title: Ad-EGFP_IL-1b(+)_2 [02exp3X3HUMxsample48adEGFPilPOSrp2-4EGFPILPOS]

description: 02exp3X3HUMxsample48adEGFPilPOSrp2-4EGFPILPOS_S0


title: Ad-EGFP_IL-1b(+)_1 [02exp3X3HUMxsample47adEGFPilPOSrp1-4EGFPILPOS]

status: Public on Sep 11 2022

type: SRA

city: La Jolla

first: Padma

last: Natarajan

state: CA

address: 10550 N.Torrey Pines Road

department: CCBB

country: USA

institute: The Scripps Research Institute

description: 02exp3X3HUMxsample47adEGFPilPOSrp1-4EGFPILPOS_S0

library_source: transcriptomic

data_processing:
library strategy: DRUG-seq
High-throughput RNAseq  library was sequenced on 100 cycle P2 flowcells with an Illumina NextSeq2000 sequencing instrument using paired-end sequencing (read1: 26 bases, read2: 94 bases, i5 and i8 indexes used 8 base reads).
A two-step demultiplexing was carried out: pooled libraries were demultiplexed using dual-index 8-base Illumina barcodes; then the individual samples from the pooled libraries were separated using 5'-end 10-base and 8-base inline barcodes on read1 and read2 respectively (BBTools; https://sourceforge.net/projects/bbmap/). The 3'-end 12-base UMI sequences from read1 were extracted using UMI-tools (Smith et al 2017, PMID: 28100584) and incorporated in read2 fastq as part of sequence ID.
The alignment ready, inline-barcode trimmed read2 fastq files (from the pre-deduplictated dataset) for 42 samples (made available as raw data files) were analyzed using nf-core/RNA-seq pipeline (v1.4.2 Ewels et al 2020, PMID: 32055031) written in the Nextflow domain specific language.
Adapter trimmed read2 were aligned to the reference genome using STAR v2.6.1d and gene abundance was estimated using featureCounts v1.6.4. Raw gene counts were then used to get differentially expressed genes using Bioconductor R package DESeq2 v1.20.0. Genes with BH- adjusted P-value <0.05 found by DESeq2 were assigned as significantly differentially expressed genes.
Genome_build: Ensembl GRCh38 release98
Supplementary_files_format_and_content: raw gene counts, Transcripts per million per sample; differentially expressed genes from DESeq2

molecule: total RNA

organism: Homo sapiens

source_name: Ad-EGFP-transduced TC28a2 cells with IL-1b stimulation

extract_protocol:
Total RNA was isolated with Direct-zol RNA MicroPrep kit (Zymo Research) according to manufacturer’s protocol.
Libraries were constructed using an early access High Throughput RNAseq Prep kit (Twist Bioscience).

tag: cell type

value: TC28a2 cells

tag: genotype/variation

value: Ad-EGFP-transduced

tag: tag

value: with IL-1b stimulation


title: Non-Ad_IL-1b(+)_4 [02exp3X3HUMxsample43adNOADilPOSrp4-3NOADILPOS]

description: 02exp3X3HUMxsample43adNOADilPOSrp4-3NOADILPOS_S0

source_name: Non-transduced TC28a2 cells with IL-1b stimulation

value: Non-transduced


title: Non-Ad_IL-1b(+)_5 [02exp3X3HUMxsample44adNOADilPOSrp5-3NOADILPOS]

description: 02exp3X3HUMxsample44adNOADilPOSrp5-3NOADILPOS_S0


title: Non-Ad_IL-1b(+)_6 [02exp3X3HUMxsample45adNOADilPOSrp6-3NOADILPOS]

description: 02exp3X3HUMxsample45adNOADilPOSrp6-3NOADILPOS_S0


title: Non-Ad_IL-1b(+)_1 [02exp3X3HUMxsample40adNOADilPOSrp1-3NOADILPOS]

description: 02exp3X3HUMxsample40adNOADilPOSrp1-3NOADILPOS_S0


title: Non-Ad_IL-1b(+)_2 [02exp3X3HUMxsample41adNOADilPOSrp2-3NOADILPOS]

description: 02exp3X3HUMxsample41adNOADilPOSrp2-3NOADILPOS_S0


title: Non-Ad_IL-1b(+)_7 [02exp3X3HUMxsample46adNOADilPOSrp7-3NOADILPOS]

description: 02exp3X3HUMxsample46adNOADilPOSrp7-3NOADILPOS_S0


title: IgG control

description: Sample 3 (04HAKLF4IgG_S98_L001_R1_001.fastq.gz)

library_source: genomic

data_processing:
The nf-core/chipseq pipeline (version 1.2.2; Ewels et al.,2020) written in the Nextflow domain specific language was used to perform the primary analysis of the samples.
The ChIP-seq reads were aligned to the UCSC hg38  reference genome using the BWA aligner (Li and Durbin, 2010) .
Mapped reads were further converted to normalised bigWig files files scaled to 1 million mapped reads using BEDTools for presentation as genome browser tracks  (Quinlan et al, 2010).
Th peak calling was performed using MACS2 in narrowPeak mode.
Genome_build: UCSC GRCh38
Supplementary_files_format_and_content: bigWig, narrowPeak

molecule: genomic DNA

source_name: TC28a2 cells transfected with HA-KLF4

extract_protocol:
Cells were cross-linked with 1% formaldehyde, and after lysis of cells, chromatin was fragmented by sonication. Protein-DNA complexes were purified with anti-HA tag antibody.
Libraries were constructed with ThruPLEX DNA-seq Kit (Takara Bio), according to manufacturer’s instruction.

value: transfected with HA-KLF4

tag: antibody

value: Rabbit IgG (Cell Signaling Technology)


title: Ad-KLF4_IL-1b(-)_5 [02exp3X3HUMxsample37adKLF4ilNEGrp5-2KLF4ILNEG]

description: 02exp3X3HUMxsample37adKLF4ilNEGrp5-2KLF4ILNEG_S0

source_name: Ad-KLF4-transduced TC28a2 cells without IL-1b stimulation

value: without IL-1b stimulation


title: Ad-KLF4_IL-1b(-)_4 [02exp3X3HUMxsample36adKLF4ilNEGrp4-2KLF4ILNEG]

description: 02exp3X3HUMxsample36adKLF4ilNEGrp4-2KLF4ILNEG_S0


title: Ad-KLF4_IL-1b(-)_2 [02exp3X3HUMxsample34adKLF4ilNEGrp2-2KLF4ILNEG]

description: 02exp3X3HUMxsample34adKLF4ilNEGrp2-2KLF4ILNEG_S0


title: Ad-KLF4_IL-1b(-)_1 [02exp3X3HUMxsample33adKLF4ilNEGrp1-2KLF4ILNEG]

description: 02exp3X3HUMxsample33adKLF4ilNEGrp1-2KLF4ILNEG_S0


title: Ad-KLF4_IL-1b(-)_3 [02exp3X3HUMxsample35adKLF4ilNEGrp3-2KLF4ILNEG]

description: 02exp3X3HUMxsample35adKLF4ilNEGrp3-2KLF4ILNEG_S0


title: Ad-EGFP_IL-1b(-)_4 [01exp3X3HUMxsample22adEGFPilNEGrp4-1EGFPILNEG]

description: 01exp3X3HUMxsample22adEGFPilNEGrp4-1EGFPILNEG_S0

source_name: Ad-EGFP-transduced TC28a2 cells without IL-1b stimulation


title: Ad-EGFP_IL-1b(-)_5 [01exp3X3HUMxsample23adEGFPilNEGrp5-1EGFPILNEG]

description: 01exp3X3HUMxsample23adEGFPilNEGrp5-1EGFPILNEG_S0


title: Ad-EGFP_IL-1b(-)_6 [01exp3X3HUMxsample24adEGFPilNEGrp6-1EGFPILNEG]

description: 01exp3X3HUMxsample24adEGFPilNEGrp6-1EGFPILNEG_S0


title: Ad-EGFP_IL-1b(-)_3 [01exp3X3HUMxsample21adEGFPilNEGrp3-1EGFPILNEG]

description: 01exp3X3HUMxsample21adEGFPilNEGrp3-1EGFPILNEG_S0


title: Ad-EGFP_IL-1b(+)_5 [03exp3X3HUMxsample51adEGFPilPOSrp5-4EGFPILPOS]

description: 03exp3X3HUMxsample51adEGFPilPOSrp5-4EGFPILPOS_S0


title: Non-Ad_IL-1b(-)_7 [01exp3X3HUMxsample18adNOADilNEGrp7-0NOADILNEG]

description: 01exp3X3HUMxsample18adNOADilNEGrp7-0NOADILNEG_S0

source_name: Non-transduced TC28a2 cells without IL-1b stimulation


title: Ad-EGFP_IL-1b(-)_2 [01exp3X3HUMxsample20adEGFPilNEGrp2-1EGFPILNEG]

description: 01exp3X3HUMxsample20adEGFPilNEGrp2-1EGFPILNEG_S0


title: Ad-EGFP_IL-1b(-)_1 [01exp3X3HUMxsample19adEGFPilNEGrp1-1EGFPILNEG]

description: 01exp3X3HUMxsample19adEGFPilNEGrp1-1EGFPILNEG_S0


title: Non-Ad_IL-1b(-)_4 [01exp3X3HUMxsample15adNOADilNEGrp4-0NOADILNEG]

description: 01exp3X3HUMxsample15adNOADilNEGrp4-0NOADILNEG_S0


title: Non-Ad_IL-1b(-)_2 [01exp3X3HUMxsample13adNOADilNEGrp2-0NOADILNEG]

description: 01exp3X3HUMxsample13adNOADilNEGrp2-0NOADILNEG_S0


title: Non-Ad_IL-1b(+)_3 [02exp3X3HUMxsample42adNOADilPOSrp3-3NOADILPOS]

description: 02exp3X3HUMxsample42adNOADilPOSrp3-3NOADILPOS_S0


title: Non-Ad_IL-1b(-)_5 [01exp3X3HUMxsample16adNOADilNEGrp5-0NOADILNEG]

description: 01exp3X3HUMxsample16adNOADilNEGrp5-0NOADILNEG_S0


title: Non-Ad_IL-1b(-)_3 [01exp3X3HUMxsample14adNOADilNEGrp3-0NOADILNEG]

description: 01exp3X3HUMxsample14adNOADilNEGrp3-0NOADILNEG_S0


title: Ad-KLF4_IL-1b(-)_6 [02exp3X3HUMxsample38adKLF4ilNEGrp6-2KLF4ILNEG]

description: 02exp3X3HUMxsample38adKLF4ilNEGrp6-2KLF4ILNEG_S0


title: Non-Ad_IL-1b(-)_1 [01exp3X3HUMxsample12adNOADilNEGrp1-0NOADILNEG]

description: 01exp3X3HUMxsample12adNOADilNEGrp1-0NOADILNEG_S0


title: Ad-KLF4_IL-1b(-)_7 [02exp3X3HUMxsample39adKLF4ilNEGrp7-2KLF4ILNEG]

description: 02exp3X3HUMxsample39adKLF4ilNEGrp7-2KLF4ILNEG_S0


title: Neural progenitor cells - rs557 A/G- myc

status: Public on Sep 12 2022

city: Toronto

first: Daniel

last: Schramek

state: ON

address: 600 University Ave, Room 1080

country: Canada

institute: Lunenfeld- Tanenbaum Research Institute

data_processing:
Library strategy: 4C
Read filtering of R1 fastqs for sequences beginning with respective target primer seqs (edit distance >=2)
Processing with 4cseqpipe.pl (fastq to raw format conversion): 4cseqpipe.pl -fastq2raw -convert_qual 1 -read_length 75
Processing with 4cseqpipe.pl (mapping): 4cseqpipe.pl -map -read_length 75
Processing with 4cseqpipe.pl (visualization): 4cseqpipe.pl -nearcis -calc_from 60000000 -calc_to 64000000
Genome_build: mm10
Supplementary_files_format_and_content: text, 4Cseqpipe Outputs

