+ CD4 T cell

tag: genotype

value: B6.IL21-vfp knock-in reporter mouse


title: HT-29, 9-ING-41 24 hour treatment, biological replicate 2

value: colorectal cancer

value: 9-ING-41 24 hour treatment


title: ALD1_190_scTCR

description: 10x Genomics


title: VFP+ CD69+ spleen CD4 T cells, IL-21 positive [S2plus]


title: HT-29, 9-ING-41 24 hour treatment, biological replicate 1


title: HCT-116, control, DMSO 24 hour treatment, biological replicate 2

source_name: HCT-116 human cell line


title: HCT-116, control, DMSO 24 hour treatment, biological replicate 3


title: C2


title: HT-29, 9-ING-41 24 hour treatment, biological replicate 3


title: D3 -CD4T -CGAMP

value: untreated


title: HT-29, control, DMSO 24 hour treatment, biological replicate 2

value: DMSO 24 hour treatment


title: VFP- CD69+ spleen CD4 T cells, IL-21 negative [S2_0]

value: VFP- CD4 T cell


title: HCT-116, control, DMSO 24 hour treatment, biological replicate 1


title: D3 -CD4T -BUF

value: buffer


title: D2 -CD4T -CGAMP


title: VFP- CD69+ spleen CD4 T cells, IL-21 negative [S1_0]


title: ALD1_190_scGEX

description: 10x Genomics


title: D2 -CD4T -BUF


title: VFP- CD69+ spleen CD4 T cells, IL-21 negative [S3_0]


title: VFP- CD69+ brain CD4 T cells, IL-21 negative [b3_0]

description: CD69+ CD4 T cells from the brains of Mouse Polyomvirus-infected mice at 15 dpi were sorted to purity (enriched >94% based on post-sort analysis) using a BD FACSAria II (BD Biosciences, San Diego, CA).

source_name: Brain

value: Brain


title: D4 -CD4T -BUF


title: HCT-116, 9-ING-41 24 hour treatment, biological replicate 2


title: D1 -CD4T -CGAMP


title: D1 -CD4T -BUF


title: HCT-116, 9-ING-41 24 hour treatment, biological replicate 1


title: HCT-116, 9-ING-41 24 hour treatment, biological replicate 3


title: VFP+ CD69+ brain CD4 T cells, IL-21 positive [b2plus]


title: C3

value: lung tissue


title: VFP- CD69+ brain CD4 T cells, IL-21 negative [b2_0]


title: ALD2_1226_PBMCsCD4_bulkTCR_beta

data_processing:
PCR and sequencing error correction were performed through identification and selection of unique molecular identifiers using the software MiGEC, version 1.2.6
Filtered sequences were aligned on a TCR gene reference, clonotypes were identified, grouped and CDR3 sequences were identified using the software MiXCR version 3.0.14
Clonotype tables containing clonotype counts, frequencies, CDR3 nucleotide and amino acid sequences and V(D)J genes were obtained and used for further analysis.
Assembly: Deafult MiXCR 3.0.14 VDJ reference
Supplementary files format and content: Clonotype tables (.txt)
Library strategy: TCR-Seq

extract_protocol:
Qiagen RNAeasy micro kit
miLaboratory Human TCR profiling kit. Liver biopsies were obtained in RNAlater and transferred into 2ml tubes containing 600µl RLT+ buffer + 1% -Mercaptoethanol. Tissue was disrupted using the Qiagen tissue lyser. PBMCs were isolated from paired blood samples by density gradient centrifugation (Biocoll; Biochrom, Berlin, Germany) and CD4+ T cells were enriched using CD4 Microbeads (Miltenyi Biotec). RNA was isolated from liver samples and CD4+ T cells from PBMCs using the RNeasy Micro Kit (Qiagen). TCR libraries were prepared using human TCR RNA multiplex kit (MiLaboratories), according to the manufacturer’s protocol using 24 PCR cycles (liver) and 18 PCR cycles (blood) for the 1st PCR, and 14 PCR cycles (liver) and 16 PCR cycles (blood) for the 2nd PCR amplification. Libraries were sequenced on an Illumina NovaSeq6000 machine, SP v1.5 flow cells and 300 cycles. Data of both TCRα and β chains were obtained.

