title: Brg1 reexperssed atregs subset from rko1 mice, isolated on day 7 after tam

city: Shanghai

first: Zhengyu

last: Jing

address: 393 Middle Huaxia Road, Pudong

department: School of Life Science and Technology

institute: ShanghaiTech University

data_processing:
Reads were aligned to the reference genome using Hisat2 (v2.0. 5)
The mapped reads of each sample were assembled by StringTie (v1.3.3b)
FeatureCounts  v1.5.0-p3 was used to count the reads numbers mapped each gene.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Treg cells

extract_protocol:
Total RNA was isolated from 0.1 million Tregs using RNAprep Pure Micro Kit (TIANGEN), and cDNA synthesized from mRNA using SMART-Seq® v4 Ultra™ Low Input RNA Kit (Clontech). Library was then constructed and sequenced on Illumina HiSeq platform with the PE150 strategy, which yielded 25~ 60 million reads per sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tregs were harvested from lymph nodes and spleens of various mice, including reversible KO mice treated with tamoxifen.

value: Spleen and LN

tag: age

value: 3-4 weeks


title: method_validation_hVH1-2_bait_rep2

status: Public on Feb 21 2020

type: SRA

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine (PCMM)

country: USA

institute: Boston Children's Hospital / Harvard Medical School

library_source: genomic

data_processing:
Library strategy: LAM-HTGTS-Rep-SHM-Seq
LAM-HTGTS-Rep-SHM-Seq data analysis was done by the LAM-HTGTS-Rep-SHM-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
scRNA-seq raw sequencing files were aligned to the mouse V(D)J sequence using Cell Ranger: V(D)J Pipelines (10x Genomics) and the V usage and mutation profiles were generated and visualized by Loupe V(D)J Browser.
Genome_build: mm9
Supplementary_files_format_and_content: .db.xls files were generated using LAM-HTGTS-Rep-SHM-Seq pipeline (IgBLAST); .vloup files were generated using Cell Ranger: V(D)J Pipelines (10x Genomics).

molecule: genomic DNA

organism: Mus musculus

source_name: splenic naïve B cells

extract_protocol:
Spleen and PPs were dissected out from 8-12 week old mice, prepared into single cell suspensions and purified by EasySep® Negative Selection B cell Enrichment Kit (Stem Cell Techonologies) according to the manufacturer’s protocol. Purified B cells were stained with anti-B220-PE (1:2000) (eBiosciences), anti-CD38-APC (1:200) (eBiosciences) and anti-GL7-FITC (1:200) (Biolegend). GC (B220+GL7+CD38-) and nonGC (B220+GL7-CD38+) B cells were sorted from the same sample by fluorescence-activated cell sorting (FACS). Genomic DNA from sorted cells was prepared using a DNeasy Blood and Tissue Kit (Qiagen) according to the manufacturer’s protocol.
LAM-HTGTS-Rep-SHM-Seq was derived from HTGTS-Rep-seq (Lin et. al., PNAS 2016) with several modification. All libraries were made using 400 ng genomic DNA as starting materials, so that the level of PCR amplification was kept the same among different samples. In the cases when less than 400 ng genomic DNA was obtained from GC or non-GC B cell samples, genomic DNA from JM8a3, a C57BL/6 ES cell line, was added to make the starting DNA template amount consistent among samples. The library preparation procedure was mostly done as previously described with a few modifications in the linear amplification-mediated PCR step, where we used one reaction of 50 μl instead of 8 reactions and performed 100 cycles instead of 80 cycles. scRNA-seq libraries were prepared using 10x Genomics Library Kits and sequenced on an Illumina NextSeq500 according the manufacturer’s recommendations.

tag: strain

tag: condition

value: SPF

tag: tissue

value: spleen

tag: locus (ig heavy-chain or light-chain)

value: IgH


title: Brg1 deleted aTregs subset from rKO1 mice, isolated on day 7 after tam

country: China

library_source: transcriptomic

molecule: total RNA


title: Whole blood, HSK08

type: genomic

city: Ji'nan

first: Yaran

last: Zhang

address: North industrial road

institute: Shandong Acdemy of Agricultural Sciences

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing:
Genomic DNA extracted from whole blood was genotyped using BovineHD Genotyping BeadChip (Illumina).
[matrix.txt]  Genotype: AA,AB,BB,or NC (no call), Log_R_Ratio, B_Allele_Freq

label: C-Bio and A-DNP

organism: Bos taurus

source_name: Jugular vein

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from the anti-coagulant treated whole blood was performed using proteinase K and standard phenol-chloroform extraction.

tag: gender

value: Female

tag: breed

value: Hazake cattle

tag: altitude (m)

tag: longitude

tag: latitude

value: Whole blood


title: 1098 PIX

type: RNA

city: Hennigsdorf

first: Martina

last: Schad

address: Neuendorfstrasse 16b

country: Germany

institute: OakLabs GmbH

hyb_protocol: 600 ng of each cRNA is hybridised (using Agilent Gene Expression Hybridisation Kit) on 8x60K microarrays at 65°C for 17 h in Agilent’s hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37°C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides

data_processing: Agilent’s Feature Extraction software version 11 was used to read and process the TIFF files. Furthermore default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20150612) were used to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Homo sapiens

source_name: cultured human dermal mesenchymal stem cells

label_protocol: For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate fluorescent cRNA (complementary RNA). For 1st strand synthesis, oligo-dT primer was used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP was performed.

growth_protocol: Cells were derived by enzymatic digestion of human skin tissue, expanded in adherent culture in mesenchymal stem cell-favoring medium for up to 16 passages, and positively selected for ABCB5 using a specific antibody.

extract_protocol: Total RNA was extracted using the RNeasy® Kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions.

tag: passages

value: PIX

value: skin


title: method_validation_hVH1-2_bait_rep1


title: Brg1 reexperssed tregs subset from rko1 mice, isolated on day 7 after tam

tag: cell type

value: Treg cells

tag: genotype


title: GF+SPFfeces-9_PP_IgH_GC

source_name: Peyer's Patches germinal center B cells

value: GF+SPF

value: Peyer's Patches


title: 975 PXV

value: PXV


title: Whole blood, HSK06

description: Genomic DNA extracted from whole blood was genotyped using BovineHD Genotyping BeadChip (Illumina).


title: 1024 PXV


title: Brg1 deleted tregs subset from rko1 mice, isolated on day 7 after tam


title: Brg1 deleted tregs from rko1 mice

description: rko1(without reversal)


title: 1024 PXIII

value: PXIII


title: Whole blood, HSK05


title: GF+SPFfeces-8_PP_IgH_GC


title: 975 PXII

value: PXII


title: 975 PXI

value: PXI


title: Brg1 deleted subset of tregs from mosaic females

description: Mosaic(-)

value: Spleen and LN


title: 1024 PXVI

value: PXVI


title: GF+SPFfeces-7_PP_IgH_GC


title: Brg1 expressing subset of tregs from mosaic females

description: Mosaic(+)

value: 3-4 weeks


title: Whole blood, HSK04


title: WT

description: WT


title: Whole blood, HSK03


title: GF+SPFfeces-6_PP_IgH_GC


title: 1024 PXIV

value: PXIV


title: GF+SPFfeces-5_PP_IgH_GC

value: IgH


title: NS565_SM_TyH2A_Input_1

city: Planegg-Martinsried

first: T.

middle: Nicolai

last: Siegel

address: Großhaderner Str. 9

department: Department of Physiological Chemistry

institute: Ludwig-Maximilians-Universität

description:
ratio file of ChIP to input
CpB_ws5001_ss1001_denominator_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS263_WT_ChIP_H2AZ_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

data_processing:
Reads were mapped using Bowtie 2 local
BAM files were sorted and indexed using SAMtools version 1.8
The number of reads was normalised per billion mapped reads and coverage files were generated in the wiggle format using COVERnant version 0.3.0 with the subcommand ratio
Genome_build: HGAP3_Tb427v9; from Zenodo https://doi.org/10.5281/zenodo.823671
Supplementary_files_format_and_content: wiggle format containing coverage tracks

organism: Trypanosoma brucei brucei

source_name: T. brucei SM bloodstream form

growth_protocol: Cells were grown in HMI-11 medium to a density of 0.9 mio cells per ml. For constitutive overexpression of TY1-H2A, 1 µg/µl Doxycylin was added to the medium.

extract_protocol:
In brief, 2 x 10e8 cells were harvested, crosslinked in 1% formaldehyde, lysed using 200 µM digitonin (final concentration) and chromatin was fragmented using 1 U/µl MNase (Sigma-Aldrich). Immunoprecipitation was performed using Dynabeads Protein G (Invitrogen) coupled to 10 µg monoclonal, purified BB2 mouse antibody. Bound material was washed and eluted, and cross-links were reversed at 65 °C for ~11 h in the presence of 300 mM NaCl (final concentration). see Wedel et al. 2017 #1 (DOI: 10.15252/embj.201695323) and Wedel et al. 2017 #2 (10.1016/j.exppara.2017.03.003 )
ChIP-seq libraries were constructed using 35 ng of immunoprecipitated or input DNA for sequencing on an Illumina platform. Following blunt-ending and poly(A)-tailing, Y-shaped adapters (Ford et al., 2014) containing the Illumina Truseq-Adapter-sequences are ligated to each end of a DNA molecule. The library concentrations were determined in duplicates using Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. Q32854) for Qubit 2.0 Fluorometer (Invitrogen, cat. no. Q32866). ChIP-seq libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, cat. no. KK4824) according to the manufacturer’s instruction and sequenced in paired-end mode with 2 x 76 cycles using an Illumina NextSeq 500 platform.

tag: chip antibody


title: NS525_ssRNAseq_HAT1KD2T1_48h_2

description:
Replicate RNA-seq datasets were merged using Samtools and indexed
ERCC_ws101_ss101_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_numerator_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz

data_processing:
Adapter sequences were removed from the raw sequencing files using Cutadapt
Reads were mapped using BWA-mem
BAM files were sorted and indexed using SAMtools version 1.8 and unmapped, PCR or optical duplicates, not primary aligned and supplementary aligned reads were removed from the alignment files (SAM flag: 3332)
Differential gene expression analysis was conducted with the DESeq2 package from R/Bioconductor
wig files were generated using COVERnant version 0.3.0 with the subcommand ratio including the additional parameters –factor_numerator and –factor_denominator
Genome_build: hybrid genome (HGAP3_Tb427v9 and the sequences of the 92 ERCC spike-in transcripts; from Zenodo https://doi.org/10.5281/zenodo.823671)
Supplementary_files_format_and_content: wiggle format containing coverage tracks

source_name: T. brucei 2T1 bloodstream form

growth_protocol: Cells were grown in HMI-11 medium for 48 h up to a density of 0.9 mio cells per ml. For depletion of HAT1 or HAT2, cells were treated with 1 µg/ml Doxycylcin for 48 h.