organism: Mus musculus

source_name: Neural progenitor cells

growth_protocol:
Primary Neural stem cells were grown in Lamin/poly-L-ornithine coated plates, NeuroCult™ NS-A Basal Medium supplemented with 2mM glutamine, 75ug/ml BSA, 2ug/ml heparin, anti-anti,  N2, W21 and 10 ng/ml of both EGF and bFGF.
all samples grown in the same conditions

extract_protocol:
Cell cultures were fixed with 1% PFA for 10 minutes before glycine inactivation and PBS wash
libraries were prepared for sequencing using standard Illumina protocols

value: ES-derived neural progenitor cells

tag: strain

tag: anchor

value: Myc anchored

tag: treatment

value: untreated


title: L02_SMC3_WT_ChIP

city: Shanghai

first: Hu

last: Haolin

state: Shanghai

address: Fenglin Road

country: China

institute: Zhongshan Hospital

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeq X Ten output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trim Galore v0.65, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.45. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to RPKM) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample),normalized by RPKM

source_name: cell line

growth_protocol: DMEM with 10% FBS and 1X P/S, Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor PICO.
ChIP-seq libraries were prepared using the Vazyme DNA Library Preparation Kit complemented with Vazyme DNA Barcodes from Vazyme. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at ~300bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: tissue

value: cell line

tag: cell line

value: human liver cell line

tag: genotype

value: WT


title: PLC_CTCF_WT_ChIP

value: Human hepatocellular carcinoma cell line


title: L02_H3K27ac_WT_ChIP

value: H3K27ac(Active Motif,39133)


title: L02_CTCF_WT_ChIP


title: Ad-EGFP_IL-1b(-)_7 [02exp3X3HUMxsample25adEGFPilNEGrp7-1EGFPILNEG]

description: 02exp3X3HUMxsample25adEGFPilNEGrp7-1EGFPILNEG_S0


title: PLC_SMC3_WT_ChIP


title: Cyclin B1 +ve [H11]

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
Bisulfite converted
GEO report for rows E-H CCNB1 +ve.txt

data_processing:
adapter and quality trimming using Trim Galore (v0.6.2)
mapped to GRCh38 using Bismark v0.22.1
reads were quantified in 5 Mb windows spaced every 2.5 Mb across the genome, with windows of aberrantly high and low read count excluded
Log transformed datasets were normalised per probe by subtracting the median for that probe, which converts data to log2-fold change in copy number relative to average (the average copy number for each probe being the genomic copy number)
Enrichment normalisation for the 10th and 90th percentiles was then applied to each dataset normalise differences in total read count and distribution.
Assembly: GRCh38
Supplementary files format and content: Normalised total read counts for the CCNB1 negative and CCNB1 positive datasets are provided as separate files

source_name: colorectal tumour

growth_protocol: COLO205 cell lines were provided by the laboratory of Dr. Simon J Cook (Babraham Institute). Cells were cultured in RPMI-1640 media supplemented with 10% (v/v) foetal bovine serum, penicillin (100 U/mL), streptomycin (100 mg/mL) and 2 mM glutamine at 37 °C in a humidified incubator with 5% (v/v) CO2.

extract_protocol:
Cells were glyoxal-fixed and stained for CCNB1 as previously described (Channathodiyil and Houseley, 2021) and single cells sorted by flow cytometry to collect CCNB1 positive and CCNB1 negative cells in a 96-well plate.
Bisulfite conversion was carried out using EZ Methylation Direct bisulfite reagent (Zymo) and desulfonation and purification of converted DNA with magnetic beads (Zymo) on the Bravo automated workstation (Agilent) with DNA eluted into the master mix for the first-strand synthesis. Random priming and extension were performed followed by purification of the resulting DNA fragments. Second strand synthesis was then performed and the resulting fragments amplified with 14 PCR cycles. Amplified libraries were pooled (2 pools of 48 libraries each) and purified using 0.7× Ampure XP beads.
Single cell bisulfite libraries were then prepared as (CLark et al 2017)

treatment_protocol: COLO205 cells were treated with 1uM selumetinib for 48 hours

value: colorectal tumour

value: BRAF V600E

value: selumetinib (48h, 1uM)


title: Cyclin B1 +ve [H08]


title: Cyclin B1 +ve [H07]


title: Cyclin B1 +ve [H04]


title: Non-Ad_IL-1b(-)_6 [01exp3X3HUMxsample17adNOADilNEGrp6-0NOADILNEG]

description: 01exp3X3HUMxsample17adNOADilNEGrp6-0NOADILNEG_S0

value: TC28a2 cells


title: Cyclin B1 +ve [H03]


title: Cyclin B1 +ve [H12]


title: Cyclin B1 +ve [H09]


title: Cyclin B1 +ve [G12]


title: Cyclin B1 +ve [G10]


title: Cyclin B1 +ve [H05]


title: Cyclin B1 +ve [H02]


title: Cyclin B1 +ve [G09]


title: Cyclin B1 +ve [H01]


title: PLC_H3K27ac_WT_ChIP


title: Cyclin B1 +ve [G08]


title: Cyclin B1 +ve [G05]


title: Cyclin B1 +ve [G04]


title: Cyclin B1 +ve [G06]


title: Cyclin B1 +ve [G07]


title: Cyclin B1 +ve [G03]


title: Cyclin B1 +ve [G02]


title: Cyclin B1 +ve [G01]


title: Cyclin B1 +ve [F11]


title: Cyclin B1 +ve [F12]


title: Cyclin B1 +ve [F09]


title: Cyclin B1 +ve [H10]


title: Cyclin B1 +ve [F10]


title: Cyclin B1 +ve [F06]


title: Cyclin B1 +ve [F07]


title: Cyclin B1 +ve [F05]


title: Cyclin B1 +ve [F04]


title: Cyclin B1 +ve [F02]


title: Cyclin B1 +ve [E11]


title: Cyclin B1 +ve [F03]


title: Cyclin B1 +ve [E10]


title: Cyclin B1 +ve [E07]


title: Cyclin B1 +ve [E12]


title: Cyclin B1 +ve [E04]


title: Cyclin B1 +ve [E05]


title: Cyclin B1 +ve [E08]


title: Cyclin B1 -ve [D12]

description:
Bisulfite converted
GEO report for rows A-D CCNB1 -ve.txt


title: Cyclin B1 -ve [D10]


title: Cyclin B1 +ve [E02]


title: Cyclin B1 -ve [D06]


title: Cyclin B1 -ve [D11]


title: Cyclin B1 -ve [D09]


title: Cyclin B1 -ve [D07]


title: Cyclin B1 -ve [D08]


title: Cyclin B1 -ve [D04]


title: Cyclin B1 -ve [D02]


title: Cyclin B1 -ve [D05]


title: Cyclin B1 -ve [D01]


title: Cyclin B1 -ve [D03]


title: Cyclin B1 -ve [C12]


title: Cyclin B1 -ve [C10]


title: Cyclin B1 -ve [C09]


title: Cyclin B1 -ve [C11]


title: 52: ECRS_rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: eosinophilic chronic rhinosinusitis_1

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19

source_name: eosinophilic chronic rhinosinusitis_1

extract_protocol:
Total RNAs were extracted from the cells with miRNeasy Kit (QIAGEN), according to the manufacturer’s protocol.
NGS library preparation was performed using the SMARTer® Stranded Total RNA Sample Prep Kit-Pico Input Mammalian (Clontech, TaKaRa) according to the manufacturer’s instructions.

tag: disease state

value: eosinophilic chronic rhinosinusitis (ECRS)

value: nasal epithelial cells


title: 72: ECRS_rep2

description: eosinophilic chronic rhinosinusitis_2

source_name: eosinophilic chronic rhinosinusitis_2


title: Cyclin B1 +ve [E03]


title: Cyclin B1 -ve [C08]


title: 88: NECRS_rep1

description: non-eosinophilic chronic rhinosinusitis_1

value: non-eosinophilic chronic rhinosinusitis (NECRS)


title: Cyclin B1 -ve [C06]


title: Cyclin B1 -ve [C05]


title: 90: NECRS_rep2

description: non-eosinophilic chronic rhinosinusitis_2


title: Cyclin B1 -ve [C03]


title: Cyclin B1 +ve [E06]


title: Cyclin B1 -ve [C04]


title: BRL-3A si-hnrnpa2b1-2

first: dongsheng

last: xiao

address: No.151 Libing Road, Zhangjiang Hi-Tech Park Pudong, Shanghai 201203, P.R. China

institute: Shanghai Biotechnology Corporation

data_processing:
The main steps of applying Seqtk for filtering are as follows:1、Remove the sequence of joints contained in reads；2、Remove bases with 3 'end mass Q less than 20, that is, the base error rate is less than 0.01，among,Q=-10logerror_ratio；3、Remove reads with length less than 25；4、Remove ribosome RNA reads of the species。
Spliced mapping algorithm of Hisat2 (version:2.0.4) was applied to Genome mapping of preprocessed reads，Take default parameters. The alignment result generated by Mapping is BAM file
Application Stringtie (version: 1.3.0)in Hisat2 than after each gene Fragments could count to count, and then use TMM (trimmed mean of M values) normalization method, finally calculated using perl script FPKM value of each gene.
In order to make gene expression levels between different genes and samples comparable, reads were transformed into FPKM (Fragments Per Kilobase of exon model Per Million mapped reads) to standardize gene expression
EdgeR was used for gene analysis of differences between samples, and multiple hypothesis test and correction were carried out after p-value was obtained. The threshold value of p-value was determined by controlling FDR (False Discovery Rate), and the p-value after correction was q-value.Meanwhile, we calculate Fold-change according to FPKM.
Genome_build: Rnor_6.0

organism: Rattus norvegicus

source_name: BRL-3A cell line

growth_protocol: The BRL-3A rat liver cell line （ATCC） were cultured in glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal bovine serum (FBS) (Life Technologies, Carlsbad, CA) at 37°C with humidified air and 5% CO2

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All of siRNAs were transfected into cells applying lipofectamine 2000 (Life Technologies, Carlsbad, CA) according to manufacture's protocol for 48h then haverst cells. The cultured BRL-3A cells were collected and added to trizol for lysis after storage at -80.

value: Sprague-Dawley

value: Liver

tag: age

value: hypertriglyceridemia


title: BRL-3A si-hnrnpa2b1-3


title: BRL-3A si-hnrnpa2b1-1


title: Cyclin B1 -ve [C02]


title: BRL-3A NC-3


title: Cyclin B1 -ve [B12]


title: Lib07, p. falciparum, severe

city: Kigali

first: Abdoelnaser

middle: Mahmmod

last: Degoot

state: Kigali

address: KN 3Rd

department: Research Department

country: Rwanda

institute: African Institute for Mathematical Sciences

data_processing:
The sequencing data were de-multiplexed, quality-filtered, and clustered based on the unique molecular identifiers to accurately quantify the frequencies of unique TCR clones.
The V, D and J gene segments of each uniquely identified clonal sequence were determined by alignment to germline sequences found in the ImMunoGeneTics database.
The nucleotide sequences were subsequently translated into amino acid sequences.
For VDJ annotation, CDR3 regions were identified as the subsequence occurring between the last conserved cysteine found at the 3’ end of the Vβ and the conserved phenylalanine found at the 5’ end of the Jβ gene segment.
CDR3 sequences with stop codons were classified as out-of-frame or non-productive sequences.
Assembly: IMGT/IgBlast
Supplementary files format and content: Tab-separated files that contain incolde IgBlast clonotype, count, frequency, CDR3 nucleotide sequence, CDR3 amino acid sequence, productive status, chain type, and V-D-J gene segment.

source_name: PBMCs

extract_protocol:
Total RNA was extracted from PBMC obtained from malaria positive and negative controls.
Library preparation and sequencing were performed according to the miodx Clonomap™ immune repertoire sequencing assay using the Illumina MiSeq platform.