value: Blood

value: T cell, CD4+


title: ALD2_1226_PBMCsCD4_bulkTCR_alpha

value: ALD


title: VFP- CD69+ brain CD4 T cells, IL-21 negative [b1_0]


title: KV_HI1_20191114

description: Total RNAs extracted from PMNs from this donor D5 were of lower quality (lower RNA integrity [RIN] values), affecting overall RNA-seq data quality

organism:
Homo sapiens
Influenza A virus

tag: influenza a strain

value: Influenza A pH1N1

value: Co-culture

value: nHBEC


title: KV_HI3_20200130


title: ALD2_1226_liver_bulkTCR_alpha

value: Liver

value: T cell


title: VFP+ CD69+ brain CD4 T cells, IL-21 positive [b1plus]

value: VFP+ CD4 T cell

value: B6.IL21-vfp knock-in reporter mouse


title: KV_HI4_20200130


title: ALD1_190_PBMCsCD4_bulkTCR_beta


title: ALD2_1226_liver_bulkTCR_beta


title: ALD1_190_liver_bulkTCR_beta


title: ALD1_190_PBMCsCD4_bulkTCR_alpha


title: ALD1_190_liver_bulkTCR_alpha


title: VFP+ CD69+ brain CD4 T cells, IL-21 positive [b3plus]


title: whole body discarding last third from the cloaca, 37dph, rep1 [ATAC-seq]

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

data_processing:
Alignment of reads with Bowtiew2
Duplicated removal and correction of start position with Bedtools
Peak calling with MACS2 and IDR algorithm
Assembly: Turbot genome: http://ftp.ensembl.org/pub/release-107/fasta/scophthalmus_maximus/dna/
Supplementary files format and content: IDR peaks in BED format
Supplementary files format and content: bigWig format for displaying in a genome browser track

organism: Scophthalmus maximus

extract_protocol:
Turbots at different stages were collected to reach 75,000 cells per sample. 3dpf stage was treated with 1mg/ml pronase in 1X PBS to remove the chorion. Cells were lysated after incubation with 10mM Tris, 10mM NaCl, 3mM MgCl2, 0.1% NP40 for transposition reaction and PCR amplification.
Transposition with Tn5 enzyme and PCR amplification

tag: developmental stage

value: 37 days post hatching


title: whole body discarding last third from the cloaca, 23dph, rep2 [ATAC-seq]

value: 23 days post hatching


title: whole body discarding last third from the cloaca, 37dph, rep2 [ATAC-seq]


title: whole body discarding last third from the cloaca, 23dph, rep1 [ATAC-seq]


title: whole body discarding last third from the cloaca, 15dph, rep1 [ATAC-seq]

value: 15 days post hatching


title: whole body discarding last third from the cloaca, 15dph, rep2 [ATAC-seq]


title: Medial prefrontal cortex,CCI operation contralateral (Right side), Day 28 after operation [C4R]

city: Shanghai

first: Qimin

last: Zheng

address: 131 Dongan Road,Xuhui District

department: Institutes of Brain Science

institute: Fudan University

data_processing:
Hisat2 v 2.0.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Hisat2Hisat2 (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2 (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using Hisat2
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Brain tissue

extract_protocol:
RNA was harvested using TransZol Up Plus RNA Kit (Cat#ER501-01，Trans) 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  Illumina mRNA sample preparation kits following manufacturer's protocols.

value: Brain tissue

value: WT

value: chronic constriction injury of sciatic nerve operation

tag: time

value: Day 28


title: Medial prefrontal cortex,Naïve mice, Day 28  habituation [N1]

value: no treatment


title: Medial prefrontal cortex,Naïve mice, Day 28  habituation [N2]


title: whole, 3dpf, rep2 [ATAC-seq]

source_name: whole animal

value: whole animal

value: 3 days post fertilization


title: Medial prefrontal cortex,CCI operation ipsilateral (Left side), Day 28 after operation [C4L]


title: Medial prefrontal cortex,CCI operation contralateral (Right side), Day 28 after operation [C3R]


title: Medial prefrontal cortex,CCI operation ipsilateral (Left side), Day 28 after operation [C3L]


title: whole, 3dpf, rep1 [ATAC-seq]


title: VFP+ CD69+ spleen CD4 T cells, IL-21 positive [S1plus]

value: Spleen


title: Medial prefrontal cortex,Naïve mice, Day 28  habituation [N4]


title: Medial prefrontal cortex,CCI operation ipsilateral (Left side), Day 28 after operation [C2L]