extract_protocol:
In brief, total RNA was extracted from 4.5 x 10e7 cells grown to a density of 0.9 x 10e6 cells/ml using the NucleoSpin RNA kit (Macherey-Nagel; cat. no. 740955.10). 3.8 µl of 1 M RNAse-free dithiothreitol (Sigma-Aldrich; cat. no. 10197777001) and 1 μl of 1:10 Ambion ERCC RNA Spike-In Mix (ThermoFisherScientific; cat. no. 4456739) were added to the cell lysis buffer. Ribosomal RNA was depleted from 2 µg of total RNA; see Kraus et al. 2019 (DOI: 10.1038/s41598-019-48692-2).
cDNA was synthesized using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs; cat. no. E7420), strand specific RNA-seq libraries were generated. Library concentrations were determined in duplicates using Qubit dsDNA HS Assay Kit (Invitrogen, cat. no. Q32854) for Qubit 2.0 Fluorometer (Invitrogen, cat. no. Q32866). Strand-specific RNA-sequencing libraries were quantified using the KAPA Library Quantification Kit (KAPA Biosystems, cat. no. KK4824) according to the manufacturer’s instruction and sequenced in paired-end mode on an Illumina NextSeq 500 sequencer 2 x 76 cycles; see Kraus et al. 2019 (DOI: 10.1038/s41598-019-48692-2)

tag: genotype/variation


title: NS526_ssRNAseq_HAT1KD2T1_48h_3


title: NS563_SM_TyH2A_ChIP_1

description:
ratio file of ChIP to input
CpB_ws5001_ss1001_numerator_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS565_SM_TyH2A_Input_1_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS563_SM_TyH2A_ChIP_1_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz

value: monoclonal, purified BB2 mouse antibody; purified from hybridoma cells (Bastin et al. 1996)


title: Whole blood, HSK01

value: Female

value: Hazake cattle


title: NS564_SM_TyH2A_ChIP_2

description:
ratio file of ChIP to input
CpB_ws5001_ss1001_numerator_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_numerator_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_numerator_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: Whole blood, FZ11

value: Fuzhou cattle

value: Whole blood


title: GF+SPFfeces-3_PP_IgH_GC


title: NS524_ssRNAseq_HAT1KD2T1_48h_1


title: NS354_ssRNAd_HAT2KD2T1_48h_3

description:
Replicate RNA-seq datasets were merged using Samtools and indexed
ERCC_ws101_ss101_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_numerator_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz


title: GF+SPFfeces-2_PP_IgH_GC


title: Whole blood, FZ10


title: NS353_ssRNAd_HAT2KD2T1_48h_2


title: NS352_ssRNAd_HAT2KD2T1_48h_1


title: NS351_ssRNAd_WT3

description:
Replicate RNA-seq datasets were merged using Samtools and indexed
ERCC_ws101_ss101_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_denominator_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws101_ss101_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws1_ss1_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT1KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_forward.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_reverse.wig.gz
ERCC_ws5001_ss1001_ratio_RNAseq_WT_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted_vs_RNAseq_HAT2KD2T1_merged_F3332_to_HGAP3_Tb427v9_ERCC_bwa.sorted.wig.gz

source_name: T. brucei WT bloodstream form Lister 427

value: WT


title: Whole blood, FZ09


title: NS566_SM_TyH2A_Input_2

description:
ratio file of ChIP to input
CpB_ws5001_ss1001_denominator_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_denominator_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_denominator_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz
CpB_ws5001_ss1001_ratio_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_forward.wig.gz
CpB_ws5001_ss1001_ratio_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted_reverse.wig.gz
CpB_ws5001_ss1001_ratio_NS566_SM_TyH2A_Input_2_to_HGAP3_Tb427v9_bwt2.sorted_vs_NS564_SM_TyH2A_ChIP_2_to_HGAP3_Tb427v9_bwt2.sorted.wig.gz


title: GF+SPFfeces-1_PP_IgH_GC

value: GF+SPF


title: NS320_ssRNAd_WT1


title: SFB-5_PP_IgH_GC

value: GF+SFB

value: Peyer's Patches


title: Whole blood, FZ08


title: GF+SPFfeces-4_PP_IgH_GC


title: SFB-5_PP_IgH_nonGC

source_name: Peyer's Patches naïve B cells


title: Whole blood, FZ07


title: SFB-4_PP_IgH_GC


title: SFB-4_PP_IgH_nonGC


title: Whole blood, FZ06


title: Whole blood, FZ05


title: 6-H3

city: Guangzhou

first: Qian

last: Gui

state: Guangdong

address: 74 Zhongshan 2nd Rd

department: Department of Biomedical Informatics

institute: Sun Yat-sen University

data_processing:
Trimmomatic used to remove the Illumina adapters and low quality bases or reads
Short-read alignments were further generated by aligning preprocessed reads with the index genome using HISAT2
Transcripts per million reads (TPM) value was quantified with StringTie and used as the gene expression levels
Genome_build: Yeast (Saccharomyces cerevisiae) S288C reference genome version R64-2-1
Supplementary_files_format_and_content: abundance files include TPM values for each Sample

organism: Saccharomyces cerevisiae

growth_protocol: Each strain of the pRPL5-GFP cassette was inoculated into 5 ml of YPD medium (1% yeast extract, 2% peptone, 2% glucose), then cultured overnight at 30 °C and 250 rpm.

extract_protocol:
Total RNA was then extracted from cell lysates using the Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions. The quality of RNA was determined by A260/A230 ratio, A260/A280 ratio and concentration using NanoDrop. An A260/A230 ratio > 2 and an A260/A280 ratio of the range of 1.8 to 2.2 were considered acceptable.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 6-H6


title: 6-H1


title: 6-H8


title: BY4743-2

source_name: wild type

value: wild type


title: Whole blood, FZ04


title: 6-G5


title: 6-G12


title: NS350_ssRNAd_WT2


title: SFB-3_PP_IgH_nonGC


title: 6-F6


title: 6-F5


title: Whole blood, FZ02


title: 6-F4


title: SFB-2_PP_IgH_GC


title: 6-G11


title: 6-F3


title: SFB-2_PP_IgH_nonGC


title: 6-F2


title: Whole blood, FZ01


title: 6-E7


title: 6-G6


title: SFB-1_PP_IgH_GC


title: SFB-3_PP_IgH_GC


title: Whole blood, HSK02


title: Whole blood, DZ20

value: Dianzhong cattle


title: 6-E6


title: 6-E4


title: GF-10x3_PP_IgH_GC

value: GF


title: 6-E3


title: 6-E12


title: Whole blood, DZ18


title: Whole blood, DZ16


title: Whole blood, DZ17


title: GF-8x3_PP_IgH_GC


title: GF-9x3_PP_IgH_GC


title: 6-E11


title: 6-E10


title: 6-D8


title: 6-D3


title: 6-D6


title: 6-D1


title: 6-D2


title: Whole blood, FZ03


title: Whole blood, DZ15


title: GF-6x3_PP_IgH_GC


title: 6-E1


title: GF-5x3_PP_IgH_GC


title: 6-C8


title: GF-5x3_PP_IgH_nonGC


title: Whole blood, DZ12


title: Whole blood, DZ19


title: 6-E2


title: SFB-1_PP_IgH_nonGC


title: 6-D7


title: GF-7x3_PP_IgH_GC


title: 6-C5


title: GF-4x3_PP_IgH_GC


title: GF-4x3_PP_IgH_nonGC


title: Whole blood, DZ11


title: 6-B3


title: 6-C1


title: 6-C3


title: Whole blood, DZ10


title: Whole blood, DZ13


title: Whole blood, DZ14


title: 6-B2


title: 6-A3


title: Whole blood, DZ09


title: GF-3x3_PP_IgH_GC


title: 6-A2


title: 6-C7


title: 5-H9


title: 6-C6


title: GF-3x3_PP_IgH_nonGC


title: Whole blood, DZ08


title: 5-H8


title: GF-2x3_PP_IgH_GC


title: Whole blood, DZ07


title: 5-H6


title: 5-H5


title: GF-2x3_PP_IgH_nonGC


title: Whole blood, DZ06


title: 5-H4


title: 5-H2


title: GF-1x3_PP_IgH_GC


title: 5-H11


title: Whole blood, DZ05


title: 5-H1


title: Whole blood, DZ04


title: 5-G8


title: 5-G9


title: SPF-18_PP_IgH_GC

value: SPF


title: 5-G6


title: SPF-17_PP_IgH_GC


title: Whole blood, DZ02


title: Whole blood, DZ01


title: 5-G5


title: 5-G2


title: 5-G3


title: 5-G4


title: SPF-16_PP_IgH_GC


title: 5-G11


title: Whole blood, CNSD12

value: Chuannan Mountain cattle


title: SPF-15_PP_IgH_GC


title: Whole blood, CNSD11


title: 5-G10


title: 5-G1


title: 5-H10


title: SPF-15_PP_IgH_nonGC


title: 5-F9


title: GF-1x3_PP_IgH_nonGC


title: Whole blood, CNSD10


title: 5-F6


title: SPF-14_PP_IgH_GC


title: 5-F4


title: SPF-16_PP_IgH_nonGC


title: Whole blood, CNSD08


title: Whole blood, DZ03


title: SPF-13_PP_IgH_GC


title: 5-F11


title: SPF-14_PP_IgH_nonGC


title: Whole blood, CNSD09


title: 5-F2


title: Whole blood, CNSD06


title: SPF-12_PP_IgH_GC


title: 5-G12


title: 5-F3


title: Whole blood, CNSD05


title: 5-F10


title: Whole blood, CNSD07


title: 5-E8


title: 5-F1


title: 5-E6


title: 5-E5


title: SPF-10_PP_IgH_GC


title: 5-E2


title: Whole blood, CNSD04


title: SPF-9_PP_IgH_GC


title: 5-F5


title: Whole blood, CNSD03


title: 5-E11


title: SPF-8_PP_IgH_GC


title: 5-E10


title: Whole blood, CNSD02


title: 5-E9


title: SPF-7_PP_IgH_GC


title: Whole blood, CNSD01


title: 5-D9


title: 5-E1


title: 5-D8


title: 5-D7


title: SPF-6_PP_IgH_GC


title: 5-D6


title: Whole blood, BHB14

value: Bohai Black cattle


title: 975 PX

value: PX

value: skin


title: 5-D5


title: SPF-6_PP_IgH_nonGC

value: IgH


title: 5-D4


title: SPF-5_PP_IgH_GC


title: 5-D2


title: 5-E12


title: Whole blood, BHB12

value: Female


title: 5-D11


title: Whole blood, BHB11


title: 5-D10


title: 5-D1


title: SPF-5_PP_IgH_nonGC


title: Whole blood, BHB10


title: 5-C8


title: SPF-4_PP_IgH_GC


title: 5-C7


title: 5-C9


title: SPF-4_PP_IgH_nonGC


title: 5-C6


title: Whole blood, BHB08


title: 5-C4


title: Whole blood, BHB13


title: SPF-3_PP_IgH_nonGC


title: 5-C5


title: SPF-3_PP_IgH_GC


title: Whole blood, BHB07


title: 5-C3


title: 5-C2


title: SPF-2_PP_IgH_GC


title: Whole blood, BHB06


title: 5-C11


title: SPF-2_PP_IgH_nonGC


title: 5-C1


title: Whole blood, BHB05


title: 5-B8


title: Whole blood, BHB04


title: SPF-1_PP_IgH_GC


title: 5-B9


title: 5-B6


title: Whole blood, BHB09


title: SPF-1_PP_IgH_nonGC


title: Whole blood, BHB03


title: 5-B5


title: 5-B4


title: 5-B3


title: Whole blood, BHB02


title: 5-B2


title: NP10d-4_SP_IgL_nonGC

value: NP-CGG IP immunization 10 day

value: spleen

value: IgL


title: 5-B11


title: 5-A8


title: NP10d-3_SP_IgL_GC

source_name: splenic germinal center B cells


title: 5-A6


title: NP10d-3_SP_IgL_nonGC


title: 5-A5


title: Whole blood, AX08

value: Anxi cattle

value: Whole blood


title: Whole blood, AX09


title: 5-B7


title: 5-A3


title: 5-A12


title: 5-A10


title: 5-A1


title: NP10d-2_SP_IgL_nonGC


title: Whole blood, AX07


title: 4-H9


title: NP10d-2_SP_IgL_GC


title: Whole blood, AX06


title: NP10d-4_SP_IgL_GC


title: Whole blood, AX05


title: NP10d-1_SP_IgL_GC


title: 4-H8


title: 4-H7


title: Whole blood, BHB01


title: 4-H5


title: 4-H4


title: Whole blood, AX04


title: NP10d-1_SP_IgL_nonGC


title: 4-H2


title: NP10d-5_SP_IgH_GC


title: Whole blood, AX03


title: 4-H11


title: NP10d-5_SP_IgH_nonGC


title: 4-H10


title: Whole blood, AX02


title: Whole blood, AX01


title: 4-G8


title: 4-G6


title: NP10d-4_SP_IgH_nonGC


title: NP10d-3_SP_IgH_GC


title: 4-G7


title: 4-G9


title: 4-G5


title: Whole blood, APJZ11

value: Apeijiaza cattle


title: 4-G3


title: NP10d-4_SP_IgH_GC


title: 4-G2


title: Whole blood, APJZ10


title: Whole blood, APJZ12


title: 4-G12


title: 4-G10


title: NP10d-2_SP_IgH_GC


title: 4-G4


title: Whole blood, APJZ09


title: 4-F7


title: 4-G1


title: NP10d-2_SP_IgH_nonGC


title: Whole blood, APJZ08


title: 4-F4


title: Whole blood, APJZ07


title: NP10d-1_SP_IgH_GC


title: 4-F2


title: 4-F11


title: 4-E8


title: NP10d-1_SP_IgH_nonGC


title: Whole blood, APJZ06


title: 4-E7


title: 4-E3


title: FrB_dKO_M2_A34

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: Total RNA was extracted from FrB pro-B cells. mRNAseq was carried out from polyadenylated transcripts using the SMART-Seq v4 Ultra low input RNA kit from Clontech