value: PBMCs

value: TCR Beta

value: Severe malaria


title: BRL-3A NC-2


title: Lib05, p. falciparum, severe


title: BRL-3A NC-1


title: Cyclin B1 -ve [B11]


title: Lib03, p. falciparum, severe


title: Lib09, p. falciparum, severe


title: Lib02, p. falciparum, severe


title: Lib10, p. falciparum, severe


title: Cyclin B1 -ve [B10]


title: Lib22, p. falciparum, uncomplicated

value: Uncomplicated


title: Cyclin B1 -ve [B09]


title: Lib04, p. falciparum, severe


title: Cyclin B1 -ve [B06]


title: Lib20, p. falciparum, uncomplicated


title: Lib17, p. falciparum, uncomplicated


title: Lib21, p. falciparum, uncomplicated


title: Cyclin B1 -ve [B08]


title: Lib16, p. falciparum, uncomplicated


title: S4-3 Cold acclimation four times input

city: Lanzhou

first: Zezhong

last: Su

address: YuZhong

institute: Lanzhou University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: Arabidopsis thaliana
Supplementary files format and content: bigWig, excel

organism: Arabidopsis thaliana

source_name: plants stems and leaves

growth_protocol: Soil culture after the germination, 2-week seedlings

extract_protocol:
0.5 g of Arabidopsis thaliana leaves were ground into a fine power with liquid nitrogen and cross-linked, filtered, and washed to obtain chromatin.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: cold memory (S1:4°C for 6 h, then at room temperature for 18 h; S4:4°C for 6 h, then at room temperature for 18 h, repeated four times), and then placed at 0°C for 6 h, and control groups with normal growth conditions.

value: plants stems and leaves

tag: chip antibody


title: S4-2 Cold acclimation four times input


title: S4-3 Cold acclimation four times IP


title: Lib14, p. falciparum, uncomplicated


title: Lib06, p. falciparum, severe


title: Lib15, p. falciparum, uncomplicated


title: Cyclin B1 -ve [B05]


title: Cyclin B1 -ve [B04]


title: Lib50, p. falciparum, asymptomatic

value: Asymptomatic


title: S4-1 Cold acclimation four times input


title: Cyclin B1 -ve [B03]


title: Lib13, p. falciparum, uncomplicated


title: Lib48, p. falciparum, asymptomatic


title: S1-3 Cold acclimation once input


title: MR_rep1

city: Wuhan

first: yiqian

last: yu

state: Hubei

address: Luoyu Road 237#, 430079, Wuhan, Hubei

institute: wuhan university

data_processing:
Raw sequencing data processed by Trim_Galore (v.0.6.7) for removing adapters and low-quality base pairs.
Reads were aligned with hisat2 (v.2.1.0) to GRCm38 reference genome.
Read counts were generated by featureCounts (v.2.0.1)
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: mesenchymal stem cell

extract_protocol:
Total RNA was extracted from cells  using the TRIzol reagent (Takara). Purified poly(A) mRNA was isolated from 1 mg total RNA using a Poly(A) mRNA Magnetic Isolation Module (Thermo Scientific).
RNA-seq libraries were prepared using NEBNext Super Directional RNA Library Preparation Kits (New England Biolabs)

value: limbs

value: 8 weeks

value: co-cultured with RAW cells

value: mesenchymal stem cell


title: S4-1 Cold acclimation four times IP


title: Cyclin B1 -ve [B02]

value: colorectal tumour

value: BRAF V600E

value: selumetinib (48h, 1uM)


title: Lib19, p. falciparum, uncomplicated


title: Cyclin B1 -ve [B01]


title: MRL_rep2

value: co-cultured with LPS stimulated RAW cells


title: Lib45, p. falciparum, asymptomatic


title: S1-2 Cold acclimation once input


title: MRL_rep1


title: Lib43, p. falciparum, asymptomatic


title: S4-2 Cold acclimation four times IP


title: Cyclin B1 -ve [A12]


title: Lib42, p. falciparum, asymptomatic


title: S1-2 Cold acclimation once IP


title: Cyclin B1 -ve [A11]


title: Cyclin B1 -ve [A10]


title: msc_rep1

value: control


title: MR_rep2


title: Lib41, p. falciparum, asymptomatic


title: S1-1 Cold acclimation once IP


title: S0-3 control : Room temperature/or before stress input


title: Cyclin B1 -ve [A09]


title: Lib47, p. falciparum, asymptomatic


title: Lib76, p. falciparum,  control

value: Control


title: S1-3 Cold acclimation once IP


title: Cyclin B1 -ve [A06]


title: ovx_rep1

source_name: bone marrow-derived macrophages

value: ovariectomized (OVX)


title: ovx_rep2


title: Lib66, p. falciparum, control

value: PBMCs


title: S0-2 control : Room temperature/or before stress input


title: msc_rep2


title: Cyclin B1 -ve [A05]


title: sham_rep2

value: sham


title: sham_rep3


title: Lib63, p. falciparum, control

value: TCR Beta


title: Cyclin B1 -ve [A04]


title: S1-1 Cold acclimation once input


title: S0-1 control : Room temperature/or before stress input


title: MGH-CP1_2

city: Charlestown

first: Yang

last: Sun

state: MA

address: 149 13th Street, CBRC 3050E

department: CBRC

institute: Massachusetts General Hospital

data_processing:
"Qphred" represents base quality values of Illunima, the Qphred=-10log10(e). Base Quality and Phred score relationship in illumina Casava 1.8
GC-content is used to detect potential AT/GC separation.
The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Novogene use STAR to accomplish the mapping. For the spieces(Human and mice) whose gene annotation information are more completed, if only need the differential expression significant genes, can map reads to the transcriptome directly. If research the study of alternative splicing, variation, the fusion gene, the alignment should be carried out at the genome level. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely
Reads will be mapped to exon, intron and intergenic.
After getting the information about distribution of mapped reads on genome area, we will focus the distribution of mapped reads on chromosome. On one hand we can get insight into how many regions on chromosome is covered, on the other hand we can get the information about transcription activity on chromosome.We calculate mapped reads density on every chromosome , then plot based on the mapped reads density. In general, the longer the chromosome is, the more reads will be mapped to the chromosome. The statistics of reads mapped to chromosome indicates the relationship between chromosome length and reads number.
Genome_build: Homo_sapiens_hg19
Supplementary_files_format_and_content: fpkm

source_name: breast cancer

growth_protocol: MDA-MB-231 cells were culture in DMEM supplied with 10% FBS and Penicillin-Streptomycin

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen 74104)
mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer.Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Cells were treated with vehicle control or MGH-CP1(10uM) for 24 hours

value: breast cancer cell

tag: agent

value: MGH-CP1 10microM 24 hours


title: sham_rep1


title: Cyclin B1 -ve [A03]


title: MGH-CP1_1


title: S0-1 control : Room temperature/or before stress IP

value: plants stems and leaves


title: ovx_rep3

value: limbs


title: S0-3 control : Room temperature/or before stress IP


title: Cyclin B1 -ve [A08]


title: CT2A

city: Daejeon

first: Heung Kyu

last: Lee

address: 291 Daehak-ro, Yuseong-gu

department: Graduate School of Medical Science and Engineering

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
Cell Ranger (10X Genomics) was used for align reads, generate gene-cell matrices and perform clustering and gene expression analysis
Samples were aligned using the mouse genome 10-3.0.0 (Mm10, 10X genomics)
Assembly: Mm10
Supplementary files format and content: Feature, barcode, matrix

source_name: Glioma infiltrated leukocyte

growth_protocol: Mice were housed in specific pathogen free (SPF) facility or KAIST, Korea. CT2A cells were cultured in DMEM supplied with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Mice were transcardially perfused with 50 ml cold DPBS to remove the blood before isolating tissues. The right hemisphere of the brain was minced into small pieces by blade and digested with 2 mg/ml collagenase IV (Worthington) and 30 μg/ml DNase I (Rhoche) at 37℃ for 30 min. Tissues were passed through a 70 μm strainer. To remove non-immune cells from tumor samples, cells were resuspended in 4 ml of 30% percoll (GE Healthcare) containing DMEM CM and loaded onto 3 ml of 70% percoll containing DPBS supplemented with 1% BCS. Immune cells and myelin were separated by centrifugation. Cells were treated with ACK lysis buffer for 5 min at RT to remove residual red blood cells. Cells were stained with anti-mouse CD45.2-APC or CD45-APC and propidium iodide. PI-negative and CD45.2/CD45-positive live immune cells were sorted with FACS Aria.
library were constructed with Single Cell 3' Reagent Kit v3 (10x genomics) following manufacturer's instruction.

treatment_protocol: Mice were intracranially injected with 100000 CT2A tumor cells

tag: injected cells

value: CT2A tumor cells

value: Brain

value: CD45.2+ immune cell


title: Lib68, p. falciparum, control


title: Cyclin B1 -ve [A02]

value: colorectal tumour


title: Cyclin B1 -ve [A01]

value: BRAF V600E


title: Control_1

value: vehicle control


title: Control_2


title: TG

data_processing:
Cell Ranger (10X Genomics) was used for align reads, generate gene-cell matrices and perform clustering and gene expression analysis
Samples were aligned using the mouse genome 10-3.0.0 (Mm10, 10X genomics)
Genome_build: Mm10
Supplementary_files_format_and_content: Feature, barcode, matrix

growth_protocol: CD169-DTR wild type or hetero mice were housed in specific pathogen free (SPF) facility or KAIST, Korea. GL261 cells were cultured in DMEM supplied with 10% FBS and 1% penicillin-streptomycin

extract_protocol:
Mice were transcardially perfused with 50 ml cold DPBS to remove the blood before isolating tissues. The right hemisphere of the brain was minced into small pieces by blade and digested with 2 mg/ml collagenase IV (Worthington) and 30 μg/ml DNase I (Rhoche) at 37℃ for 30 min. Tissues were passed through a 70 μm strainer. To remove non-immune cells from tumor samples, cells were resuspended in 4 ml of 30% percoll (GE Healthcare) containing DMEM CM and loaded onto 3 ml of 70% percoll containing DPBS supplemented with 1% BCS. Immune cells and myelin were separated by centrifugation. Cells were treated with ACK lysis buffer for 5 min at RT to remove residual red blood cells. Cells were stained with anti-mouse CD45.2-APC and propidium iodide. PI-negative and CD45.2-positive live immune cells were sorted with FACS Aria.
library were constructed with Single Cell 3' Reagent Kit v3 (10x genomics) following manufacturer's instruction.

treatment_protocol: CD169-DTR wild type or hetero mice were intraperitoneally injected with DT at -1 and +4 days of tumor injection. Mice were injected with 100000 GL261 cells intracranially.

tag: strain background

value: CD169-DTR hetero type

value: Diphthelia toxin

value: Glioma infiltrated leukocyte


title: WT

value: CD169-DTR wild type


title: shBCOR rep1

status: Public on Sep 10 2022

city: Montreal

first: Awais

last: Javed

state: Quebec

address: 110 Avenue des Pins

institute: IRCM

description: Raw ht-seq counts/Deseq2

data_processing:
RNA-Seq: Fastq reads were pre-processed using “FastQGroomer” and “Trimmomatic” algorithms (Bolger et al. 2014), then mapped against the mm10 genome using “Tophat” (Kim etal. 2013). Gene counts were generated using “htseq-count” followed by “DeSeq2” (Anders et al. 2015 ; Love et al. 2014). R-studio was used to annotate and merge data. Heatmaps were generated using Morpheus program (https://software.broadinstitute.org/morpheus/) with k-means clustering. Gene Ontology (GO) analysis (allowing to detect which terms are under- or over- represented using annotations within a specific genes set) was ran using David 6.8 tool (Huang da et al. 2009).
CUT&RUN: Fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using default parameters. Bamcoverage was used to generate bigwig files.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: Raw ht-seq counts in tabular format and excel spreadsheet results of DESeq2 analysis of RNA-seq data generated from retinal cells with BCOR knockdown
Supplementary_files_format_and_content: Bigwig tracks files and MACS2 peaks bed files for scored peaks in CUT&RUN

source_name: Retina

growth_protocol: In vivo electroporation of P0 eyes was performed as described previously (de Melo et al. 2011) using plasmid DNA at 1ug/ul (pSilencer-shBcor or empty vector pSilencer-CAG-Venus as control).