title: Medial prefrontal cortex,CCI operation contralateral (Right side), Day 28 after operation [C1R]


title: Medial prefrontal cortex,CCI operation ipsilateral (Left side), Day 28 after operation [C1L]


title: Medial prefrontal cortex,CCI operation contralateral (Right side), Day 28 after operation [C2R]


title: Medial prefrontal cortex,Naïve mice, Day 28  habituation [N3]


title: LV-MBD5 IP

city: Chongqing

first: Feng-lin

last: Tang

address: No. 1, Youyi Road, Yuzhong District, Chongqing

department: Chongqing Key Laboratory of Neurology

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Mus musculus from GEO database using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
bigWig files were generated using deepTools.
Supplementary files format and content: Mus sapiens GRCm38
Supplementary files format and content: bigWig

source_name: hippocampus

extract_protocol:
The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature by a vacuum pump, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tissue was then collected and frozen in liquid nitrogen, and grinded by tissue lyser. The grinded powder was treated with lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-FLAG antibody (Catalogue NO. F1804, Sigma‒Aldrich, USA) and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: hippocampus

value: tissue

value: Kainic acid model after MBD5 lentivirus infection one month


title: LV-MBD5 input


title: PF_NF54_Batch 2, scRNAseq

city: Stockholm

first: Mubasher

last: Mohammed

state: Stockholm lan

address: Svante Arrhenius Väg 20c, MBW, Stockholms University

department: Department of Molecular Biosciences, the Wenner-Gren Institute

institute: Stockholm University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the STAR (Version 2.5.3a)
Assembly: P. falciparum genome downloaded from PlasmoDB (PlasmoDB-39_Pfalciparum3D7_Genome.fasta)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Plasmodium falciparum

source_name: Pfalciparum, NF54

extract_protocol:
Plasmodium falciparum NF54 gametocyte producing cell line were committed to sexual stages (gametocytes) and pooled to 1% gametocytaemia and 50% hematocrit. Gametocyte were membrane fed to Anopheles gambiae adult mosquiteo and dissected at time points; 2, 4, 8, 12 and 20 hours post infection, parasites were then isolated using Micromanupulation based on Anti-Pfs25 antibody conjugated to Alea-488 and Hoechst stain. cDNA library were prepared using SMART-seq2 and ScRNA-seq data were then analyzed using various computational tools.
SMART-seq2

value: Pfalciparum, NF54

value: pfalciparum 3D7


title: PF_NF54_Batch 1, scRNAseq

value: Pfalciparum 3D7


title: 43549

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_DelDup5

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
The raw sequenced reads were aligned by Hisat2 against the Rno6.v96. 32623 ENSEMBL Gene Ids were quantified aligning to the Rno6.v96 assembly. HTSeq-count was used to generate the raw counts.
The downstream analyses were carried on with in-house bash scripts and R version 3.6 scripts using FCROS and DESeq2 packages to identify the DEGs. Raw reads and normalized counts have been deposited in GEO
Assembly: rn6

extract_protocol: Total RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for --- minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis. The Whole genome expression sequencing was performed by the platform using Illumina Hiseq 4000 and generating single-end RNA-Seq reads of 50 bps length.

tag: genetic background

value: Sprague Dawley

tag: Sex

value: M

value: Del/Dup


title: 43503

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Del3

value: Del/+


title: 43516

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Del4


title: 43495

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Del1


title: RNA-seq_BBC1115_rep2

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
Raw reads were mapped to the reference genome assembly mm10 using STAR mapping tool (Dobin et al, 2013l; PMID: 23104886).
Assembly: mm10
Supplementary files format and content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

source_name: murine AML cells

growth_protocol: Above cell lines were cultured in conditions as described in this study.

extract_protocol:
Total RNAs were extracted from ~ 1 million cells using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

treatment_protocol: treated with drugs as indicated.