data_processing:
Raw sequence reads were trimmed with Trim Galore (v 1.15 https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with default parameters.
Trimmed reads were mapped with Hisat2 (v 2.1.0) with -p 7 -t --phred33-quals --no-mixed --no-discordant parameters, the Mus_musculus.GRCm38 genome and known splice sites from the Mus_musculus.GRCm38.90 annotation
Reads mapped over genes were counted with HTSeq (v0.10.0) with f bam -r name -s no -a 10 parameters and the Mus_musculus.GRCm38.93.gtf annotation from Ensembl.
Reads mapping to immunoglobulin genes (including V, D, J gene segments, light and heavy immunoglobulin genes and T cell receptor genes) were excluded.
Genome_build: GRCh38 (mm10)
Supplementary_files_format_and_content: HTSeq Count File: read counts mapping to all annotated exons of a gene. First colum is the Ensembl ID gene identifier, second colum is the number of reads.
Raw sequence reads were trimmed with cutadapt.
Trimmed reads were mapped with STAR (v2.5.4b) and the GRCm38.p5 mouse genome.
Reads were de-duplicated using random barcodes included in the library preparation and xlink-sites for individual replicates were determined as described in König et al, 2010 Nature Structural and Molecular Biology, 17, 909-915 with iCOUNT: https://icount.readthedocs.io/en/latest/cite.html
Xlink sites from the individual replicates were pooled together.
Clusters of binding sites were identified with iCOUNT https://icount.readthedocs.io/en/latest/cite.html
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: LPS_group_grouped_xlinks.bedgraph: bedgraph file containing xlink-sites of PTBP1 identified in mitogen (LPS) activated B cells pooling  five biological replicates together. LPS_group_grouped_clusters.bedgraph: bedgraph file containing clusters of PTBP1-binding sites in mitogen (LPS) activated B cells determined from the xlink-sites identified in five biological replicates together.

source_name: FrB pro-B cells

extract_protocol:
RNA was extracted using the RNeasy Micro Kit from Qiagen (Cat. #74004)
mRNAseq libraries from polyadenylated transcripts were prepared by generating cDNA from 2 ng RNA and 9 PCR cycles per replicate with the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (cat# 634891, Takara) and by enzymatic fragmentation of 300 pg of cDNA followed by 12 PCR cycles using the Nextera XT DNA Library Preparation Kit  (cat# FC-131-1096, Illumina).

tag: genotye

value: CD79aCre/+ Ptbp1fl/fl Ptbp2fl/fl

tag: Sex

value: Male


title: 4-E11


title: 4-E10


title: FrB_dKO_M1_A22


title: Whole blood, APJZ04


title: 4-D7


title: Whole blood, APJZ03


title: FrB_dKO_F3_A28


title: 4-D4


title: 4-D9


title: Whole blood, APJZ02


title: FrB_dKO_F1_A10


title: FrB_dKO_F2_A16


title: 4-D11


title: 4-D2


title: Whole blood, APJZ01


title: 4-D1


title: SPF-11_PP_IgH_GC

value: Peyer's Patches


title: FrB_sKO_M2_A40

value: CD79aCre/+ Ptbp1fl/fl Ptbp2+/+


title: 4-C5


title: 4-E6


title: Whole blood, ALT13

value: Aletai White cattle


title: Whole blood, APJZ05


title: 4-C11


title: Whole blood, ALT12


title: 4-C12


title: FrB_sKO_M1_A24


title: FrB_sKO_F3_A38


title: Whole blood, ALT11


title: 4-B9


title: 4-B8


title: 4-C1


title: 4-B7


title: Whole blood, ALT10


title: Whole blood, ALT09


title: 4-B6


title: FrB_sKO_F1_A12


title: FrB_Ctrl_M2_A32

value: CD79a+/+ Ptbp1fl/fl Ptbp2fl/fl


title: Whole blood, ALT08


title: 4-B11


title: 4-B2


title: 4-A9


title: NP10d-3_SP_IgH_nonGC


title: 4-C4


title: Whole blood, ALT07


title: FrB_Ctrl_F3_A26


title: 4-A8


title: FrB_Ctrl_M1_A20


title: 4-A6


title: Whole blood, ALT06


title: 4-A5


title: 4-A3


title: 4-A4


title: FrB_sKO_F2_A18


title: FrB_Ctrl_F2_A14


title: FrB_Ctrl_F1_A8


title: 4-A12


title: Whole blood, ALT04


title: 4-A11


title: 4-B3


title: 3-H9


title: Whole blood, ALT03


title: 3-H8


title: 3-H4


title: 3-G9


title: Whole blood, ALT01


title: 3-H2-2


title: MmES_MeCP2_MBD_R133C

city: Utrecht

first: Tuncay

last: Baubec

address: Padualaan 8

department: Department of Biology

country: Netherlands

institute: Utrecht University

description: Enriched DNA

data_processing:
Reads were aligned to mm9 mouse genome using Bowtie directly executed from the R package QuasR with standard alignment parameters allowing up to 2 mismatches and excluding multi-mappers.
Coordinates of unique reads that map only once to the mouse genome were converted to WIG format for visualisation using qExportWig() with standard parameters in QuasR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: wig track format: read coverage per consecutive 100bp windows.

source_name: embryonic stem cell

growth_protocol: Wild type embryonic stem cells derived from mixed 129-C57Bl/6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
For cross-linking and chromatin extraction, cells were fixed for 10 minutes with 1% Formaldehyde at room temperature and incubated for 10 min on ice in presence of 1.2M Glycine. Cells were harvested and treated for 10 min with 10mM EDTA, 10mM TRIS, 0.5mM EGTA and 0.25% Triton X-100 and 10 min in 1mM EDTA, 10mM TRIS, 0.5mM EGTA and 200mM NaCl with subsequent lysis in 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate, 0.2% SDS and 300 mM NaCl for 2 hours on ice. Crosslinked chromatin was subjected to sonication in a Bioruptor Pico instrument (Diagenode) and diluted with equal volumes of 50mM HEPES, 1mM EDTA, 1% Triton X-100, 0.1% deoxycholate after successful sonication. ProteinA-dynabeads pre-cleared 150-250 µg chromatin were incubated with 40 µl blocked (1% CFSG, 100ng tRNA) Streptavidin-M280 magnetic beads over night at 4°C. Beads were washed with two rounds of 2% SDS, 1x high salt buffer, 1x LiCl Buffer and two rounds of TE. Beads were treated with RNaseA for 30 min at 37°C, Proteinase K for 3 hours at 50°C then de-crosslinked over night at 55°C. DNA was purified with Phenol-Chloroform extraction and EtOH precipitation.
ChIP-seq library using NEB ChIP library protocol with index adapters.

value: embryonic stem cells

tag: strain/background

value: mixed 129-C57Bl/6

value: wild type

tag: ChIP

value: streptavidin


title: MmES_MBD1_MBD

description: Enriched DNA


title: 3-F6

tag: strain


title: MmES_MBD1_MBD_noGFP

description: Enriched DNA


title: MmES_MBD1_MBD_R22A

description: Enriched DNA


title: 3-F9


title: 4-A1


title: MmES_bioGFP_r2

description: Enriched DNA


title: Whole blood, ALT05

value: Female

tag: tissue


title: 3-E12


title: 3-D8


title: 3-F5


title: AID-13_SP_IgH_nonGC

tag: condition

value: AID-deficient mice SPF

tag: locus (ig heavy-chain or light-chain)

value: IgH


title: MmES_CBX1_2xChro

description: Enriched DNA


title: AID-13_SP_IgH_GC

value: spleen


title: AID-12_SP_IgH_GC


title: Whole blood, ALT02

tag: gender

tag: breed


title: MmES_CBX1_1xChro

description: Enriched DNA


title: AID-12_SP_IgH_nonGC


title: 3-D1


title: 3-C8


title: CRB_SCR_52w_3

city: La Jolla

first: Shane

middle: Gary

last: Poplawski

state: CA

address: 4120 Capricorn Lane

institute: JCVI

data_processing:
Reads were aligned to the GRCm38.p3 mouse genome and transcriptome from iGenomes using TopHat
Feature counting was performed using featureCounts with the iGenomes annotation
Differential expression tests were performed using edgeR with standard settings
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: Excel Spreadsheet (Cuffdiff output)

source_name: Mouse cerebellum

extract_protocol:
For in vivo mouse samples, total RNA and DNA was extracted from the liver and the right hemisphere’s hippocampus, cortex, and cerebellum with AllPrep® DNA/RNA/miRNA kit (Qiagen).
Total RNA-seq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina – San Diego, CA) according to manufacturer’s instructions. 1µg of RNA was used as starting material and 12 PCR cycles were used to minimize bias. Library size was observed on an Agilent 2100 Bioanalyzer and quantity was determined using qPCR (KAPA Biosystems - Wilmington, MA). Libraries were sequences on an Illumina HiSeq 2500 using a 50-cycle rapid run kit or an Illumina NextSeq instrument using a 75-cycle high throughput kit. Reads were aligned to the GRCm38.p3 mouse genome and transcriptome from iGenomes using TopHat and differential expression tests were performed using featureCounts and edgeR with standard settings.

value: SCRAMBLE ASO

tag: time point

value: 52 weeks

value: cerebellum


title: 3-C2


title: 3-E4


title: AID-11_SP_IgH_GC


title: 3-C12


title: AID-11_SP_IgH_nonGC


title: MmES_bioGFP_r1

description: Enriched DNA


title: CRB_SCR_52w_2


title: 3-B4


title: AID-10_SP_IgH_GC


title: CRB_SCR_52w_1


title: CRB_ASO_52w_3

value: HDAC2 ASO


title: 3-D5


title: AID-10_SP_IgH_nonGC


title: 3-D4


title: CRB_ASO_52w_2


title: 3-B2


title: Input

city: Cleveland

first: Ruth

last: Keri

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Quality filter with FastQ
Chip-seq reads were aligned to the hg19 genome assembly using Bowtie2 with default settings
The data were sorted, indexed and filtered with Samtools-1.3.1
Peaks called to hg19 with MACS2
Rank Ordering of Super-enhancers (ROSE) used to rank enhancers in hg19 with a stitch size of 12,500bp
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 was used to generate bedgraphs. Bedgraphs were then converted to wig files.