extract_protocol:
RNA-seq: RNA extraction was performed as detailed by manufactorer (RNeasy mini kit, Qiagen).
CUT&RUN: Genomic DNA extraction was performed as per manufactorers guidelines (QIAquick Nucleotide Removal Kit).
RNA-seq: Samples quantity (RNA Integrity Number = RIN) and quality were assessed using the Agilent RNA 6000 Pico Kit (Agilent #5067-1513) on the Bioanalyzer 2100. Libraries preparation started with rRNA depletion using the Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324). 3.0 ng to 5.1 ng of total RNA were used for rRNA depletion of the total RNA. Speed-vac sublimation was performed on some samples to reduce RNA volume to 17ul in order to start the depletion reaction. rRNA depleted RNA were then purified with AGENCOURT® RNA CLEAN® XP Kit (Beckman Coulter). The samples were eluted in 8.5ul of H2O to continue the library preparation using SMARTer® Stranded RNA-Seq Kit (Takara Bio USA, Inc. #634836 or #634837).
CUT&RUN: Libraries were prepared with the KAPA DNA HyperPrep Kit (Roche 07962363001 - KK8504). This protocol includes an End-Repair/A-tailing step and an adapter ligation step followed by a PCR amplification (enrichment) of ligated fragments.
RNA-seq: The 1st strand synthesis was performed using a modified N6 primer (the SMART Stranded N6 Primer) in order to obtain full length fragments. The full-length, single-stranded (ss) cDNA fragments were purified with Agencourt DNA CleanUp AMPure® XP Kit (Beckman Coulter #A63881). PCR Enrichment + indexing step of 15 cycles was then performed using the Illumina Indexing Primer Set provided by the kit. The final enriched product (library, after PCR) was purified using Agencourt DNA CleanUp AMPure® XP Kit (Beckman Coulter #A63881). Libraries were eluted in 16 ml of elution buffer. Quality and quantification of the libraries were assessed using the Agilent High Sensitivity DNA Kit (Agilent #5067-4626) on the Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted and pooled equimolar prior to paired-end sequencing performed with 50 cycles (PE50) on a v4 flowcell (Illumina - HiSeq PE Cluster Kit v4 cBot - PE-401-4001) of the Illumina HiSeq 2500 System.
CUT&RUN: The adapters used for ligation were IDT for Illumina TruSeq UD Indexes (Illumina - 20022371). The final enriched product (library, after PCR) was purified using KAPA purification beads (Roche 07983298001 - KK8002) and a dual-SPRI size selection was performed (with KAPA beads) to select fragments between 180-500 bp. Libraries were then quantified using a Nanodrop microvolume spectrophotometer (ng/l) and quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent -5067-4626) on a Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted, pooled equimolar and sequenced in pair end 50 cycles (PE50) on a S1 flowcell (Illumina - 20012863) of the Illumina NovaSeq 6000 System.

treatment_protocol: The electroporated eyes were collected at post-natal day 21 and processed for dissection, dissociation and FACS sorting. Dissociation was done with StemPro Accutase (Thermo Fisher) for 30 minutes instead of papain and cells were treated with propidium iodide (PI) solution prior to sorting. 10 to 15% of cells were excluded due to cell death. Multiple sorted GFP+ cells samples were combined to obtain 30 000 - 70 000 cells per replicate (n=2)

value: Retinal cells

tag: mouse line

value: WT

value: P0+21 days in-vivo

tag: condition

value: shBCOR


title: Control GFP rep2

description: Raw ht-seq counts/Deseq2

tag: cell type

value: GFP


title: shBCOR rep2

description: Raw ht-seq counts/Deseq2


title: S0-2 control : Room temperature/or before stress IP

value: plants stems and leaves


title: Control GFP rep1

description: Raw ht-seq counts/Deseq2


title: GIST430

city: New York

first: Prabhjot

middle: Singh

last: Mundi

state: NY

address: 1130 St. Nicholas Avenue

department: Medicine; Systems Biology

institute: COLUMBIA UNIVERSITY HEALTH SCIENCES

library_source: transcriptomic single cell

data_processing:
Alignment with STARv2.5.3 to GRCh38 or with bowtie2 to Hg19 and mm10 for PDX samples, as indicated below
Gene-level raw counts summarization with STARv2.5.3 quant-mode. In the case of PDX samples, xenomapper tool was to generate counts from reads selectively mapping to human transcriptome and not mouse.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and viper analysis as described in manuscript.
Assembly: GRCh38.v90 or as indicated below.
Supplementary files format and content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for VIPER analysis of differential protein activity for perturbation or pharmacodynamic samples.

source_name: Cancer Cell line, CUIMC sequenced, RNASeq

growth_protocol: The cells were grown in logarithomic phase till treatment

extract_protocol:
RNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500 or NovaSeq 6000 sequencer, as indicated below for each file.

treatment_protocol: Drug perturbations profiles in cell lines were done at 24 hours, and in some cell lines also at 6 hours (short time point) after introducing drug, as indicated by appropriate column names in the sample plate maps and processed data files


title: GISTT1

value: Cancer Cell line, CUIMC sequenced, RNASeq


title: PDX_Pharmacodynamic_Plateseq

description:
demuliplexed fastq (PLATESeq platform)
PDX_Pharmacodynamic_Plateseq_counts.txt
PDX_Pharmacodynamic_Plateseq_samples_barcordes.txt
PDX_Pharmacodynamic_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: PDX tumor samples treated and vehicle control (from GIST.81050, CAR.23659, CNS.16474, PAC.05647), Multiplexed RNASeq (PLATESeq)


title: PDX_Pharmacodynamic_BC_GIST_Plate2

description:
demuliplexed fastq (PLATESeq platform)
PDX_Pharmacodynamic_BC_GIST_Plate2_counts.txt
PDX_Pharmacodynamic_BC_GIST_Plate2_samples_barcodes.txt
PDX_Pharmacodynamic_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: PDX tumor samples treated and vehicle control (from BC.32398), Multiplexed RNASeq (PLATESeq)


title: PDX_Pharmacodynamic_BC_GIST_Plate1

description:
muliplexed fastq (PLATESeq platform)
PDX_Pharmacodynamic_BC_GIST_Plate1_counts.txt
PDX_Pharmacodynamic_BC_GIST_Plate1_samples_barcodes.txt
PDX_Pharmacodynamic_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: PDX tumor samples treated and vehicle control (from GIST.81050, BC.32398), Multiplexed RNASeq (PLATESeq)


title: N2 trained PVD OLL RNA Seq

first: Xiwei

last: Liu

address: 1239 Siping Road

institute: Tongji University

data_processing:
The quality control of illumina FASTA files were conducted using the FastQC v0.11.8 and MultiQC v1.0.
For single-cell RNA-seq,first, we processed the raw data of naïve PVD and OLL cells to digital gene expression matrix using UMI-tools (v0.5.5), All the sequencing files end with “R2” contain only the barcode and UMI, while the “R1” files contain the target sequences. The barcode position is the 1st to 8th bp from the 5’ end and the UMI locates at the 9th to 16th bp from the 5’ end.
For single-cell RNA-seq,we used Seurat (v3.0.1) workflow for filtering datasets, normalization, dimension reduction and clustering cells. Cells with less than 2500 genes per cell or more than 200,000 UMI per cell were considered as outlier, and then they were removed.
For single-cell RNA-seq, we normalized data with SCTransform method under Seurat package (sctransform package version 0.2.0) and identified 500 high variable genes for downstream analyze.  After dimension reduction and clustering cells, we removed a cluster with low expression of ser-2 (The average expression level of the removed cluster about ser-2 is lower than 2, but others are between 3 to 4. Furthermore, we didn’t find any known PVD or OLL marker genes in the cluster.)
genome build: WS269
processed data files format and content: For single-cell RNA-seq tab-delimited text files include UMI counts for each sample each gene, and tab-delimited text files include corresponding barcode sequences and annotaed sample names in the UMI expression matrix.

organism: Caenorhabditis elegans

source_name: PVD and OLL neuron of worm

growth_protocol: Worms were grown at 20℃ on nematode growth media (NGM) plates seeded with bacteria (E. coli OP50) as a food source. Embryos are collected by hypochlorite-bleaching gravid adult animals and were grown at 20℃.

extract_protocol: Single Cell RNA-Seq: After dissection and washing of the single intestine or germ line in M9, a mouth pipette was used to transfer the single tissues into 2 ul of cell lysis buffer in 200-uL PCR tubes, each containing 1 U/uL RNase Inhibitor (Invitrogen, AM2684), 0.475% Triton X-100 (Sigma-Aldrich, T9284), 2.5 mM deoxynucleotide triphosphate (dNTP) mixture (Thermo, R0193) and 0.75 uM barcode-reverse transcriptase (RT) primers (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-NNNNNNNN-T25, where X represents the nucleotides of the designed cell-specific barcodes and N represents the unique molecular identifier [UMI]).To lyse each organ, the tube was first vortexed thoroughly and placed in a thermocycler at 72℃ for 3 min to release the linearized RNA molecules. Then, the reaction was immediately quenched on ice. After the reaction was centrifuged, 2.85 uL of RT mixture (50 U SuperScript II reverse transcriptase [Invitrogen, 18064071], 5U RNase Inhibitor, 1 uL 5× Superscript II first-strand buffer , 8.77 mM dithiothreitol [DTT], 1.75 uM betaine [Sigma-Aldrich, 61962], 10.5 mM MgCl2 [Sigma-Aldrich, M2393], and 1.75 uM template switch oligo [TSO] primer [AAGCAGTGGTAT CAACGCAGAGTACATrGrG+G, where rG represents riboguanosine one (+G), and +G indicates the LNAmodified guanosine]) were added into the lysate. Reverse transcription was carried out in the thermocycler at 25℃ for 5 min, 42℃ for 60 min, 50℃ for 30 min, and then 70℃ for 10 min. After reverse transcription, 7.5 uL of PCR mixture (6.25 mL 2× KAPA HiFi HotStart ReadyMix [KK2602], 300 nM ISPCR oligo [AAGCAGTGGTATCAACGCAGAGT], and 1 uM 3’ Anchored oligo [GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC]) were added to each reaction. The sample was amplified with four cycles of 98℃ for 20 s, 65℃ for 30 s, and 72℃ for 5 min, followed by 9-13 cycles of 98℃ for 20 s, 67℃ for 15 s, and 72℃ for 5 min; and finally 72℃ for 5 min.The amplified samples with different barcodes (up to 96 barcodes) were pooled together. The pooled cDNAs were first purified with DNA Clean & Concentrator™-5 (ZYMO, D4014) and eluted in 50 uL of H2O. After the sample was further purified twice with 0.8× Ampure XP beads (Beckman, A63881), the cDNAs were used for a second round of amplification with biotinylated index primer (/Biotin/CAAGCAGAAGACGGCATACGAGATindexGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC) and ISPCR oligo for an additional four cycles. Subsequently, the biotinylated cDNAs were again purified with 0.8× Ampure XP beads. Next, the cDNAs were sheared into approximately 300-bp fragments with a Covaris sonicator. The fragmented cDNAs containing barcode and UMI sequences were then enriched by using Dynabeads® MyOne™ Streptavidin C1 (Invitrogen, 65001). Libraries were prepared using KAPA Hyper Prep Kits (KK8504). The NEB U-shaped adapter was used for ligation. Finally, the adapter-ligated fragments were amplified by using an Illumina QP2 primer (CAAGCAGAAGACGGCATACGA) and a short universal primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC) for 19 cycles. The libraries were sequenced on an Illumina Hiseq Xten platform to generate 150-bp paired-end reads (sequenced by Novogene).