tag: strain

value: engineered murine acute myeloid leukemia cell line (MLL-AF9/NRAS G112D)

tag: biological replicate


title: KV_HIB4_20200130

organism:
Streptococcus pneumoniae
Homo sapiens
Influenza A virus

value: Influenza A pH1N1

tag: treatment condition

value: Co-culture

tag: human cell type

value: nHBEC

tag: s. pneumoniae strain


title: RNA-seq_BBC1115_rep1

tag: cell line


title: 43539

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_DelDup4


title: 43524

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_DelDup3


title: KV_HIB3_20200130

tag: incubation time


title: 43508

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_wt6

value: wt


title: KV_HIB1_20191114


title: 43510

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_DelDup2


title: RNA-seq_OTX015_rep1

tag: treatment


title: RNA-seq_RVX208_rep2


title: ChIP-Seq_RPB1_RPB3_IAA_1h_rep2

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

data_processing:
ChIP-Seq raw data were processed using a custom pipeline that builds on published workflows with minor modifications. Briefly, raw reads after adapter trimming and quality control with cutadapt and RseQC were aligned to a concatenated genome comprised of mouse mm10 and fly dm6 assemblies using bowtie2 with options (-very-sensitive-local) as described in the ChIP-seq section.
Only properly paired and uniquely aligned reads were retained for subsequent processing. Reads mapped to the mouse genome were normalized to total reads originating from Human HEK293T spike-in cells, and the normalization factor was calculated as previously described (Jiang et al., 2020).
SAMtools (v 0.1.19) and sambamba (v0.7.0) were used to filter unmapped reads, multiple mapped reads, and potential PCR duplicates. The final BAM files were converted to bigwig and normalized to spike-in controls using bamCoverage from deeptools.
For visualization purposes, the bigWig format tracks from two biological replicates for each treatment were merged into an averaged signal using the mean operator from the WiggleTools (v1.2) package (Zerbino, Johnson, et al. 2014).
Assembly: mm10 and hg19
Supplementary files format and content: bigwig files

source_name: mouse embryonic stem cells (V6.5)

growth_protocol: For ChIP-seq, dRPB3 or RPB3 degron cells were cultured in DMEM-KO (Thermo Fisher, Cat#10829018) supplemented with 15% FBS (Gibco, Cat#10099141C), 1× penicillin/ streptomycin (Gibco, Cat#15140122), 1 × L-glutamine (Gibco, Cat#25030081), 1 × non-essential amino acids (Gibco, Cat#11140050), 1 × nucleoside (Millipore, Cat#ES-008-D), 3 μM CHIR99021 (Selleck, Cat#S1263), 0.5 μM PD0325901 (Selleck, Cat#S1036), 143 μM 2-mercaptoethanol (Thermo Fisher, Cat#M3148) and maintained at 37℃ cell incubator with 5% CO2. The HEK293T cells were cultured in basic-DMEM (Thermo Fisher, Cat#C11995500BT) supplemented with 10% FBS (GIBCO, Cat#10099141C), and maintained at 37℃ cell incubator with 5% CO2.

extract_protocol:
Cross-linked cells were subjected to chromatin fraction isolation as reported (Ji et al., 2015), and the chromatin was pretreated with 40 U MNase (NEB, Cat#M0247), followed by sonication as previously described (Yongpeng et al., 2020). 1 μl RPB1 antibodies (Cell Signaling Technology, Cat#14958) and 30 μl Protein G beads (Thermo Fisher, Cat#10004D) were used to enrich Pol II subunit-DNA complexes.
ChIP DNA were subjected to library construction according to the instructions of the NEBNext Ultra II DNA Library Prep Kit (NEB, Cat#E7645S). 200bp-400bp DNA libraries were gel-selected, purified, and delivered to Novogene company for sequencing.

treatment_protocol: The degron cells were pretreated with 1 μg/ml Doxycycline for 12 h to induce TIR1 expression, then treated with or without 500 μM IAA for 1 h to induce target protein degradation. Then the cells were harvested and mixed with 10% HEK293T cells before cross-linking.

value: RPB3 degron mESCs treated with 1ug/ml Dox for 12 h, then treated with 500 uM IAA for 1h

tag: chip antibody

value: RPB1 (Cell Signaling Technology, Cat#14958)


title: 43502

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Del2

tag: tissue

value: hippocampus


title: 43560

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Dup5

value: Dup/+


title: RNA-seq_RVX208_rep1


title: 43559

description:
total RNA extract (Qiagen RNeasy Plus Minikit)
16p11_2_Dup4


title: ChIP-Seq_RPB1_RPB3_IAA_1h_rep1


title: ChIP-Seq_RPB1_RPB3_IAA_0h_rep2

value: RPB3 degron mESCs treated with 1ug/ml Dox for 12 h


title: RNA-seq_DMSO_rep2

value: DMSO