source_name: MDA-MB-231 cells

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27ac antibody.
Libraries were prepared using the ThruPlex DNA-seq kit from Rubicon Genomics using 20ng of ChIP DNA. Two unique tags were used. Two final pools were made. Each library was QC'ed using Qbit HS dsDNA kit for concentration and Agilent Bioanalyzer DNA HS chip for quality and fragment size. DNA was pooled based on qubit concentration, and qPCR was performed using Kappa Biosystems Illumina LIbrary Quant kit on the pool for nM concentration. DNA was then loaded onto an Illumina HiSeq 2500 50bp rapid run v2 flowcell.


title: 3-B10


title: H3K27ac_ChIPSeq_2

value: H3K27ac (Abcam, ab5079)


title: CRB_ASO_52w_1


title: 3-B1


title: AID-9_SP_IgH_GC


title: AID-9_SP_IgH_nonGC


title: H3K27ac_ChIPSeq_1


title: HPC_SCR_52w_3

source_name: Mouse hippocampus

value: hippocampus


title: 3-C10


title: 3-B8


title: AID-8_SP_IgH_GC


title: 3-C1


title: HPC_SCR_52w_2


title: 3-A5


title: AID-8_SP_IgH_nonGC


title: 3-A3


title: HPC_SCR_52w_1


title: 3-A11


title: 3-B3


title: AID-7_SP_IgH_GC


title: HPC_ASO_52w_3


title: 3-A10


title: AID-7_SP_IgH_nonGC


title: HPC_ASO_52w_2


title: AID-6_SP_IgH_GC


title: 3-A1


title: 2-H11


title: AID-6_SP_IgH_nonGC


city: San Francisco

first: Sahar

last: Houshdaran

address: 513 Parnassus Ave HSE1619

department: OB/GYN

institute: UCSF

description:
Endo IV-4 E2+P4
Genomic RNA from Endo IV eSF sample 4, treated with E2+P4.

hyb_protocol: The labeled cDNA was hybridized to Human Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: The signal intensity fluorescent images produced during the Affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner and converted into GeneChip probe results files (CEL) using Command and Expression Console software (Affymetrix).

data_processing: Gene expression data was RMA normalized in R and GeneSpring Software from Agilent Technologies.

label: biotin

source_name: Endo IV-4 E2+P4

label_protocol: Purified RNA was analyzed for quality using chip-based capillary electrophoresis (Bioanalyzer, Agilent, Inc) and quantity and purity were determined with a NanoDrop Spectrometer. The NuGen Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation and biotin-labelling.

growth_protocol: eSF were isolated from human endometrial eutopic biopsies from women with no pelvic or uterine pathology and women with stage I or stage IV endometriosis by digestion and size fractionation. The primary eSF culture cells were grown in the stromal cell medium (SCM) to 70% confluency before being passed for hormone treatment.

extract_protocol: RNA was extracted using the Macherey-Nagel NuceloSpin Tissue Kit with DNase treatment (Marcherey-Nagel Inc., Bethlehem, PA) according to manufacturers’ recommendations and stored at -80C until analysis in microarray.

treatment_protocol: eSF confluent cultures (n=4 normal, n=4 stage I endometriosis, n=4 stage IV endometriosis) were treated with 10 nM estrogen (E2), 1𝝁M progesterone (P4), 10 nM+ 1𝝁M E2+P4, or vehicle 0.1% ethanol for 14 days. Cells were collected, RNA was extracted and stored at -80C until analysis.

value: Eutopic endometrial stromal fibroblasts

tag: disease state

value: Endometriosis Stage IV

tag: treatment

tag: individual

value: Endo IV-4


title: 2-G7

tag: genotype


description:
Endo IV-4 P4
Genomic RNA from Endo IV eSF sample 4 treated with P4.

source_name: Endo IV-4 P2

tag: cell type


description:
Endo IV-4 E2
Genomic RNA from Endo IV eSF sample 4, treated with E2.

source_name: Endo IV-4 E2


title: AID-5_SP_IgH_GC


description:
Endo IV-4 Veh
Genomic RNA from Endo IV eSF sample 4, treated with vehicle.

source_name: Endo IV-4 Veh

value: vehicle


title: CTX_SCR_52w_2

source_name: Mouse cortex

tag: genotype/variation

value: cortex


title: AID-5_SP_IgH_nonGC

source_name: splenic naïve B cells


title: AID-15_PP_IgH_GC

source_name: Peyer's Patches germinal center B cells

value: Peyer's Patches


title: 2-G2


title: 2-G12


description:
Endo IV-3 Veh
Genomic RNA from Endo IV eSF sample 3, treated with vehicle.

source_name: Endo IV-3 Veh

value: Endo IV-3


description:
Endo IV-3 E2+P4
Genomic RNA from Endo IV eSF sample 3, treated with E2+P4.

source_name: Endo IV-3 E2+P4

value: Female


description:
Endo IV-3 E2
Genomic RNA from Endo IV eSF sample 3, treated with E2.

source_name: Endo IV-3 E


title: CTX_ASO_52w_2


description:
Endo IV-3 P4
Genomic RNA from Endo IV eSF sample 3 treated with P4.

source_name: Endo IV-3 P4


title: CTX_SCR_52w_1


title: HPC_ASO_52w_1


title: AID-14_PP_IgH_GC

value: AID-deficient mice SPF


title: CTX_SCR_52w_3


title: CTX_ASO_52w_3


description:
Endo IV-2 Veh
Genomic RNA from Endo IV eSF sample 2, treated with vehicle.

source_name: Endo IV-2 Veh

value: Endo IV-2


title: AID-15_PP_IgH_nonGC

source_name: Peyer's Patches naïve B cells

value: IgH


description:
Endo IV-2 E2+P4
Genomic RNA from Endo IV eSF sample 2, treated with E2+P4.

source_name: Endo IV-2 E2+P4


title: CRB_SCR_48w_3

source_name: Mouse cerebellum

value: SCRAMBLE ASO

value: 48 weeks


title: 2-G6


title: 2-F7


title: AID-13_PP_IgH_GC


title: AID-14_PP_IgH_nonGC


title: 2-F9


title: 2-F5


title: AID-13_PP_IgH_nonGC


title: CRB_SCR_48w_1

value: cerebellum


title: CRB_SCR_48w_2


description:
Endo IV-2 E2
Genomic RNA from Endo IV eSF sample 2, treated with E2.

source_name: Endo IV-2 E2


title: 2-G10


title: AID-12_PP_IgH_GC


description:
Endo IV-2 P4
Genomic RNA from Endo IV eSF sample 2 treated with P4.

source_name: Endo IV-2 P4


title: 2-F4


title: CTX_ASO_52w_1

value: HDAC2 ASO

value: 52 weeks


title: CRB_ASO_48w_3


title: 2-F3


title: CRB_ASO_48w_2


description:
Endo IV-1 E2+P4
Genomic RNA from Endo IV eSF sample 1, treated with E2+P4.

source_name: Endo IV-1 E2+P4

value: Endo IV-1


title: AID-12_PP_IgH_nonGC


description:
Endo IV-1 Veh
Genomic RNA from Endo IV eSF sample 1, treated with vehicle.

source_name: Endo IV-1 Veh

value: Eutopic endometrial stromal fibroblasts


title: 2-F10


title: AID-11_PP_IgH_GC


title: 2-F1


title: CRB_ASO_48w_1


title: AID-11_PP_IgH_nonGC


title: HPC_SCR_48w_3

source_name: Mouse hippocampus

value: hippocampus


description:
Endo IV-1 P4
Genomic RNA from Endo IV eSF sample 1 treated with P4.

source_name: Endo IV-1 P4

value: Endometriosis Stage IV


description:
Endo IV-1 E2
Genomic RNA from Endo IV eSF sample 1, treated with E2.

source_name: Endo IV-1 E2


description:
Endo I-4 Veh
Genomic RNA from Endo I eSF sample 4, treated with vehicle.

source_name: Endo I-4 Veh

value: Endometriosis Stage I

value: vehicle

value: Endo I-4


title: AID-10_PP_IgH_GC

source_name: Peyer's Patches germinal center B cells

value: Peyer's Patches


title: HPC_SCR_48w_2


title: 2-E11


title: AID-10_PP_IgH_nonGC


title: 2-D7


title: HPC_SCR_48w_1


description:
Endo I-4 E2+P4
Genomic RNA from Endo I eSF sample 4, treated with E2+P4.

source_name: Endo I-4 E2+P4

value: Female


title: AID-9_PP_IgH_GC

value: AID-deficient mice SPF


title: 2-D4


title: AID-9_PP_IgH_nonGC


title: HPC_ASO_48w_2


title: HPC_ASO_48w_1


title: HPC_ASO_48w_3


title: 2-C8


title: AID-8_PP_IgH_nonGC


description:
Endo I-4 P4
Genomic RNA from Endo I eSF sample 4 treated with P4.

source_name: Endo I-4 P2


title: 2-D3


description:
Endo I-3 Veh
Genomic RNA from Endo I eSF sample 3, treated with vehicle.

source_name: Endo I-3 Veh

value: Endo I-3


title: CTX_SCR_48w_3

source_name: Mouse cortex

value: cortex


title: 2-E2


description:
Endo I-3 P4
Genomic RNA from Endo I eSF sample 3 treated with P4.

source_name: Endo I-3 P4


title: 2-C6


title: AID-7_PP_IgH_GC

value: IgH


title: 2-C11


title: AID-7_PP_IgH_nonGC

source_name: Peyer's Patches naïve B cells


description:
Endo I-4 E2
Genomic RNA from Endo I eSF sample 4, treated with E2.

source_name: Endo I-4 E2


title: 2-B1


title: CTX_SCR_48w_1

value: SCRAMBLE ASO

value: 48 weeks


title: AID-6_PP_IgH_GC


title: AID-8_PP_IgH_GC


title: CTX_ASO_48w_3

value: HDAC2 ASO


title: AID-6_PP_IgH_nonGC


title: 2-A6


title: 2-A4


description:
Endo I-2 Veh
Genomic RNA from Endo I eSF sample 2, treated with vehicle.

source_name: Endo I-2 Veh

value: Endo I-2


title: CTX_ASO_48w_2


title: CTX_ASO_48w_1


title: AID-5_PP_IgH_nonGC


title: 2-A12


title: AID-5_PP_IgH_GC


title: CTX_SCR_48w_2


title: 10xGenomics_SPF-17_PP_IgH_GC

data_processing:
LAM-HTGTS-Rep-SHM-Seq data analysis was done by the LAM-HTGTS-Rep-SHM-Seq bioinformatics pipeline (Github address: https://github.com/Yyx2626/HTGTSrep), using IgBLAST with default parameters for qualified reads mapping. Only reads with more than 98% of the sequences having a sequencing Quality Score ≥20 were kept; only joined reads (R1 and R2 had an overlap region ≥10 bp and mismatch rate ≤8%) were kept.
scRNA-seq raw sequencing files were aligned to the mouse V(D)J sequence using Cell Ranger: V(D)J Pipelines (10x Genomics) and the V usage and mutation profiles were generated and visualized by Loupe V(D)J Browser.
Genome_build: mm9
Supplementary_files_format_and_content: .db.xls files were generated using LAM-HTGTS-Rep-SHM-Seq pipeline (IgBLAST); .vloup files were generated using Cell Ranger: V(D)J Pipelines (10x Genomics).

value: SPF


title: CRB_SCR_40w_2

source_name: Mouse cerebellum

value: 40 weeks

value: cerebellum


title: 1-H8


description:
Endo I-2 E2+P4
Genomic RNA from Endo I eSF sample 2, treated with E2+P4.