treatment_protocol: PA14 Training: Cultivate naïve group worms on a standard 6 cm NGM plate seeded with bacteria OP50. For 72 hr training, a suspension of 200 ul of the fresh PA14 bacteria was spread on the middle of the plate to form a wide barrier lawn and 50 ul of fresh OP50 suspension was dropped to form a small lawn on one side of the PA14 barrier, and training plates were incubated at 26 ℃ for 48 h before use. Embryos were collected by bleaching and hatching at 20 ℃ on the other side of PA14 barrier on 72 hr training plates. After embryos hatching, 72 hours later, day1 adult worm were collected by washing with M9 buffer for three times and then dropped on the 10 cm test plates to do binary choice assay.

value: PA14 trained

value: PVD and OLL neuron of worm

tag: protocol

value: Single Cell RNA-Seq


title: N2 trained germline RNA Seq

data_processing:
The quality control of illumina FASTA files were conducted using the FastQC v0.11.8 and MultiQC v1.0.
For barcoded tissue raw files, R2 contains the barcode (1st to 8th bp from 5' end)  and UMI (9th to 16th bp from 5' end) and R1 contains the biological read.
For barcoded tissue RNA-seq,raw FASTQ data was first trimed by the sequencing company using fastp software under parameters of -q 5, -u 50 -n 15 -l 15. The trimmed fasta files were used for the following analysis.
For barcoded tissue RNA-seq,UMI-tools v1.0.0 was used, following the associated online tutorial (https://umi-tools.readthedocs.io/en/latest/Single_cell_tutorial.html), to find tissue barcode whitelist, and to extract and filter tissue barcodes and UMIs. All the read files end with number 1 contain only the barcode and UMI. The barcode position is the 1st to 8th bp from the 5’ end and the UMI locates at the 9th to 16th bp from the 5’ end, while the number 2 files contain the target sequences. Before mapping the sequencing reads to a reference genome, the algorithm identified barcodes were manually re-filtered according to experimental data record. Mapping the barcodes and UMIs labeled reads against the reference C. elegans genome (WS269) was conducted using STAR v2.7.1a. By Subread package v1.6.4 function featureCounts the reads were assigned to Wormbase (WS269) released genes. The assigned reads were sorted and converted into BAM files by Samtools v1.9. Then UMI-tools v1.0.0 was again used to count UMIs per gene per tissue and to generate a matrix containing these data. And then according to experiment record, transcription data of worms that chose PA14 after a binary choice test (annotated by tissue names contain “pa” in-between) were excluded from the following analysis.
For barcoded tissue RNA-seq,mapping the barcodes and UMIs labeled reads against the reference C. elegans genome (WS269) was conducted using STAR v2.7.1a
For barcoded tissue RNA-seq,by Subread package v1.6.4 function featureCounts the reads were assigned to Wormbase (WS269) released genes.
For barcoded tissue RNA-seq,the assigned reads were sorted and converted into BAM files by Samtools v1.9.
For barcoded tissue RNA-seq,then UMI-tools v1.0.0 was again used to count UMIs per gene per tissue and to generate a matrix containing these data for the following analysis.
genome build: WS269
processed data files format and content: For barcoded tissue RNA-seq tab-delimited text files include UMI counts for each sample each gene and tab-delimited text files include corresponding barcode sequences and annotaed sample names in the UMI expression matrix.

source_name: worm germline

extract_protocol: Barcoded tissue RNA-Seq protocol: We established the Single-organ cDNA amplification and library construction method according to the Single cell cDNA amplification and library construction with minor modifications.After dissection and washing of the single intestine or germ line in M9, a mouth pipette was used to transfer the single tissues into 2 ul of cell lysis buffer in 200-uL PCR tubes, each containing 1 U/uL RNase Inhibitor (Invitrogen, AM2684), 0.475% Triton X-100 (Sigma-Aldrich, T9284), 2.5 mM deoxynucleotide triphosphate (dNTP) mixture (Thermo, R0193) and 0.75 uM barcode-reverse transcriptase (RT) primers (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-NNNNNNNN-T25, where X represents the nucleotides of the designed cell-specific barcodes and N represents the unique molecular identifier [UMI]).To lyse each organ, the tube was first vortexed thoroughly and placed in a thermocycler at 72℃ for 3 min to release the linearized RNA molecules. Then, the reaction was immediately quenched on ice. After the reaction was centrifuged, 2.85 uL of RT mixture (50 U SuperScript II reverse transcriptase [Invitrogen, 18064071], 5U RNase Inhibitor, 1 uL 5× Superscript II first-strand buffer , 8.77 mM dithiothreitol [DTT], 1.75 uM betaine [Sigma-Aldrich, 61962], 10.5 mM MgCl2 [Sigma-Aldrich, M2393], and 1.75 uM template switch oligo [TSO] primer [AAGCAGTGGTAT CAACGCAGAGTACATrGrG+G, where rG represents riboguanosine one (+G), and +G indicates the LNAmodified guanosine]) were added into the lysate. Reverse transcription was carried out in the thermocycler at 25℃ for 5 min, 42℃ for 60 min, 50℃ for 30 min, and then 70℃ for 10 min. After reverse transcription, 7.5 uL of PCR mixture (6.25 mL 2× KAPA HiFi HotStart ReadyMix [KK2602], 300 nM ISPCR oligo [AAGCAGTGGTATCAACGCAGAGT], and 1 uM 3’ Anchored oligo [GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC]) were added to each reaction. The sample was amplified with four cycles of 98℃ for 20 s, 65℃ for 30 s, and 72℃ for 5 min, followed by 9-13 cycles of 98℃ for 20 s, 67℃ for 15 s, and 72℃ for 5 min; and finally 72℃ for 5 min.The amplified samples with different barcodes (up to 96 barcodes) were pooled together. The pooled cDNAs were first purified with DNA Clean & Concentrator™-5 (ZYMO, D4014) and eluted in 50 uL of H2O. After the sample was further purified twice with 0.8× Ampure XP beads (Beckman, A63881), the cDNAs were used for a second round of amplification with biotinylated index primer (/Biotin/CAAGCAGAAGACGGCATACGAGATindexGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC) and ISPCR oligo for an additional four cycles. Subsequently, the biotinylated cDNAs were again purified with 0.8× Ampure XP beads. Next, the cDNAs were sheared into approximately 300-bp fragments with a Covaris sonicator. The fragmented cDNAs containing barcode and UMI sequences were then enriched by using Dynabeads® MyOne™ Streptavidin C1 (Invitrogen, 65001). Libraries were prepared using KAPA Hyper Prep Kits (KK8504). The NEB U-shaped adapter was used for ligation. Finally, the adapter-ligated fragments were amplified by using an Illumina QP2 primer (CAAGCAGAAGACGGCATACGA) and a short universal primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGAC) for 8-10 cycles. The libraries were sequenced on an Illumina Hiseq Xten platform to generate 150-bp paired-end reads (sequenced by Novogene).

value: germline of worm

value: Barcoded tissue RNA-Seq protocol


title: N2 trained intestine RNA Seq

source_name: worm intestines

value: intestine of worm


title: PDX_Pharmacodynamic_GIST_TruSeq

description:
PDX_Pharmacodynamic_GIST_TruSeq_counts.txt
PDX_Pharmacodynamic_GIST_TruSeq_samples.txt
PDX_Pharmacodynamic_Plateseq_viperanalyzeddifferentialproteinactivity.txt

source_name: PDX tumor samples treated and vehicle control (from GIST.81050), RNASeq (TruSeq)


title: PAC.05647 PDX P0 passage tumor sample

source_name: PDX tumor sample, RNASeq

value: PDX tumor sample, RNASeq

value: PDX of pancreatic cancer


title: N2 naive intestine RNA Seq

value: naive


title: BC.97359 PDX P0 passage tumor sample

value: PDX of breast cancer


title: N2 trained bulk-RNA Seq rep3

data_processing:
The quality control of illumina FASTA files were conducted using the FastQC v0.11.8 and MultiQC v1.0.
Bulk RNA-seq reads were quantified and pseudoaligned to C. elegans reference transcriptome (WS269) using Kallisto v0.46.0 quant with 200 bootstrapping.
genome build: WS269
processed data files format and content: For bulk RNA-seq, tab-delimited text files for each sample, include length,efficient length, estamated counts and TPM values for each transcript

source_name: bulk worms

extract_protocol:
For bulk RNA-Seq, after behavior tests, N2 worms were collected from naive-OP50, trained-OP50, trained-PA14 part respectively. Worms were washed in M9 buffer for 3 times. Total RNA were extracted as standard Trizol(Takara) method. After grinded in 1 ml Trizol, the worms were added in 200ml chloroform and centrifuge at 4℃. The upper water phase was precipitated in equal isopropanol overnight. After centrifuging at 4℃ and removing supernatant, the precipitate was total RNA and washed by 70% alcohol for 2 times. The total RNA was dissolved in DEPC water.
Bulk RNA-Seq library was constructed by sequencing company WuxiNextCode for a standard illumina PE150 platform.

value: whole worm

value: Bulk RNA-Seq protocol


title: mock NK cell

type: RNA

city: Kashihara

first: Takayuki

last: Morimoto

state: Nara prefecture

address: 840 Shijo-Cho

department: Department of Neurosurgery

institute: Nara Medical University

hyb_protocol: Following labeling, 5.2 ug of cDNA were hybridized for 16 hr at 45 degree C on Clariom S Human Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G system.

data_processing: The data analysis were used Transcriptome Analysis Console Ver.4.0.  Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA),  Expression Analysis was perfoermed using ebayes ANOVA.

label: biotin

source_name: primary human NK cell

label_protocol: The fragmented 5.2 μg of single-stranded cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent that is covalently linked to biotin. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

growth_protocol: PBMCs were obtained from 16 mL heparinized peripheral blood from healthy volun-teers (31 and 41-year-old men). The CD3 fraction of the PBMCs was depleted by the RosetteSepTM Human CD3 Depletion Cocktail (STEMCELL Technologies, Vancouver, Canada). The CD3-depleted PBMCs were placed in a T25 culture flask (Corning, Steuben, NY, USA) containing AIM V medium (Life Technologies) supplemented with 10% autologous plasma, 50 ng/mL recombinant human IL-18 (rhIL-18, Medical & Bio-logical Laboratories Co., Ltd., Nagoya, Japan), and 3000 IU/mL rhIL-2 (Novartis, Basel, Switzerland) at 37 °C in a humidified atmosphere containing 5% CO2 for 14 days. The AIM V medium containing 3000 IU/mL rhIL-2 was replenished as necessary.   LAK (Lymphocyte Activated Killer) cells were obtained the PBMCs which were cultured in AIM-V medium supplemented with 5% autologous plasma and 3000 IU/mL rhIL-2 at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA of mock NK cells and TIGIT knockout NK cells was exacted by using NucleoSpin RNA (Takara Bio, Shiga, Japan).

value: mock

value: primary human NK cell


title: CNS.16474 PDX P0 passage tumor sample

value: PDX of meningioma


title: N2 trained bulk-RNA Seq rep1


title: N2 trained bulk-RNA Seq rep2


title: CAR.23659 PDX P0 passage tumor sample

value: PDX of colon cancer


title: TIGIT knockout NK cell

value: TIGIT knockout


title: N2 naive bulk-RNA Seq rep3


title: GIST.81050 PDX P0 passage tumor sample

value: PDX of GIST sarcoma


title: N2 naive bulk-RNA Seq rep2


title: BC.32398 PDX P0 passage tumor sample


title: N2 naive PVD OLL RNA Seq

value: PVD and OLL neuron of worm


title: N2 naive bulk-RNA Seq rep1


title: CAR.23659 patient tumor sample [paired-end]

source_name: Patient tumor sample, liver metastasis from colon cancer, RNASeq

value: colon cancer


title: CAR.23659 patient tumor sample [single]

value: Patient tumor sample, liver metastasis from colon cancer, RNASeq


title: N2 naive germline RNA Seq

value: germline of worm

value: Barcoded tissue RNA-Seq protocol


title: GIST.81050 patient tumor sample#3

description: paired-end (two lanes)

source_name: Patient tumor sample 3, peritoneal metastasis from GIST sarcoma * PDX developed from this, RNASeq

value: GIST sarcoma


title: GM18505, stress-treated, crispr-control

city: Houston

first: Annie

middle: W.

last: Shieh

state: Texas

address: 1825 Pressler St

department: Brown Foundation Institute Of Molecular Medicine

institute: University of Texas Health Science Center

library_source: other

data_processing:
Adapter and polyA sequences as well as 4 nucleotides at the 5’ end were removed from each read using FASTX-Toolkit
Trimmed reads mapped to human rRNA, tRNA and snoRNA sequences were removed
Remaining sequence reads were mapped to the GRCh38 human genome using TopHat2, allowing 2 mismatches
Unique reads were summarized using featureCounts of the Subread package
Assembly: GRCh38
Supplementary files format and content: Excel sheet containing quantification of ribosome protected fragments mapped to each Ensembl gene / spike-in (row) for each sample (column)
Library strategy: Ribo-Seq

molecule: other

extract_protocol:
Ribosome footprint isolated and subsequent ribosome protected RNA fragments extracted following Hornstein et al 2016 (PMID 27380875)
Sequencing library constructed using Clontech SMARTER smRNA SEQ KIT

value: EBV-transformed lymphoblastoid B-cell lines (LCL)

value: WT

value: Sodium Arsenite


title: GM19204, stress-treated, crispr-treated


title: GM19204, stress-treated, crispr-control


title: CNS.16474 patient tumor sample

source_name: Patient tumor sample, meninges recurrence from grade II meningioma, RNASeq

value: meningioma


title: BC.97359 patient tumor sample

source_name: Patient tumor sample, chest wall metastasis from breast cancer, RNASeq

value: breast cancer


title: GM18505, stress-treated, crispr-treated


title: GM19193, stress-treated, crispr-treated


title: GM19193, stress-treated, crispr-control


title: GIST.81050 patient tumor sample#2

description: paired-end (two lanes)

source_name: Patient tumor sample 2, peritoneal metastasis from GIST sarcoma, RNASeq


title: GM18505, stress-control, crispr-control

value: Control


title: GM18505, stress-control, crispr-treated


title: GM19204, stress-control, crispr-control


title: GIST.81050 patient tumor sample#1

description: paired-end (two lanes)

source_name: Patient tumor sample 1, peritoneal metastasis from GIST sarcoma, RNASeq


title: BC.32398 patient tumor sample

source_name: Patient tumor sample, brain metastasis from breast cancer, RNASeq


title: GM19204, stress-control, crispr-treated


title: GM19193, stress-control, crispr-treated


title: 25, S-methoprene, rep3 [F_25_J_3]

city: Providence

first: Corinne

last: Hutfilz

state: Rhode Island

address: 171 Meeting St.

institute: Brown University

description: virgin female adult dissected fat body. 25 days old.

data_processing:
FastQC data assessment
Adapter trimming via Trimgalore! and Cutadapt
Alignment to dm6 reference genome using Bowtie2 (--no-discordant)
Conversion to .bam via Samtools
Removal of optical duplicates via Picard tools and Samtools
Differential expression analyzed via DESeq2
Assembly: dm6
Supplementary files format and content: comma-separated values (.csv). Data represent the set of genes that become differentially expressed in response to temperature, but not S-methoprene or juvenile hormone status.

organism: Drosophila melanogaster

source_name: Fat body

growth_protocol: All flies were reared at 25C on agar-based standard diet. Virgins were collected and divided into the appropriate conditions within 8 hours post-eclosion. Flies remained in those conditions for 25 days, at which time flies were sacrificed and dissected for fat body tissue.

extract_protocol:
Fat body was harvested by dissection using 25 flies per replicate, using only those flies whose ovaries displayed the proper response to S-methoprene supplementation or temperature effect. Flies with either S-methoprene or at 25C had large, viable ovaries, whereas flies at 11C with ethanol displayed the regressed ovarian morphology characteristic of diapause.
Tissue was homogenized in Trizol™ with steel beads and total RNA was extracted using the Direct-zol™ RNA MicroPrep kit from Zymo Research. RNA concentration and purity was assessed via Nanodrop™ and Qubit™ technologies prior to library preparation, which was completed at Novogene facilities. Briefly, mRNA was isolated from total RNA via using magnetic beads coated with polyT oligomers. mRNA was then fragmented and cDNA synthesized, followed by end repair, A-tailing, Illumina adapter ligation, size selection, PCR amplification and purification. The final concentrations and purity of libraries were then assessed via Qubit™ and qPCR. Fragment size distribution was assessed via bioanalyzer.

treatment_protocol: Flies were supplemented with 10 uL of 99% ethanol once every 2 days, or supplemented with 10 uL 39.4 mm S-methoprene diluted in 99% ethanol every 2 days. Treatment was administered via volatilization.

value: Fat body


title: 25, S-methoprene, rep5 [F_25_J_5]


title: GM19193, stress-control, crispr-control


title: 25, S-methoprene, rep6 [F_25_J_6]


title: 25, S-methoprene, rep4 [F_25_J_4]


title: 25, S-methoprene, rep2 [F_25_J_2]


title: 25, EtOH, rep6 [F_25_E_6]


title: 25, EtOH, rep5 [F_25_E_5]


title: Input_Oregon_Prepupa_10h_APF

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to the dm6 genome by Hisat2 (using UseGalaxy.eu online tools)
Bam files were filtered to MAPQ>5. BigWig files were generated using  bamCoverage 3.0.2 with scores representing number of reads normalized by the size of the library. Final bigwig files were obtained using bigwigcompare tool as ratio of ChIP signal to Input. Scores represent number of reads normalized by the size of the library.
Assembly: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary files format and content: bigwig
Supplementary files format and content: Scores represent number of reads normalized by the size of the library.

source_name: whole prepupa

growth_protocol: The flies of Oregon-R-modENCODE stock were used (corresponds to Bloomington stock #25211). Embryos were collected in the fly cages for 2h using apple juice agar plates. Then plates were incubated at the 25°C for the required period of time. The time after egg laying (AEL) was calculated starting from the moment the agar plates were placed in the fly cages. L3 larvae, corresponding to the puff stages 1-3 full gut and puff stages 7-9 empty gut, were collected by culturing larvae in the fly media supplemented with 0.05% bromophenol blue to mark the guts of feeding animals. Prepupae corresponding to 0-1 hour after puparium formation (APF) were collected according to description of this developmental stage: white motionless prepupae starting to evert their anterior spiracles. Prepupae corresponding to later developmental stages were collected at the stage of white prepupa and then incubated at the 25°C for the required period of time

extract_protocol:
Crosslinking was performed with 0,7% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-2000 bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: stock

value: Oregon-R-modENCODE (Bloomington stock 25211)

tag: developmental stage

value: Prepupa 10h APF

value: whole prepupa

value: no treatment


title: Input_Oregon_Embr_2-4h

source_name: whole embryo

value: Embryos 2-4h AEL

value: whole embryo


title: ChIP_PolS5P_Oregon_Prepupa_10h_APF

description: Antibodies against RNA polymerase II CTD repeat (phospho S5) (Ab5131) Abcam


title: Input_Oregon_Embr_6-8h

value: Embryos 6-8h AEL


title: 25, EtOH, rep2 [F_25_E_2]


title: Input_Oregon_White_prepupa_0h_APF

value: White prepupae 0h APF


title: 25, EtOH, rep4 [F_25_E_4]


title: 25, EtOH, rep1 [F_25_E_1]


title: 25, EtOH, rep3 [F_25_E_3]


title: Input_Oregon_L3 PS1-3 full gut

source_name: whole larva

value: L3 larvae PS1-3 full gut

value: whole larva


title: ChIP_PolS2P_Oregon_Prepupa_10h_APF

description: Antibodies against RNA polymerase II CTD repeat (phospho S2) (Ab5095) Abcam


title: ChIP_Brd4-Fs(1)h_Oregon_White_prepupa_0h_APF

description: Rabbit polyclonal antibodies against ), Brd4/Fs(1)h (120–386 aa) were obtained and described previously in our lab (Mazina et al (2018) Biochim. Biophys. Acta Gene Regul. Mech. 1861, 178–189; Mazina et al (2017) Russ. J. Genet. 2, 178–186)


title: ChIP_Rpb3_Oregon_Prepupa_10h_APF

description: Rabbit polyclonal antibodies against Rpb3 (1-275 aa) were obtained and described previously in our lab (Mazina et al (2018) Biochim. Biophys. Acta Gene Regul. Mech. 1861, 178–189; Mazina et al (2017) Russ. J. Genet. 2, 178–186)


title: 11, S-methoprene, rep4 [F_11_J_4]


title: 11, S-methoprene, rep5 [F_11_J_5]


title: 11, S-methoprene, rep6 [F_11_J_6]


title: 11, S-methoprene, rep3 [F_11_J_3]


title: ChIP_PAF1_Oregon_White_prepupa_0h_APF

description: Rabbit polyclonal antibodies against PAF1 (1–234 aa) were obtained and described previously in our lab (Mazina et al (2018) Biochim. Biophys. Acta Gene Regul. Mech. 1861, 178–189; Mazina et al (2017) Russ. J. Genet. 2, 178–186)


title: 25, S-methoprene, rep1 [F_25_J_1]


title: ChIP_PolS5P_Oregon_White_prepupa_0h_APF


title: ChIP_NELF-E_Oregon_White_prepupa_0h_APF

description: Rabbit polyclonal antibodies against NELF E (2–279 aa) were obtained and described previously in our lab (Mazina et al (2018) Biochim. Biophys. Acta Gene Regul. Mech. 1861, 178–189; Mazina et al (2017) Russ. J. Genet. 2, 178–186)


title: 11, S-methoprene, rep2 [F_11_J_2]


title: 11, S-methoprene, rep1 [F_11_J_1]


title: 11, EtOH, rep5 [F_11_E_5]


title: 11, EtOH, rep6 [F_11_E_6]


title: ChIP_PolS2P_Oregon_White_prepupa_0h_APF


title: ChIP_Spt5_Oregon_White_prepupa_0h_APF

description: Rabbit polyclonal antibodies against Spt5 (917–1117 aa) were obtained and described previously in our lab (Mazina et al (2018) Biochim. Biophys. Acta Gene Regul. Mech. 1861, 178–189; Mazina et al (2017) Russ. J. Genet. 2, 178–186)


title: ChIP_Rpb3_Oregon_White_prepupa_0h_APF


title: ChIP_Brd4-Fs(1)h_Oregon_L3 PS1-3 full gut


title: 11, EtOH, rep4 [F_11_E_4]


title: ChIP_PAF1_Oregon_L3 PS1-3 full gut


title: 11, EtOH, rep3 [F_11_E_3]


title: 11, EtOH, rep2 [F_11_E_2]


title: 11, EtOH, rep1 [F_11_E_1]


title: ChIP_Rpb3_Oregon_L3 PS1-3 full gut


title: ChIP_NELF-E_Oregon_L3 PS1-3 full gut


title: ChIP_PolS2P_Oregon_L3 PS1-3 full gut


title: ChIP_PAF1_Oregon_Embr_6-8h


title: ChIP_Brd4-Fs(1)h_Oregon_Embr_6-8h


title: ChIP_NELF-E_Oregon_Embr_6-8h


title: ChIP_Spt5_Oregon_Embr_6-8h


title: SGC7901 cells_shControl_rep3

city: Shenzhen

first: Songcheng

last: Yin

address: 628 Zhenyuan Road

institute: The Seventh Affiliated Hospital of Sun Yat-sen 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. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
The de-duplicated consensus sequences were used for standard RNA-seq analysis. They were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: All_samples_rpkm.txt: Tab-delimited text file includes RPKM values for all Samples.