source_name: Endo I-2 E2+P4

value: Eutopic endometrial stromal fibroblasts


title: 10xGenomics_SPF-12_PP_IgH_GC


title: CRB_SCR_40w_1


title: 10xGenomics_SPF-11_PP_IgH_GC


description:
Endo I-2 E2
Genomic RNA from Endo I eSF sample 2, treated with E2.

source_name: Endo I-2 E2

value: Endometriosis Stage I


description:
Endo I-1 E2+P4
Genomic RNA from Endo I eSF sample 1, treated with E2+P4.

source_name: Endo I-1 E2+P4

value: Endo I-1


description:
Endo I-3 E2
Genomic RNA from Endo I eSF sample 3, treated with E2.

source_name: Endo I-3 E2


title: 1-H6


description:
Endo I-2 P4
Genomic RNA from Endo I eSF sample 2 treated with P4.

source_name: Endo I-2 P4


description:
Endo I-3 E2+P4
Genomic RNA from Endo I eSF sample 3, treated with E2+P4.

source_name: Endo I-3 E2+P4


description:
Endo I-1 Veh
Genomic RNA from Endo I eSF sample 1, treated with vehicle.

source_name: Endo I-1 Veh

value: vehicle


title: 1-H4


description:
Endo I-1 P4
Genomic RNA from Endo I eSF sample 1 treated with P4.

source_name: Endo I-1 P4


title: 10xGenomics_SPF-10_PP_IgH_GC

source_name: Peyer's Patches germinal center B cells

value: Peyer's Patches


title: 1-H11


title: 1-H10


title: CRB_SCR_40w_3


description:
Endo I-1 E2
Genomic RNA from Endo I eSF sample 1, treated with E2.

source_name: Endo I-1 E2

value: Female


title: CRB_ASO_40w_2


title: GF+SPFfeces-10_PP_IgH_nonGC

value: GF+SPF


description:
NUP4-Veh
Genomic RNA from NUP eSF sample 4, treated with vehicle.

value: Normal


title: CRB_ASO_40w_1


title: GF+SPFfeces-9_PP_IgH_nonGC


description:
NUP4-P4
Genomic RNA from NUP eSF sample 4 treated with P4.


title: HPC_SCR_40w_3

source_name: Mouse hippocampus

value: hippocampus


title: GF+SPFfeces-8_PP_IgH_nonGC

value: IgH


description:
NUP4-E2
Genomic RNA from NUP eSF sample 4, treated with E2.


title: HPC_SCR_40w_2

value: SCRAMBLE ASO


title: CRB_ASO_40w_3


description:
NUP3-Veh
Genomic RNA from NUP eSF sample 3, treated with vehicle.


title: GF+SPFfeces-7_PP_IgH_nonGC


title: 1-G5


title: HPC_ASO_40w_3


title: HPC_SCR_40w_1


title: 1-G2


title: GF+SPFfeces-5_PP_IgH_nonGC


title: HPC_ASO_40w_2


title: GF+SPFfeces-6_PP_IgH_nonGC


title: HPC_ASO_40w_1


title: 1-H1


title: GF+SPFfeces-4_PP_IgH_nonGC


title: GF+SPFfeces-3_PP_IgH_nonGC


title: 1-G12


title: 1-F6-1


description:
NUP3-P4
Genomic RNA from NUP eSF sample 3 treated with P4.


title: 1-G11


title: 1-F4-2


title: CTX_SCR_40w_3

source_name: Mouse cortex

value: cortex


title: GF+SPFfeces-2_PP_IgH_nonGC


description:
NUP3-E2
Genomic RNA from NUP eSF sample 3, treated with E2.


description:
NUP4-E2+P4
Genomic RNA from NUP eSF sample 4, treated with E2+P4.


title: CTX_SCR_40w_2


description:
NUP2-Veh
Genomic RNA from NUP eSF sample 2, treated with vehicle.


title: 1-F4-1


title: GF+SPFfeces-1_PP_IgH_nonGC


description:
NUP2-P4
Genomic RNA from NUP eSF sample 2, treated with P4.


description:
NUP2-E2+P4
Genomic RNA from NUP eSF sample 2, treated with E2+P4.


title: CTX_SCR_40w_1


title: 1-F3-2


title: GF-10x3_PP_IgH_nonGC

value: GF


title: 1-F11


description:
NUP3-E2+P4
Genomic RNA from NUP eSF sample 3, treated with E2+P4.


description:
NUP2-E2
Genomic RNA from NUP eSF sample 2, treated with E2.


title: CTX_ASO_40w_3

value: HDAC2 ASO


title: GF-9x3_PP_IgH_nonGC


title: CTX_ASO_40w_2


title: 1-E2-2


description:
NUP1-Veh
Genomic RNA from NUP eSF sample 1, treated with vehicle.


title: 1-G6


title: CTX_ASO_40w_1


title: GF-8x3_PP_IgH_nonGC


title: 1-E10-2


title: 1-E10-1


title: GF-7x3_PP_IgH_nonGC


title: CRB_SCR_4w_3

value: 4 weeks


title: MousePeriMac_untreated [24.14]

city: Sydney

first: Sheila

last: Donnelly

state: NSW

address: Corner Thomas St & Harris St

department: School of Life Sciences

country: Australia

institute: University of Technology Sydney

data_processing:
Quality control analysis to check libraries quality using FASTQC
Removal of adapters, low quality reads, and reads <18nt using Cutadapt.
Reads aligned to Mus musculus mature miRBase sequences using Bowtie 1.2. Aligned reads omitted and unaligned reads retained.
Reads aligned to Fasciola hepatica mature miRBase sequences using Bowtie1.2. Aligned reads retained and raw counts quantified.
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: Tab delimited text file of read counts of Fasciola hepatica mature miRNA sequences found in sequenced RNA from F.hepatica infected Mus musculus peritoneal macrophage.

extract_protocol:
Macrophages were extracted from peritoneal cells using the Macrophage isolation kit (Peritoneum), mouse (Miltenyi Biotec #130-110-434) for total RNA extraction using RNAzol RT (MRC, #RN 190).
Libraries were prepared using standard Illumina protocol after using TruSeq Small RNA Library Prep Kit

treatment_protocol: Female adult BALB/c mice were infected with Fasciola hepatica metacecariae, and peritoneal cells were extracted at different time points post infection.

value: BALB/c

value: female

value: Untreated

value: peritoneal macrophages


title: CRB_SCR_4w_2

value: cerebellum


title: 1-D7-2


title: GF-6x3_PP_IgH_nonGC


title: MousePeriMac_untreated [23.13]


title: SPF-18_PP_IgH_nonGC

value: SPF


title: CRB_SCR_4w_1


title: 1-D7-1


title: SPF-17_PP_IgH_nonGC

value: Peyer's Patches


title: MousePeriMac_5day [22.12]

value: Fasciola hepatica infection, 5 days post


description:
NUP1-E2
Genomic RNA from NUP eSF sample 1, treated with E2.

value: Female

value: Eutopic endometrial stromal fibroblasts


description:
NUP1-P4
Genomic RNA from NUP eSF sample 1, treated with P4.

value: Normal


description:
NUP1-E2+P4
Genomic RNA from NUP eSF sample 1, treated with E2+P4.


title: CRB_ASO_4w_3


title: 1-D4-1


title: SPF-13_PP_IgH_nonGC

value: IgH


title: CRB_ASO_4w_2


title: MousePeriMac_5day [21.11]


title: SPF-12_PP_IgH_nonGC


title: 1-D3-2


title: MousePeriMac_72hr [20.1]

value: Fasciola hepatica infection, 72hr post


title: CRB_ASO_4w_1


title: SPF-11_PP_IgH_nonGC


title: 1-D2-1


title: MousePeriMac_72hr [19.9]


title: HPC_SCR_4w_3

value: SCRAMBLE ASO

value: hippocampus


title: 1-D11-2


title: SPF-10_PP_IgH_nonGC


title: MousePeriMac_24hr [18.8]

value: Fasciola hepatica infection, 24hr post


title: HPC_SCR_4w_1

value: 4 weeks


title: SPF-9_PP_IgH_nonGC


title: 1-D11-1


title: HPC_SCR_4w_2


title: MousePeriMac_24hr [17.7]

value: BALB/c


title: 1-C5-2


title: MousePeriMac_18hr [16.6]

value: female

value: Fasciola hepatica infection, 18hr post


title: HPC_ASO_4w_3

value: HDAC2 ASO


title: 1-C5-1


title: MousePeriMac_18hr [15.5]

value: peritoneal macrophages


title: HPC_ASO_4w_2


title: NP10d-5_SP_IgL_GC

source_name: splenic germinal center B cells

value: NP-CGG IP immunization 10 day

value: spleen

value: IgL


title: 1-C12-2


title: SPF-7_PP_IgH_nonGC

source_name: Peyer's Patches naïve B cells

value: SPF

value: Peyer's Patches


title: HPC_ASO_4w_1


title: NP10d-5_SP_IgL_nonGC

source_name: splenic naïve B cells


title: 1-C12-1


title: MousePeriMac_12hr [13.3]

value: Fasciola hepatica infection, 12hr post


title: MmES_TKO_MeCP2_MBD_r2

description: Enriched DNA

source_name: embryonic stem cell

value: embryonic stem cells

value: mixed 129-C57Bl/6

value: streptavidin


title: 1-B8-1


title: MousePeriMac_6hr [12.2]

value: Fasciola hepatica infection, 6hr post


title: CTX_SCR_4w_2

value: SCRAMBLE ASO

value: cortex


title: MousePeriMac_6hr [11.1]

value: BALB/c


title: MmES_TKO_MeCP2_MBD_r1

description: Enriched DNA


title: CTX_SCR_4w_1

value: 4 weeks


title: 1-B4-2


title: SPF-8_PP_IgH_nonGC

value: IgH


title: PTBP1 iCLIP replicate 5

description:
Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. 5' Barcode used for iCLIP demultiplexing and deduplication CTTNNNN
iCLIP

source_name: Splenic B cells, LPS 48h

extract_protocol:
30*10^6 cells were used in each immunoprecipitation and were lysed in 50 mM Tris-HCL pH7.4, 100mM NaCl, 1% NP-40 and 0.1% SDS lysis buffer.
See Monzon-Casanova, E. et al. The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers. Nat. Immunol. 45, 471 (2018).

tag: genotye

value: Female


title: 1-B3-1


title: CTX_ASO_4w_3

value: HDAC2 ASO


title: MmES_TAF3_2xPhd_r2

description: Enriched DNA

value: wild type


title: PTBP1 iCLIP replicate 4

description:
Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. 5' Barcode used for iCLIP demultiplexing and deduplication TCTNNNN
iCLIP

tag: Sex


title: MousePeriMac_12hr [14.4]

value: female

value: peritoneal macrophages


title: MmES_TAF3_2xPhd_r1

description: Enriched DNA

tag: strain/background


title: 1-B11-2


title: PTBP1 iCLIP replicate 3

description:
Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. 5' Barcode used for iCLIP demultiplexing and deduplication CCCNNNN
iCLIP


title: CTX_SCR_4w_3


title: MmES_PCchro_Taf3phd_r1

description: Enriched DNA

tag: ChIP


title: CTX_ASO_4w_2


title: CTX_ASO_4w_1


title: 1-C11-1

tag: strain


title: PTBP1 iCLIP replicate 2

description:
Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. 5' Barcode used for iCLIP demultiplexing and deduplication AGTNNNN
iCLIP


title: MmES_PC_2xChro_r2

description: Enriched DNA


title: PTBP1 iCLIP replicate 1

description:
Splenic B cells isolated by negative MACS sorting were stimulated ex vivo with LPS for 48h. 5' Barcode used for iCLIP demultiplexing and deduplication GGCNNNN
iCLIP


title: 1-B11-1


title: 1-B10-2


title: CRB_SCR_2w_1

source_name: Mouse cerebellum

value: 2 weeks

tag: tissue

value: cerebellum


title: 1-B10-1


title: 1-B1-1


title: CRB_SCR_2w_2


title: MmES_MeCP2_MBD_r2

description: Enriched DNA


title: Control [Bisulfite-seq (reduced respresentation)]

city: Chongqing

first: Jing

last: Wang

address: Yuzhong District Petroleum Road on the 1st

institute: Chongqing Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Genome_build: miRNAs annotation data were downloaded from miRBase21
Genome_build: mRNAs and lncRNAs annotation data were retrieved from GENCODE rn6
Genome_build: DNA annotation data were retrieved from GENCODE rn5
Supplementary_files_format_and_content: tab-delimited text files of lncRNA, miRNA and mRNA include RPKM values for each Sample; tab-delimited text files of methylation include methylation site and methylation level for each Sample

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and DNA was harvested using DNA extraction kit. Then constructe  RRBS libraries.
RRBS libraries were prepared for sequencing using standard Illumina protocols

value: Sprague-Dawley

value: hippocampus

tag: age

value: 7 weeks

tag: agent

value: corn oil


title: MmES_PCchro_Taf3phd_r2

description: Enriched DNA

value: embryonic stem cells

value: mixed 129-C57Bl/6

value: streptavidin


title: Control [miRNA-Seq]

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and RNA was harvested using RNA extraction kit. Then constructe  RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Control [RNA-Seq]

treatment_protocol: B[a]P was dissolved in corn oil. The B[a]P-treated rat was administered by oral gavage each day in a dose of 2.0mg/kg B[a]P and the control rat was also administered by oral gavage but with equivalent volume of corn oil. Oral gavage for 7 weeks.


title: CRB_ASO_2w_3


title: CRB_ASO_2w_2


title: MmES_MeCP2_MBD_r1

description: Enriched DNA


title: B[a]P-treated [miRNA-Seq]

value: B[a]P


title: HPC_SCR_2w_3

value: SCRAMBLE ASO


title: MmES_MeCP2_MBD_R106W

description: Enriched DNA


title: B[a]P-treated [RNA-Seq]


title: 1-A5-1


title: B[a]P-treated [Bisulfite-seq (reduced respresentation)]


title: MmES_H3K9me3

description: Enriched DNA

value: antibody


title: 1-A8-2


title: CRB_SCR_2w_3


title: MmES_MeCP2_MBD_T158M

description: Enriched DNA


title: HPC_SCR_2w_1


title: MmES_H3K27me3

description: Enriched DNA


title: CD326neg_LLC_day14 (3'SAGE-seq)

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

country: Japan

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Trimommatic-v0.36 and PRINSEQ-0.20.4. Filtered reads were mapped to Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Total tag number was adjusted to 1 million tags, and between-sample normalization was performed by using Microsoft R Open-3.3.3 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

molecule: polyA RNA

extract_protocol:
Tumors and draining axillary lymph nodes (LNs) were collected at day 10 or 14 post tumor inoculation, cut into small fragments and digested for 45 min at 37 °C with 0.2% collagenase (Wako, Osaka, Japan) and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO).The cells were then subjected to 40/70 % Percoll (GE Healthcare, Buckinghamshire, UK) gradient and leukocytes were recovered from the interphase. Resulting cells were pretreated with Fc Block (anti-mouse CD16/CD32 mAb; clone 2.4G2, BioXcell, West Lebanon, NH, USA), then stained with a mixture of fluorophore-conjugated anti-mouse mAbs. Tumor-infiltrating lineage- Ly-6C- MHC class II+ CCR7+ tDCs, lineage- CCR7- MHC class II+ cells and CD326- migratory DCs in the dLN were purified by cell sorting. Then, we performed transcriptome analysis on these cells by 3’ SAGE-seq.
PolyA RNAs were isolated and amplified from donor fibroblasts according to the protocol described in (Huang H, Nucleic Actd Res, 2014) with some modifications. Briefly, 0.5 pmol of biotin-TEG-adapter-dT25 primers was bound to 20 μL of Dynabeads M270 streptavidin (Thermo Fisher Scientific). The washed beads (20 uL) were added to each cell lysis buffer containing 10,000 sorted fibroblasts and incubated for 30 min at room temperature with gentle rotation. Beads were washed once with wash buffer A [0.1% LiDS, 10 mM Tris-HCl (pH 7.5), 150 mM LiCl, and 1 mM EDTA] and three times with wash buffer B [10 mM Tris-HCl (pH 7.5), 150 mM LiCl, and 1 mM EDTA]. Beads were then suspended in 10 μL of RT mix 1 [1× SSIV buffer (Thermo Fisher Scientific), 2 mM dNTP, 2 M betaine (Sigma-Aldrich), 12 mM MgCl2, and 3.2 U/μL RNaseIn Plus (Promega)] and incubated for 90 s at 70ºC, 5 min at 35ºC, and immediately cooled on ice. RT mix 2 [10 μL; 1× SSIV buffer, 10 mM DTT (Thermo Fisher Scientific), 10 U/μL Superscript IV (Thermo Fisher Scientific), and 2 M betaine (Sigma-Aldrich)] was added, and reverse transcription was performed for 5 min at 35ºC and 15 min at 50ºC. Beads were washed once with cell lysis buffer, twice with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], once with Tris-HCl (pH 8.0) and 20 μL of RNase H mix [1× first-strand buffer (Life Technologies, Carlsbad, CA, USA), 5 mM DTT, 0.6 U RNase H (Thermo Fisher Scientific)], and incubated for 20 min at 37ºC to digest reverse-transcribed mRNA. Beads were washed, 20 μL of TdT mix [50 mM Tris-HCl (pH 8.0), 100 mM KCl, 3 mM MgCl2, 1 mM CoCl2 (Roche), 0.65 mM dATP (Thermo Fisher Scientific), and 15.2 U/μL TdT (Roche)] was added on an ice-chilled aluminum rack, and polyA-tailing was performed for 3 min at 37ºC. The reaction was stopped by adding 5 μL of 0.5 M EDTA, and the enzyme was heat-inactivated by incubation for 10 min at 65ºC. Beads were washed, 20 μL of second-strand synthesis mix [1× KAPA Hifi ReadyMix (KAPA Biosystems, Wilmington, MA, USA) and 0.4 µM anchored tagging primer] was added, and second-strand synthesis was performed according to the following program: 95ºC for 2 min, 98ºC for 20 s, 44ºC for 2 min, 72ºC for 7 min, and hold at 4ºC. Beads were washed, and 1/4 of the beads were used for the first round of whole-transcript amplification (WTA) in 25 μL of first-round WTA mix [1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.4 µM anchored tagging primer, and 0.4 µM 3′ WTA primer] using the following program: 95ºC for 3 min, five cycles of 98ºC for 20 s, 65ºC for 15 s, and 72ºC for 7 min, followed by 72ºC for 5 min and a hold at 4ºC. PCR products were purified twice with 0.6× AmPure XP beads (Beckman Coulter) and eluted with 23 μL of nuclease-free water. Second-round WTA mix [27 μL; 1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.614 µM 5′ WTA primer, and 0.614 µM Biotin-TEG-3′ WTA primer] was added, and the second round of WTA was performed using the following program: 95ºC for 3 min, nine cycles of 98ºC for 20 s, 65ºC for 15 s, and 72ºC for 7 min, followed by 72ºC for 5 min and a hold at 4ºC. PCR products were purified twice with 0.6× AmPure XP beads and eluted with 25 μL of Tris-HCl (pH 8.0). Amplified whole transcripts were quantified using a Nanodrop 1000 (Thermo Fisher Scientific), and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific).
3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Briefly, 150 ng of the whole-transcript library was restriction digested with NlaIII (New England Biolabs, Ipswich, MA, USA) for 2 h at 37ºC, and biotinylated 3′-tail transcripts were immobilized on Dynabead M-280 streptavidin beads (Thermo Fisher Scientific). Beads were washed, and 10 pmol of the CS1-EcoP15I-NlaIII adapter was ligated using a DNA ligation kit (Mighty Mix; Takara) for 30 min at 16ºC. Beads were washed three times with B&W-T buffer, once with 10 mM Tris-HCl (pH 8.0), suspended in 200 μL of EcoP15I digestion mix [1× NEBuffer 3.1, 1 mM ATP, and 0.2 U EcoP15I (New England Biolabs)], and digested for 16 h at 37ºC in a tightly sealed screw-cap tube with gentle rotation. Supernatant was purified using a Nucleospin Gel&PCR clean-up kit (Takara) and eluted twice with 12.5 μL of nuclease-free water. End-repair/polyA-tailing/ligation reactions were performed using NEBNext Ultra II modules (New England Biolabs) and 1.875 pmol of CS2-adapter according to manufacturer instructions. Reaction products were purified using a Qiagen MinElute Column (Qiagen, Hilden, Germany) and eluted with 13 μL of nuclease-free water. Barcoding mix [14.25 μL; 1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.614 µM IonA-BC[N]-CS1-primer, and 0.614 µM Ion-trP1-CS2 primer] was added into 10.75 μL of elutant, and PCR enrichment was performed using the following program: 98ºC for 45 s, nine cycles of 98ºC for 15 s, 65ºC for 30 s, and 72ºC for 90 s, followed by 72ºC for 1 min and a hold at 4ºC. Reaction products were purified using double-size selection of AmPure XP beads (0.8× → 0.8×) and eluted with 10 μL of Tris-HCl (pH 8.0). The size distribution of each library was analyzed using an Agilent DNA high-sensitivity kit (Agilent Technologies, Santa Clara, CA, USA), and library concentration was quantified using a KAPA library quantification kit for Ion Torrent (KAPA Biosystems). Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

treatment_protocol: C57BL/6 mice were received subcutaneous injections of 5 x 10^5 tumor cells (B16 or LLC) in the flank.

tag: tumor model

value: Lewis lung carcinoma subcutaneous tumor

value: draining axillary lymph nodes

value: CD326- migratory dendritic cells

tag: time

value: cell sorting at day14 post-tumor inoculation


title: 1-A8-1


title: CD326neg_LLC_day10 (3'SAGE-seq)

value: cell sorting at day10 post-tumor inoculation


title: CRB_ASO_2w_1

value: HDAC2 ASO

tag: time point

value: 2 weeks


title: HPC_ASO_2w_3


title: CD326neg_B16_day14 (3'SAGE-seq)

value: B16 subcutaneous tumor


title: MmES_EedKO_CBX7_2xChro_r2

description: Enriched DNA

value: Eed-KO


title: HPC_ASO_2w_2

value: hippocampus


title: 1-A5-2


title: MmES_EedKO_CBX7_2xChro_r1

description: Enriched DNA


title: CD326neg_B16_day10 (3'SAGE-seq)


title: MmES_H3K4me3

description: Enriched DNA

value: wild type


title: 1-A4-1


title: CTX_SCR_2w_3

value: cortex


title: CCR7pos_LLC_day14 (3'SAGE-seq)

value: subcutaneous tumor

value: lineage-negative (CD3, CD19, NK1.1, Ly-6G, Ter-119) Ly-6C- MHC class II+ CCR7+ tumor-infiltrating dendritic cells


title: CCR7pos_LLC_day10 (3'SAGE-seq)


title: HPC_SCR_2w_2


title: CTX_SCR_2w_2


title: 1-A10-1


title: CCR7pos_B16_day14 (3'SAGE-seq)


title: CTX_SCR_2w_1


title: CCR7pos_B16_day10 (3'SAGE-seq)