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen), DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit.
2 μg total RNAs were used for stranded RNA sequencing library preparation using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: human gastric cancer cell line


title: SGC7901 cells_shControl_rep2

value: WT


title: SGC7901 cells_shControl_rep1


title: SGC7901 cells_shPUM1_rep3

value: PUM1 knockdown


title: SGC7901 cells_shPUM1_rep1


title: SGC7901 cells_shPUM1_rep2


title: ChIP_PolS5P_Oregon_Embr_6-8h


title: ChIP_PolS2P_Oregon_Embr_6-8h


title: ALG-1 S642A IP rep1

city: Québec

first: Miguel

last: Quévillon Huberdeau

state: Québec

address: 9 Rue McMahon

department: Département de biologie moléculaire, de biochimie médicale et de pathologie

institute: Université Laval

description: small RNA analysis

data_processing:
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 2 mismatches are considered
Assembly: C. elegans WS215
Supplementary files format and content: sequence and read number for the analysis

source_name: Cloning ALG-1 S642A IP small RNA

growth_protocol: Worms were grown on NGM plates with OP50 at 20 °C.

extract_protocol:
RNAs were extracted with TRIzol.
RNAs were linked with Truseq LT/V1/V2 linkers using the standard 5' and 3' ligation methods. Amplicons with ~20 nt inserts were selected for sequencing. The samples were multiplexed with 8 nt indexes in the 3' linker. 5' RNA ligation and 3' RNA ligation.

treatment_protocol: For cloning 22G-RNA, the sample is treated with 0.5 μM PIR-1 at 20 °C for 2 hours in the ligation condition

value: Gravid adults

tag: genotype/variation


title: MCF-10A TGFβ treatment rep1

city: Chengdu

first: Wenrong

address: No. 17, Block 3, Southern Renmin Road

institute: West China Hospital, Sichuan University

data_processing:
The sequenced raw reads were obtained from the Illumina instrument
The raw reads were assessed by fastp and fastqc to remove adaptor or low-quality sequences. Then the clean reads were mapped to human GRCh37 genome using STAR v2.5.3a with the parameters recommended by CIRCexplorer2 pipeline
CIRCexplorer2 pipeline was exployed to identify circRNA candidates. The R package DESeq2 was utilized to determine the differentially expressed circRNA between the WT and TGFβ groups. To obtain the relative RPM value of circRNA, The number of back-spliced junction reads of each circRNA was counted and normalized by the number of uniquely mapped reads of the library
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw back-spliced junction reads count for each sample
Supplementary_files_format_and_content: Matrix table with RPM values for every circRNA and every sample

growth_protocol: MCF-10A was maintained in DMEM/Ham’s F-12 nutrient mixture (GIBCO) with 5% horse serum (GIBCO), 20 ng/ml−1 EGF (Peprotech), 10 µg/ml insulin, 0.5 µg/ml hydrocortisone (Sigma), 100 ng/ml cholera toxin.

extract_protocol:
To identify circRNAs that are regulated by TGFβ, the breast epithelial MCF10A cells were continuously treated with TGFβ for three days before harvested by TRIzol for RNA exaction and circRNA analysis.
RNA libraries were prepared for sequencing using standard rRNA-minus and strand-specific Illumina protocols

treatment_protocol: TGF-beta (5ng/ml, 72h)

tag: treatment

value: TGF[beta], 72h


title: MCF-10A WT rep2


title: Pigmentary mosaicismPB_263.21

type: genomic

city: CDMX

first: consuelo

last: salas

state: CDMX

address: INSURGENTES SUR 3700C

country: Mexico

institute: Instituto Nacional de Pediatria

description:
Mosaicism > 15-20%
peripheral blood DNA

hyb_protocol: Digestion and ligation, PCR amplification, purification of PCR products, quantification and fragmentation, labelling, array hybridization, wash and scan. CytoScan® technology (Thermo FisherScientific Inc).

data_processing:
Data was analyzed with ChAS 4.2 software. For the interpretation of these results, our database was used. internal data and the following databases: DGV, Cytogenomics Array Group CNV Database, Ensembl Resources, OMIM, UCSC, ClinGen, ClinVar and CHD wiki
By Array46 750k, no variation was detected in the number of copies that have not previously been described as benign or polymorphisms without clinical significance. By Array46 Optima, it has been detected a complete mosaic duplication of chromosome 12 (30%). The sample corresponds to a male individual compatible with mosaic trisomy 12.

label: Biotin

source_name: peripheral blood__PM263.21

growth_protocol: Biological samples (peripheral blood and fibroblasts) were grown with culture medium and under standard conditions for the cell type

extract_protocol: DNA was isolated from peripheral blood and fibroblast using the Gentra® PureGene® Blood kit, (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: No treatment

tag: disease

value: Pigmenatry mosaicism


title: Pigmentary mosaicismPB_264.21

description:
Mosaicism > 15-20%
peripheral blood DNA

scan_protocol: Digestion and ligation, PCR amplification, purification of PCR products, quantification and fragmentation, labelling, array hybridization, wash and scan. CytoScan® technology (Thermo FisherScientific Inc).

source_name: peripheral blood__PM264.21


title: ChIP_PolS5P_Oregon_L3 PS1-3 full gut

tag: tissue


title: ChIP_Rpb3_Oregon_Embr_6-8h


title: ChIP_Spt5_Oregon_L3 PS1-3 full gut


title: MCF-10A WT rep1

tag: cell line


title: ChIP_Brd4-Fs(1)h_Oregon_Embr_2-4h


title: Pigmentary mosaicismSkin_132.19

description:
Mosaicism >~20%
Fibroblasts DNA

source_name: dark skin_PM132.19

label_protocol: Digestion and ligation, PCR amplification, purification of PCR products, quantification and fragmentation, labelling, array hybridization, wash and scan. CytoScan® technology (Thermo FisherScientific Inc).


title: Pigmentary mosaicismPB_262.21

description:
Mosaicism > 15-20%
peripheral blood DNA

source_name: peripheral blood__PM262.21


title: ChIP_PAF1_Oregon_Embr_2-4h


title: LP_sgCbfa2t3_QuantSeq_rep3

city: Isehara

first: Hiroyuki

last: Hosokawa

address: 143 Shimokasuya

department: Immunology

institute: Tokai Univ

data_processing:
ChIP-seq; Sequencing data were mapped to the mouse genome build NCBI37/mm10 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory and visualized in the UCSC-genome browser (http://genome.ucsc.edu) (Speir et al., 2016).  ChIP peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”.  Peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr).  Only reproducible high quality peaks, with a normalized peak score ≥ 15, were considered for further analysis.
QuantSeq; Adaptor sequences were trimmed from the raw RNA-seq reads with fastp. Trimmed reads of each sample were mapped to the reference mouse genome mm10 by using STAR and normalized to 1 million reads in the original library. Genes with an average of 10 or more reads in either group were subjected for further analysis.  Differentially Expressed Genes (DEGs) were defined with P < 0.05, |log2FC| > 1, and TPM > 10 based on measurements from three biologically independent replicates for each sample type.
Assembly: mm10
Supplementary files format and content: Processed files include BED-files  All genomic coordinates are relative to mm10 mouse assembly.

source_name: LP cells

growth_protocol: A LP cell line was cultured on OP9 monolayers using OP9 medium (α-MEM, 10% FBS, 50 μM β-mercaptoethanol, Pen-Step-Glutamine) supplemented with 10 ng/ml of SCF (Pepro Tech Inc), 10 ng/ml of IL-7 (Pepro Tech Inc) and 10 ng/ml of Flt3L (Pepro Tech Inc).  Every 2-3 days, cultured cells were disaggregated, filtered through 40-um nylon mesh, and re-cultured on new OP9 monolayers with medium containing cytokines above.

extract_protocol: Total RNA was isolated from samples of 3 × 105 cultured cells using a RNeasy Micro Kit (Qiagen).  500 ng of total RNA was subjected to the 3’mRNA library preparation with QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (LEXOGEN) according to the manufacturer’s instructions.  After the PCR step, size distribution and yield of the library was determined by the D1000 high sensitivity tape station (Agilent) or Agilent High Sensitivity DNA kit on the bioanalyzer (Agilent).  The pooled libraries were loaded on the Illumina Nextseq500 platform and analyzed by 75bp single read.

tag: strain

value: LP

value: Cultured on OP9

tag: chip (antibody)

tag: sgrna


title: LP_sgCbfa2t3_QuantSeq_rep2


title: ALG-1 S642E IP rep3

description: small RNA analysis

source_name: Cloning ALG-1 S642E IP small RNA


title: EAU

city: Tianjin, China

first: hong

last: nian

address: 251 Fukang Road, Nankai District

institute: Tianjin Medical University Eye Hospital

hyb_protocol: Each slide was hybridized with Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Agilent) in hybridization Oven (Agilent) at 55°C, 20 rpm for 20 hours according to the manufacturer’s instructions. After hybridization, slides were washed by Gene Expression Wash Buffer Kit (Agilent).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent).

source_name: CD4+ T cells

label_protocol: miRNA in total RNA was labeled by miRNA Complete Labeling and Hyb Kit following the manufacturer’s instructions.

growth_protocol: CD4+ T cells were isolated and purified from the spleen and draining lymph nodes of naive and EAU mice.

extract_protocol: Total RNA was extracted from the CD4+ T cells of Naive and EAU mice with TRIzol reagent.

treatment_protocol: For induction of EAU, female C57BL/6 mice were injected intraperitoneally (i.p.) with 800 ng of pertussis toxin and immunized subcutaneously (s.c.) at over six spots on the tail base and flank with uveitogenic peptide IRBP1–20 emulsified in CFA containing mycobacterium tuberculosis strain H37RA (0.8 mg per mouse).

tag: gender

value: female

tag: age

value: 10 week

tag: disease status

value: EAU mice

value: CD4+ T cells from spleen and draining lymph nodes


title: MCF-10A TGFβ treatment rep2


title: ChIP_Spt5_Oregon_Embr_2-4h

value: Oregon-R-modENCODE (Bloomington stock 25211)

value: Embryos 2-4h AEL

value: whole embryo

value: no treatment


title: CD-tumor

first: Chae Won

last: Kim

address: 291, Daehak-ro, Yuseong-gu  E7 Rm 5101

data_processing:
Using cellranger 'mkfastq' module to demultiplexes raw base call files generated by Illumina sequencers into FASTQ files
Using cellranger 'count' to perform alignment, filtering, barcode counting and UMI counting
Assembly: Mm10
Supplementary files format and content: h5 file including matrix, barcodes, and features

source_name: brain

extract_protocol:
Isolate single cells from mouse brain tissues by using percoll gradient and sort CD45-positive immune cells by FACS
Chromiun Single Cell 3' RNA library v3

treatment_protocol: 4 week-aged mice were fed with control diet or high-salt diet and GL261 cells were intracranailly injected. Brain tissues were harvested at day 20 post tumor injection

value: brain

value: control diet


title: ALG-1 S642E IP rep2

description: small RNA analysis


title: ALG-1 Wild type IP rep3

description: small RNA analysis

source_name: Cloning ALG-1 WT IP small RNA

value: N2 (bristol)


title: ChIP_NELF-E_Oregon_Embr_2-4h


title: ALG-1 S642A IP rep3

description: small RNA analysis


title: ALG-1 S642E IP rep1

description: small RNA analysis


title: LP_sgCbfa2t3_QuantSeq_rep1


title: CKO5

city: Guangzhou

first: Wei

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include count and TPM values for each Sample
Supplementary_files_format_and_content: differential genes expression analysis

source_name: Liver

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Mice were fed with HFD for 8weeks

value: HFD for 8weeks

tag: genotype

value: Cpt1a L-/-


title: LP_sgCbfa2t2_QuantSeq_rep2


title: LP_sgCbfa2t2_QuantSeq_rep3


title: CKO3


title: LP_sgCbfa2t2_QuantSeq_rep1


title: ChIP_Rpb3_Oregon_Embr_2-4h


title: ALG-1 S642A IP rep2

description: small RNA analysis

value: Gravid adults


title: LP_sgZbtb1_QuantSeq_rep3


title: ALG-1 Wild type IP rep2

description: small RNA analysis


title: CKO1


title: ALG-1 Wild type IP rep1

description: small RNA analysis


title: 11, S-methoprene, rep4

data_processing:
FastQC data assessment
Adapter trimming via Trimgalore! and Cutadapt
Alignment to dm6 reference genome using Bowtie2 (--no-discordant and a maximum fragment length of 1000 bp)
Mitochondrial read removal via Shell and Samtools
Conversion to .bam via Samtools
Removal of optical duplicates via Picard tools and Samtools
Peaks called using MACS2 (min.FDR cutoff 0.05 and parameters --nomodel, --shift -100, --extsize 200, --keep-dup-all and –call-summits)
Blacklisted regions removed via Bedtools intersect
Differential accessibility analyzed via DiffBind
Assembly: dm6
Supplementary files format and content: comma-separated values (.csv). Data represent the set of loci that become accessible or inaccessible in response to temperature, but not S-methoprene or juvenile hormone status.