title: MmES_CBX7chrW35A_TAF3phd_r1

description: Enriched DNA

value: embryonic stem cells

value: mixed 129-C57Bl/6

value: streptavidin


title: MmES_CBX7chr_TAF3phdDW890AA

description: Enriched DNA


title: HPC_ASO_2w_1


title: MmES_CBX7chrW35A_TAF3phd_r2

description: Enriched DNA


title: CTX_ASO_2w_3


title: CCR7neg_LLC_day14 (3'SAGE-seq)

value: Lewis lung carcinoma subcutaneous tumor

value: lineage-negative (CD3, CD19, NK1.1, Ly-6G, Ter-119) Ly-6C- MHC class II+ CCR7- tumor-infiltrating myeloid cells


title: MmES_CBX7_2xChroW35A

description: Enriched DNA


title: CTX_ASO_2w_2


title: CCR7neg_LLC_day10 (3'SAGE-seq)


title: CRB_SCR_3d_3

value: SCRAMBLE ASO

value: 3 days

value: cerebellum


title: MmES_CBX7_2xChro_r1

description: Enriched DNA


title: MmES_CBX7chro_TAF3phd_r1

description: Enriched DNA


title: CTX_ASO_2w_1

value: HDAC2 ASO


title: CCR7neg_B16_day14 (3'SAGE-seq)

value: cell sorting at day14 post-tumor inoculation


title: MmES_CBX7_1xChro

description: Enriched DNA


title: CCR7neg_B16_day10 (3'SAGE-seq)

value: B16 subcutaneous tumor

value: cell sorting at day10 post-tumor inoculation


title: CRB_SCR_3d_2


title: SAS

city: chiba

first: Toshiaki

last: Ando

state: chiba

address: 1-8-1 inohana chuo-ku

department: Grad. Sch. Med

institute: Chiba Univ

description: untreated

hyb_protocol: 1 ug of each labeled cRNA was fragmented by adding 5 uL 10X Blocking Agent and 1 uL of 25 X Fragmentation Buffer, then heated the mixture at 60C for 30 min, finally 25 ul 2X Hybridization buffer was added to dilute the labeled cRNA. 50 uL of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed for scanning.

scan_protocol: The microarrays were scanned using Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. For each sample the gProcessedSignal was extracted from the Agilent Feature Extraction Files as raw intensities.

source_name: notreated squamous carcinoma, tongue

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/ug cRNA) were measured by NanoDrop ND-1000.

growth_protocol: All cells were grown in Dulbecco's modified Eagle medium (DMEM) (Sigma, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS) (Sigma) and 50 units/ml penicillin and streptomycin (Sigma).

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer's instructions. Quality of total RNA was determined using Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Extracted RNA samples were stored separately at −80 °C until use.

treatment_protocol: notreated

value: squamous epithelium

tag: cell line

value: SAS


title: HNOKs

description: untreated

source_name: notreated human normal oral keratinocytes

value: HNOKs


title: Sa3

description: untreated

source_name: notreated squamous carcinoma, maxillary gingiva


title: HSC3

description: untreated


title: MmES_CBX1_2xChro_noGFP

description: Enriched DNA

value: wild type


title: MmES_CBX1_2xChroW42A

description: Enriched DNA


title: MmES_CBX7_2xChro_r2

description: Enriched DNA


title: CRB_SCR_3d_1


title: Non-affected_donor3 [D3_N_A]

city: Stockholm

first: Anna

last: Rao

address: Alfred Nobels Alle 8

department: Center for Infectious Medicine (CIM)

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from non-affected colon tissue

hyb_protocol: 5 ug fragmented and biotinylated ssDNA were hybridized for 16 hr at 45C to Affymetrix Clariom D human arrays according to standard protocol. Washing and staing were performed using Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scannned using an Affymetrix Gene Chip Scanner 3000 7G.

data_processing:
CEL files were analyzed in Transcriptome Analysis Console (v. 4.0) using the SST-RMA method.
Please note the the analysis was performed on both gene- and exon level in Transcriptome Analysis Console (TAC) and thus the CHP files contain exon/junction data together with gene level data.

source_name: Non-affected colon tissue

label_protocol: Sense target cDNA was prepared from 150 ng of total RNA using the Affymetrix GeneChip WT Plus (Applied Biosystems P/N 902281). cDNA was fragmented and biotin-labeled using the GeneChip(tm) WT Terminal Labeling Kit (Applied Biosystems P/N 900670).

extract_protocol: Muscle and adipose tissues were removed and a small piece (approximately 2x2mm) of the remaining non-affected as well as cancer-associated colon tissue was preserved in RNAlater (Ambion) at 4°C for a maximum of 2 weeks. Subsequently, RNAlater buffer was removed and total RNA was isolated using the RNeasy kit (cat no. 217004, Qiagen) according to the manufacturer’s instructions.

tag: donor id

tag: age (yrs)

tag: gender

value: male

tag: tumor stage

value: II

tag: tumor location

value: Descending

value: non-affected colon


title: Tumor_border_donor3 [D3_T_B]

description: Gene expression data from the tissue at the border of colonic tumor

source_name: Tissue at the border of colonic tumor

value: tumor border colon


title: whole_blood_D3_IL4

city: New York

first: Joseph

middle: C

last: Devlin

state: NY

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the hg38 reference genome
Uniquely mapped indices (UMI) determined by HTSeq-counts
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

source_name: whole blood

growth_protocol: Blood was drawn from healthy human donors according to our IRB protocol (S14-02129). 1 mL of blood per tube was then added to TruCulture tubes and inverted gently to mix.

extract_protocol:
RNA for each donor was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Stimulations were added to appropriate tubes at the following final concentrations: buffer control (PBS), 500 U/mL IFN-b1a (referred to as IFN-b) (Carrier Free; R&D Systems), 10 ng/mL IFN-g (Carrier Free, R&D Systems), 100 ng/mL IFN-l2 (referred to as IFN-l) (Carrier Free, R&D Systems), 78.125 ng/mL IL-4 (Carrier Free, R&D Systems), 100 IU/mL IL-10 (Carrier Free, R&D Systems), and 100 IU/mL IL-13 (Carrier Free, R&D Systems). Tubes were inverted gently to mix. Tubes were incubated for 4 hours at 37°C with gentle rotation. Tubes were spun for 10 minutes at 450 x g without break. Supernatants were removed, and the pellets were resuspended in 2 mL of PAXGENE reagent. Tubes were incubated at room temperature for 2 hours and placed at 4°C overnight. RNA was then isolated using the PAXGene protocol.

value: whole blood

tag: donor

tag: stimulation


title: Non-affected_donor2 [D2_N_A]

value: III

value: Right colic flexure


title: CRB_ASO_3d_3

tag: genotype/variation

value: 3 days

value: cerebellum


title: Tumor_donor3 [D3_T]

description: Gene expression data from the central colonic tumor tissue

source_name: Central colonic tumor tissue

value: colon tumor


title: CRB_ASO_3d_1

value: HDAC2 ASO


title: whole_blood_D3_IL10


title: Tumor_border_donor2 [D2_T_B]


title: MIC 3 hpm_Hi-C

city: Hefei

first: xiaoyuan

last: song

address: Huangshan Road

institute: University of Science & Technology of China

data_processing:
Raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908) and the HiCExplorer tools 2.1.4 (PMID:29335486)
hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh
TAD and compartment were found with HiCExplorer (2.1.4)
Loop calling was performed with Juicer (1.5)
Genome_build: TetrahymenaMicro2016, TetrahymenaMacro2014
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila cells

growth_protocol: Tetrahymena thermophila strains B2086, Cu428, B2086 with Smc1-HA (gift from Dr. Josef Loidl) and Cu428 with Rec8-GFP (gift from Dr. Josef Loidl) were used for Hi-C and HiChIP experiments. Cells were cultured at 30°C in 1x SPP medium (10g Protease peptone, 2g Dextrose, 1g Yeast extract, 0.03g Sequestrene (Fe-EDTA), add water to final 1 liter and autoclave prior to use). For conjugation, cells were first starved in 10mM Tris-HCl Ph7.4 to a final density of approximately 2.5x105 cells/ml for 24 hours at 30°C without shaking. Then we mixed equal numbers of cells representing the two different mating types and incubated at 30°C for 1.5 hours, 3 hours or 24 hours without disturbing, until collecting the cells for the subsequent experiments.

extract_protocol:
We crosslinked conjugated Tetrahymena theromphila cells at 1.5 hpm, 3 hpm and 24 hpm (hpm: hours post-mixing) with 1% formaldehyde for 10 minutes at room temperature. For Hi-C, we followed in-situ Hi-C protocol, the Tetrahymena cells were lysed. Then the lysed cells, isolated MIC or MAC were digested by MboI or HindIII overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Then the DNA were de-crosslinked at 65°C overnight with Proteinase K and DNA were purified. For HiChIP, the Tetrahymena cells were lysed and then digested by MboI or HindIII overnight at 37℃. DNA fragment ends were filled and labeled with dCTP, dGTP, dTTP and biotin-dATP. Proximity ligation was performed at room temperature for 4 hours. Following the in situ ligation, we fragmented the ligated chromatin with sonication. Then the crosslinked protein/DNA was immunoprecipitated using antibodies to HA (rabbit, Cell Signaling Technology C29F4 or Abcam ab9110) and then purified by Protein A+G immunomagnetic beads. The amount of MboI or HindIII enzyme, antibody, and beads are determined by the number of cells in each sample. After immunoprecipitation, DNA was eluted from the beads by incubating at 65°C for 4 hours with Proteinase K and purified.
Both Hi-C and HiChIP DNA were sonicated and binding to M280 beads, then end-repair, dA-tailing and adapter ligation on beads. After PCR amplification and DNA purification, the libraries were sequenced on HiSeq X Ten using 150bp paired-end reads.

tag: developmental stages

value: 3 hours post-mixing

tag: hi-c digest enzyme

value: HindIII


title: MIC 24 hpm_Hi-C

tag: strain

value: 24 hours post-mixing


title: MIC 1.5 hpm_Hi-C

value: 1.5 hours post-mixing


title: whole_blood_D3_IL13

tag: tissue


title: Fast muscle, D72

city: Bodø

first: Ioannis

last: Konstantinidis

state: Nordland

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
Raw sequencing files were trimmed using trimmomatic v0.33 with the following parameters: PE -phred33, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
The trimmed reads were aligned to the Nile tilapia genome (NCBI assembly GCA_001858045.3) using the STAR aligner with default settings and paired-end mode
The mapped reads were used as input to htseq-count to calculate count numbers for each gene using the gff3 genome annotation from the above mentioned genome assembly
Differentially expression (DE) analysis was performed using the edgeR package in R. The DE analysis required that each gene should be expressed with at least 1 count per million in more than 25% of the samples.
P-values were adjusted for multiple testing using the Benjamini-Hochberg correction
Genome_build: GCA_001858045.3
Supplementary_files_format_and_content: csv files with counts per gene

organism: Oreochromis niloticus

source_name: Fast muscle

extract_protocol:
Fast muscle was stored in DNA/RNA Shield (Zymo Research, USA). RNA was extracted after homogenizing the tissue within the DNA/RNA Shield using the Quick-RNA miniprep plus kit (Zymo Research) according to manufacturer's protocol and recommendations.
[modification protocol]  After extracting the total RNA as described above, rRNA depletion was performed using the Ribo-Zero Gold rRNA removal kit (Illumina).
RNA libraries were prepared using the NEBNext Ultra II directional RNA library prep kit for Illumina.
RNA-Seq on a single HiSeq4000 lane (Illumina)

value: Fast muscle

tag: age

value: 5 months

tag: treatment

value: Domestication

tag: replicates


title: MAC 24 hpm_Hi-C


title: Fast muscle, D70


title: Fast muscle, D68


title: whole_blood_D3_IFNgamma

value: IFNgamma


title: whole_blood_D3_IFNbeta

value: IFNbeta


title: CRB_ASO_3d_2

tag: time point


title: Tumor_donor2 [D2_T]

value: male


title: Tumor_donor1 [D1_T]

value: female

value: Transverse


title: Tumor_border_donor1 [D1_T_B]

value: III

value: tumor border colon


title: Non-affected_donor1 [D1_N_A]

value: non-affected colon


title: HPC_SCR_3d_2

source_name: Mouse hippocampus

value: SCRAMBLE ASO

value: 3 days

value: hippocampus


title: Fast muscle, D66


title: whole_blood_D3_Buffer

value: whole blood

value: Buffer


title: HPC_SCR_3d_1


title: whole_blood_D2_IL4


title: Fast muscle, D63


title: HPC_SCR_3d_3


title: MAC 3 hpm_Hi-C

value: 3 hours post-mixing

value: HindIII


title: HPC_ASO_3d_3

value: HDAC2 ASO


title: Smc1-HA 24 hpm_HiChIP rep2

data_processing:
Library strategy: HiChIP
Raw HiC data were processed through the HiC-Pro (2.10.0) pipeline (PMID: 26619908) and the HiCExplorer tools 2.1.4 (PMID:29335486)
hic files were generated using HiC-Pro (2.10.0) script: hicpro2juicebox.sh
TAD and compartment were found with HiCExplorer (2.1.4)
Loop calling was performed with Juicer (1.5)
Genome_build: TetrahymenaMicro2016, TetrahymenaMacro2014
Supplementary_files_format_and_content: hic files contain the HiC contact matrix at different resolution

value: B2086:Smc1-HA and Cu428:Rec8-GFP

value: 24 hours post-mixing

value: MboI

tag: hichip antibody

value: Anti-HA tag antibody ChIP Grade, abcam, ab9110


title: whole_blood_D2_IL10


title: HPC_ASO_3d_2


title: Fast muscle, D53

value: Fast muscle

value: 5 months

value: Domestication


title: MAC 1.5 hpm_Hi-C

value: 1.5 hours post-mixing


title: whole_blood_D2_IL13


title: Smc1-HA 24 hpm_HiChIP rep1

value: HA-Tag (C29F4) Rabbit mAb, Cell Signaling Technology


title: CTX_SCR_3d_3

source_name: Mouse cortex

value: SCRAMBLE ASO

value: cortex


title: Fast muscle, W72

value: Wild


title: HPC_ASO_3d_1

value: 3 days

value: hippocampus


title: Smc1-HA 3 hpm_HiChIP rep2

value: 3 hours post-mixing


title: Fast muscle, W70


title: whole_blood_D2_IFNlambda

value: whole blood

value: IFNlambda


title: MmES_PC_2xChro_r1

description: Enriched DNA

tag: cell type

value: embryonic stem cells

tag: strain/background

value: mixed 129-C57Bl/6

value: wild type

tag: ChIP

value: streptavidin


title: Fast muscle, W68

value: Fast muscle


title: Smc1-HA 3 hpm_HiChIP rep1

value: B2086:Smc1-HA and Cu428:Rec8-GFP

value: HindIII


title: CTX_SCR_3d_2


title: whole_blood_D2_IFNgamma

value: IFNgamma


title: Fast muscle, W66

value: 5 months


title: Smc1-HA 1.5 hpm_HiChIP rep2

value: 1.5 hours post-mixing

value: MboI

value: Anti-HA tag antibody ChIP Grade, abcam, ab9110


title: CTX_SCR_3d_1

value: SCRAMBLE ASO

value: 3 days

value: cortex


title: whole_blood_D2_Buffer

value: whole blood

value: Buffer


title: Smc1-HA 1.5 hpm_HiChIP rep1

value: HA-Tag (C29F4) Rabbit mAb, Cell Signaling Technology


title: Fast muscle, W63

value: Wild


title: Cell 24 hpm_Hi-C rep2

value: 24 hours post-mixing


title: Fast muscle, W53


title: whole_blood_D1R_IL13


title: whole_blood_D1R_IL4


title: CTX_ASO_3d_1

value: HDAC2 ASO


title: YMB9813 Input rep1

city: Worcester

first: Richard

middle: E

last: Baker

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

data_processing:
Basecalls performed using Illumina RTA v2.4.11
ChIP-seq reads were aligned to the sacCer3 genome assembly using Bowtie version 1.0.0 with the following parameters: -n2 -3 40 -m3 --best --strata
Peaks were called using MACS version 2.1.1.20160226 in paired-end mode with the following settings:  -g 1.21e7 --keep-dup auto -B --SPMR
Regions in common between the replicate peak calls were identified using the merge function of bedtools v2.25.0.
Genome_build: sacCer3
Supplementary_files_format_and_content: narrowPeak files were generated during peak calling; scores are -10*log10qvalue
Supplementary_files_format_and_content: Averaged enrichment of the merged replicate peaks was calculated during the bedtools merge and reported in column 5 of the bed files.

organism: Saccharomyces cerevisiae S288C

source_name: sonicated spheroplasts

growth_protocol: Cells were grown to logarithmic phase of growth in a 2% raffinose synthetic complete medium at 30 degrees C.

extract_protocol:
Spheroplasts were prepared, washed, and lysed in detergent containing  buffer with protease inhibitors. Lysate was sonicated to obtain DNA fragments of average size 100 bp.
Libraries were prepared using Illumina Nextera DNA Library Kit #FC-121-1031

treatment_protocol: Galactose was added to the media to a final concentration of 2% for 2 hrs at 30 degrees C to induce Cse4 expression from the GAL promoter.

tag: genetic background

value: psh1delta pGAL-6His-3HA-cse4 K215/216R

tag: antibody


title: CTX_ASO_3d_2


title: YMB9813 Input rep2


title: whole_blood_D1R_IL10

tag: donor


title: CTX_ASO_3d_3


title: YMB9813 ChIP rep2

value: anti-HA agarose beads (A2095, Sigma)


title: whole_blood_D1R_IFNlambda

tag: stimulation

value: IFNlambda


title: YMB9813 ChIP rep1


title: whole_blood_D1R_IFNgamma

value: IFNgamma


title: YMB9245 Input rep2

value: psh1delta pGAL-6His-3HA-cse4 K215/216A


title: whole_blood_D2_IFNbeta

value: IFNbeta


title: Hep3B-RIP-DDX24_repeat1

city: Zhuhai

first: Tianze

last: Liu

address: 52 Mei Hua Dong Road

institute: The Fifth Affiliated Hospital of Sun Yat-sen University

description: DDX24 binding RNAs were pulled down by DDX24 antibody in Hep3B cells

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg38 whole genome using the STAR aligner according to ENCODE-DCC/long-rna-seq-pipeline.
The aligned reads were then assigned to genes (Gencode v26) using subread package (featureCounts) with the following setting:  -T 16 -p -s 2 -t exon -g gene_id.
Then DESeq2 was used to calculate statistically significant difference between the RIP-seq and Input.
And  the results were filtered using the following specifications: (DDX24 RIP / Input) Log2 Fold Change ≥1, p< 0.05, protein-coding gene.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include baseMean, log2FoldChange, P-values for each sample.

source_name: human hepatocellular carcinoma cells

growth_protocol: HCC cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum, 100U/ml penicillin, and 100 ug/ml streptomycin. All cells were maintained in a humidified incubator at 5% CO2 and 37°C.

extract_protocol:
Lysate input and DDX24 RIP samples with TRIzol reagent. After separated by chloroform, the RNA was precipitated using isopropyl alcohol. Then wash RNA by 75% ethanol and Dissolve it in RNase-free water.
RNA libraries were prepared for sequencing using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®(NEB #E7760) with rRNA depletion workflow.

treatment_protocol: HCC cells were harvested using cell scraper.After centrifuge, the cell pellet were resuspended with Polysomal Lysis Buffer and incubated on ice for 15 min. After the lysates were centrifuged, the supernatants were pre-cleared with Dynabeads Protein G. The lysate was then diluted in NT2 buffer. One tenth of the supernatant was saved as input and the rest of the lysate was utilized to conduct an RIP assay at 4°C overnight using DDX24 antibody. The next day, Dynabeads Protein G was added, and the mixtures were incubated at 4°C for three hours, followed by five washes with NT2 buffer. The RIP material was utilized for RNA extraction.

value: human hepatocellular carcinoma cells

tag: passages

value: human


title: Hep3B-RIP-DDX24_repeat2


title: Hep3B-RIP-Input_repeat2


title: Hep3B-RIP-Input_repeat1


title: whole_blood_D1R_IFNbeta


title: Cell 1.5 hpm_Hi-C rep1

tag: developmental stages

value: 1.5 hours post-mixing

value: MboI


title: Cell 3 hpm_Hi-C rep2

value: 3 hours post-mixing

tag: hi-c digest enzyme


title: YMB9245 Input rep1


title: Cell 1.5 hpm_Hi-C rep2

tag: strain


title: Cell 24 hpm_Hi-C rep1


title: Cell 3 hpm_Hi-C rep1


title: whole_blood_D1R_Buffer

tag: tissue

value: whole blood


title: Sample_R18062694-Hep3B-siRNA-2-Hep3B-siRNA-2

data_processing:
A NuGEN Ovation RNA-Seq System was used for RNA sequencing.
Read counts for each gene were normalized into FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Genes with log2FC≥2.3, fold change, *p<0.05 were identified as differentially expressed and were normalized using respective negative and vector control.
Gene sets from biological process gene ontology for analysis of different signaling pathways (including apoptosis, cell growth, and death gene expression) were downloaded from the KEGG pathway database (https://david.ncifcrf.gov/).
Genome_build: hg19
Supplementary_files_format_and_content: Excel files include FPKM, log2FoldChange, P-values values for each sample

extract_protocol:
Total cells RNA was purified using TRIzol reagent.
RNA libraries were prepared for sequencing using  a NuGEN Ovation RNA-Seq System.

tag: lentivirus


title: YMB9245 ChIP rep2


title: Sample_R18062693-Hep3B-siRNA-1-1-Hep3B-siRNA-1-1


title: ASC-shYBX1-rep3

city: Beijing

first: Shuai

last: Ma

address: No.15, Da Tun road

institute: Chinese Academy of Sciences

description: ASCs transduced with lentiviral vectors expressing shYBX1

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to hg19 genome using hisat2 software.
Reads were counted by featureCounts.
Differentially expressed genes were calculated by DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: The fomat of processed data is tab seprated file. And, the content is featureCounts reads count.

source_name: primary YBX1-knockdown-human-ASCs

growth_protocol: Primary human ASCs were cultured ASC culture medium containing α-MEM with 1× GlutaMAX supplement (Gibco), 10% FBS (Gibco), 1% penicillin/streptomycin and 1 ng/ml bFGF was added to 0.1% gelatin-coated plates.

extract_protocol:
Total RNA was extracted by TRIzol (Thermo Fisher Scientific). Genomic DNA was removed
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Lentiviral particles were collected from the supernatant of HEK293T cells by ultracentrifugation at 64,300 × g and 4°C for 135 min and were used to transduce ASCs.

value: human cell

tag: treatment


title: YMB8953 Input rep2

value: psh1delta pGAL-6His-3HA-CSE4


title: ASC-shYBX1-rep2

value: ASCs transduced with lentiviral vectors expressing shYBX1


title: ASC-shGL2-rep3

description: ASCs transduced with lentiviral vectors expressing shGL2

source_name: primary GL2-knockdown-human-ASCs


title: ASC-shYBX1-rep1


title: Sample_R18062692-Hep3B-siNC-Hep3B-siNC

value: non-silencing hairpin RNA


title: YMB8953 Input rep1


title: ASC-shGL2-rep2

value: ASCs transduced with lentiviral vectors expressing shGL2


title: YMB8953 ChIP rep2