extract_protocol:
Fat body was harvested by dissection using 25 flies per replicate, using only those flies whose ovaries displayed the proper response to S-methoprene supplementation or temperature effect. Flies with either S-methoprene or at 25C had large, viable ovaries, whereas flies at 11C with ethanol displayed the regressed ovarian morphology characteristic of diapause.
Nuclear extraction and library preparation protocols were adapted from Cources et al., 2017 and Davie et al., 2015 using the omni-ATAC adaptation. The NEBNext™ Illumina library quantification kit from New England Biosciences was used to measure final library concentration (Ref # E7630S, lot 10013445). The Nextera™ DNA library prep kit from Illumina (Ref # 15028212, lot 20256848) was used to tagment DNA, ligate adapter sequences and amplify fragments. Adapter sequences used are available (Supplemental table X). The quality of ATAC-seq libraries was assessed via Bioanalyzer (Agilent) prior to sequencing.

value: Fat body


title: CKO2


title: Naïve

value: naive mice


title: 11, EtOH, rep4


title: alg-1(S642E) total RNA rep3

description: small RNA analysis

source_name: Cloning alg-1(qbc46[S642E]) small RNA


title: LP_sgZbtb1_QuantSeq_rep1

value: LP

value: Cultured on OP9


title: CKO4


title: 25, S-methoprene, rep4


title: ChIP_PolS2P_Oregon_Embr_2-4h


title: ChIP_PolS5P_Oregon_Embr_2-4h


title: WT3

value: Wild type


title: alg-1(S642E) total RNA rep1

description: small RNA analysis


title: 11, S-methoprene, rep3


title: 25, EtOH, rep4


title: LP_sgLmo2_QuantSeq_rep2


title: WT4


title: WT2


title: LP_sgLmo2_QuantSeq_rep3


title: alg-1(S642A) total RNA rep3

description: small RNA analysis

source_name: Cloning alg-1(qbc23[S642A]) small RNA


title: alg-1(S642E) total RNA rep2

description: small RNA analysis


title: LP_sgZbtb1_QuantSeq_rep2


title: LP_sgLmo2_QuantSeq_rep1


title: LP_sgCont_QuantSeq_rep3

value: sgCont


title: 11, EtOH, rep3

source_name: Fat body


title: WT5


title: alg-1(S642A) total RNA rep2

description: small RNA analysis


title: LP_sgCont_QuantSeq_rep2


title: Otx2 Adult rep2

description: Bamcoverage .bigwig file/MACS2 peak calling .bed file

data_processing:
Library strategy: CUT&RUN
RNA-Seq: Fastq reads were pre-processed using “FastQGroomer” and “Trimmomatic” algorithms (Bolger et al. 2014), then mapped against the mm10 genome using “Tophat” (Kim etal. 2013). Gene counts were generated using “htseq-count” followed by “DeSeq2” (Anders et al. 2015 ; Love et al. 2014). R-studio was used to annotate and merge data. Heatmaps were generated using Morpheus program (https://software.broadinstitute.org/morpheus/) with k-means clustering. Gene Ontology (GO) analysis (allowing to detect which terms are under- or over- represented using annotations within a specific genes set) was ran using David 6.8 tool (Huang da et al. 2009).
CUT&RUN: Fastq reads were aligned using bowtie2 mm9 genome on Galaxy platform. MACS2 was used for peak calling using default parameters. Bamcoverage was used to generate bigwig files.
Genome_build: mm9, mm10
Supplementary_files_format_and_content: Raw ht-seq counts in tabular format and excel spreadsheet results of DESeq2 analysis of RNA-seq data generated from retinal cells with BCOR knockdown
Supplementary_files_format_and_content: Bigwig tracks files and MACS2 peaks bed files for scored peaks in CUT&RUN

source_name: Retina

extract_protocol:
RNA-seq: RNA extraction was performed as detailed by manufactorer (RNeasy mini kit, Qiagen).
CUT&RUN: Genomic DNA extraction was performed as per manufactorers guidelines (QIAquick Nucleotide Removal Kit).
RNA-seq: Samples quantity (RNA Integrity Number = RIN) and quality were assessed using the Agilent RNA 6000 Pico Kit (Agilent #5067-1513) on the Bioanalyzer 2100. Libraries preparation started with rRNA depletion using the Ribo-Zero™ Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre for Illumina #MRZG12324). 3.0 ng to 5.1 ng of total RNA were used for rRNA depletion of the total RNA. Speed-vac sublimation was performed on some samples to reduce RNA volume to 17ul in order to start the depletion reaction. rRNA depleted RNA were then purified with AGENCOURT® RNA CLEAN® XP Kit (Beckman Coulter). The samples were eluted in 8.5ul of H2O to continue the library preparation using SMARTer® Stranded RNA-Seq Kit (Takara Bio USA, Inc. #634836 or #634837).
CUT&RUN: Libraries were prepared with the KAPA DNA HyperPrep Kit (Roche 07962363001 - KK8504). This protocol includes an End-Repair/A-tailing step and an adapter ligation step followed by a PCR amplification (enrichment) of ligated fragments.
RNA-seq: The 1st strand synthesis was performed using a modified N6 primer (the SMART Stranded N6 Primer) in order to obtain full length fragments. The full-length, single-stranded (ss) cDNA fragments were purified with Agencourt DNA CleanUp AMPure® XP Kit (Beckman Coulter #A63881). PCR Enrichment + indexing step of 15 cycles was then performed using the Illumina Indexing Primer Set provided by the kit. The final enriched product (library, after PCR) was purified using Agencourt DNA CleanUp AMPure® XP Kit (Beckman Coulter #A63881). Libraries were eluted in 16 ml of elution buffer. Quality and quantification of the libraries were assessed using the Agilent High Sensitivity DNA Kit (Agilent #5067-4626) on the Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted and pooled equimolar prior to paired-end sequencing performed with 50 cycles (PE50) on a v4 flowcell (Illumina - HiSeq PE Cluster Kit v4 cBot - PE-401-4001) of the Illumina HiSeq 2500 System.
CUT&RUN: The adapters used for ligation were IDT for Illumina TruSeq UD Indexes (Illumina - 20022371). The final enriched product (library, after PCR) was purified using KAPA purification beads (Roche 07983298001 - KK8002) and a dual-SPRI size selection was performed (with KAPA beads) to select fragments between 180-500 bp. Libraries were then quantified using a Nanodrop microvolume spectrophotometer (ng/l) and quality was assessed using the Agilent High Sensitivity DNA Kit (Agilent -5067-4626) on a Bioanalyzer 2100. The libraries were then quantified by q-PCR to obtain their nanomolar (nM) concentration. Libraries were diluted, pooled equimolar and sequenced in pair end 50 cycles (PE50) on a S1 flowcell (Illumina - 20012863) of the Illumina NovaSeq 6000 System.

value: Retinal cells

tag: mouse line

value: WT

value: Adult

tag: condition


title: alg-1(S642A) total RNA rep1

description: small RNA analysis


title: 11, S-methoprene, rep2


title: LP_sgCont_QuantSeq_rep1


title: Otx2 Adult rep1

tag: cell type


title: 25, EtOH, rep3


title: LP_1%input_rep2

extract_protocol: Ten million of LP cells were fixed with 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min at RT followed by an additional 10 min with addition of formaldehyde up to 1 %.  The reaction was quenched by addition of 1/10 volume of 0.125 M glycine and the cells were washed with HBSS (Gibco).  Pelleted nuclei were dissolved in lysis buffer (0.5 % SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8) and PIC) and sonicated on a Bioruptor (Diagenode) for 18 cycles of 30 sec. sonication followed by 30 sec. rest, with high power.  Five ug of anti-Zbtb1 Abs (a mixture of 2.5 ug of S303-242A (Bethyl) and 2.5 ug of ab79455 (Abcam)) or anti-Cbfa2t3 (a mixture of 2.5 ug of 17190-1-AP (Proteintech) and 2.5 ug of sc-373691 (Santa Cruz)) were pre-bound to Dynabeads anti-Rabbit Ig or Protein A/G (Invitrogen) and then added to the diluted chromatin complexes.  The samples were incubated overnight at 4 °C, then washed and eluted for 6 h at 65 °C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 50 mM NaCl, 1 % SDS, and 50 ug/ml proteinase K).  Precipitated chromatin fragments were cleaned up using ChIP DNA Clean & Concentrator (Zymo).  ChIP-seq libraries were constructed using NEBNext Ultra II DNA Library Prep with Sample Purification Beads (E7103S, NEB) and NEBNext Multiplex Oligos for Illumina (E7500S, NEB), and sequenced on Illumina NextSeq500 in single read mode with the read length of 75 nt.

value: none (input)


title: N2 total RNA rep3

description: small RNA analysis

source_name: Cloning N2 small RNA


title: 11, EtOH, rep2


title: N2 total RNA rep2

description: small RNA analysis


title: BCOR Adult rep2

value: BCOR


title: 25, S-methoprene, rep2


title: N2 total RNA rep1

description: small RNA analysis


title: BT20

data_processing:
Alignment with STARv2.5.3 to GRCh38 or with bowtie2 to Hg19 and mm10 for PDX samples, as indicated below
Gene-level raw counts summarization with STARv2.5.3 quant-mode. In the case of PDX samples, xenomapper tool was to generate counts from reads selectively mapping to human transcriptome and not mouse.
Variance stabilization (normalization) with DESeq2 (R bioconductor package)
Gene expression signature and viper analysis as described in manuscript.
Assembly: GRCh38.v90 or as indicated below.
Supplementary files format and content: Tab delimited text output of raw counts from STAR alignment and gene count quantification. Tab delimited text output for VIPER analysis of differential protein activity for perturbation or pharmacodynamic samples.

source_name: Cancer Cell line, CUIMC sequenced, RNASeq

extract_protocol:
RNAs were extracted using polyA selection kits, TruSeq
For PLATEseq multiplexed platform protocol details, see reference PMID: 28740083.
RNA Sequencing was performed on an Illumina NextSeq 500 or NovaSeq 6000 sequencer, as indicated below for each file.


title: 25, EtOH, rep2


title: LP_1%input_rep1


title: WT1


title: ASPC1

value: Cancer Cell line, CUIMC sequenced, RNASeq


title: LP_aCbfa2t3_ChIP_rep1

value: anti-Cbfa2t3 (a mixture of 2.5 ug of 17190-1-AP (Proteintech) and 2.5 ug of sc-373691 (Santa Cruz))


title: BCOR Adult rep1


title: Otx2 P0 rep2


title: Otx2 P0 rep1


title: LP_aCbfa2t3_ChIP_rep2

value: anti-Cbfa2t3 (a mixture of 2.5 ug of 17190-1-AP (Proteintech) and 2.5 ug of sc-373692 (Santa Cruz))


title: 11, S-methoprene, rep1