title: Zglp1KO_cloneE5_c0_n2

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: 3'-RNAseq amplified from 1ng RNA

data_processing:
RNA-sequence reads were processed mainly as described previously (Nakamura, 2015, GSE63266).  In brief, all RNA-seq reads were processed with cutadapt v1.9.1 (Martin, 2011, EMBnet.journal) to remove library adaptor and poly-A tail sequences and low quality bases with the options "-e 0.1", "-q 20", "-n 2", "-O 1", "-m 30", "-a CTCGAGGGCGCGCCGGATCC", "-g CTCGAGGGCGCGCCGGATCC", "-a AAAAAAAAAAAAAAAAAAAA", and "-a TTTTTTTTTTTTTTTTTTTT".
Reads of 30 bases or longer were used for mapping onto the mouse genome (mm10) and ERCC spike-in RNA sequences using TopHat v2.1.0/Bowtie v1.1.2 (Trapnell, 2009, Bioinformatics;Langmead, 2009, Genome Biol) with the "--bowtie1", "--library-type fr-secondstrand" and "--no-coverage-search" options.  Mapped reads were sorted by genome coordinates using SAMtools v1.3 {Li, 2009, Bioinformatics}, and read counts per gene were counted using HTSeq-count (HTSeq v0.9.1 (Anders, 2015, Bioinformatics)) with the default settings and converted to RPM.  All transcript references were extended up to 10 kb at the transcription termination site for maximum read recovery as described previously (Nakamura, 2015, GSE63266).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

source_name: PGC like cells

growth_protocol: The ESC culture, EpiLC induction, and PGCLC induction were performed as described previously (Hayashi, 2011, Cell;Hayashi, 2012, Science;Ohta, 2017, EMBOJ) with a few modifications.  H18 BVSC and BDF1-2-1 BVSC ESCs were cultured in N2B27 medium (prepared based on previous reports (Ying, 2008, Nature ;Hayashi, 2013, Nat Protocol)) with 2 chemical inhibitors: 0.4 µM PD0325901 (Stemgent, 04-0006) and 3 µM CHIR99021 (BioVision, 1677-5) and 1,000 U/ml LIF (Merck Millipore, ESG1107) on a dish coated with 0.01% poly-L-ornithine (Sigma-Aldrich, P3655) and Laminin (300 ng/ml for H18 and 100 ng/ml for BDF1-2-1, respectively; BD Biosciences, 354232).  EpiLCs were induced by plating ESCs on a dish coated with 16.7 µg/ml human plasma fibronectin (Merck Millipore, FC010) in N2B27 medium containing 20 ng/ml activin A (Peprotech, 120-14), 12 ng/ml bFGF (Thermo Fisher Scientific, 13256-029) and 1% KSR (Thermo Fisher Scientific, 10828-028).  At 42–46 hrs of EpiLC culture, PGCLCs were induced under a floating condition by plating 4000 EpiLCs in the wells of a low-cell-binding U-bottom 96-well Lipidure-coat plate (Thermo Fisher Scientific, 81100525) in GMEM (Thermo Fisher Scientific, 11710-035) with 500 ng/ml BMP4 (R&D Systems, 314-BP), 100 ng/ml SCF (R&D Systems, 455-MC), 1000 U/ml LIF, 50 ng/ml EGF (R&D Systems, 2028-EG), 15% KSR, 0.1 mM nonessential amino acids (NEAA) (Thermo Fisher Scientific, 11140), 1 mM sodium pyruvate (Thermo Fisher Scientific, 11360), 2 mM L-glutamine (Thermo Fisher Scientific, 25030), 0.1 mM 2-mecaptoethanol (2-ME) (Thermo Fisher Scientific, 21985-023), and 100 U/ml penicillin and 0.1 mg/ml streptomycin (Thermo Fisher Scientific, 15140). PGCLC mitotic expansion culture was performed as previously described {Ohta, 2017, EMBOJ}.  Briefly, four days after PGCLC induction, BV+ PGCLCs were sorted by a flow cytometer (BD, FACSAriaIII) onto m220 feeder cells, which express a membrane-bound form of SCF {Dolci, 1991, Nature;Majumdar, 1994 J Biol Chem}, in a 0.1% gelatin (Sigma-Aldrich, G1890)-coated well.  The expansion culture was maintained in GMEM containing 100 ng/ml SCF, 10 µM Forskolin (Sigma-Aldrich, F3917), 10 µM Rolipram (Abcam, ab120029), 2.5% FBS (Thermo Fisher Scientific, 10437-028), 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 2 mM L-glutamine, 0.1 mM 2-ME, 100 U/ml penicillin and 0.1 mg/ml streptomycin.

extract_protocol:
For transcriptome analysis, total RNAs of ESCs, EpiLCs, day 4 (c0) PGCLCs (BV-sorted), c3, c4, c5, c7, and c9 cultured PGCLCs (SC-sorted) were extracted and purified using an RNeasy Micro Kit or NucleoSpin RNA XS Kit.  For each sample, 3' ends of mRNAs were enriched/amplified from 1 ng of total RNAs as the starting material as previously reported ( Nakamura, 2015, GSE63266).
The cDNA library preparation for Nextseq500 (Illumina) was performed as previously reported (Nakamura, 2015, GSE63266, Ishikura, 2016, GSM2328360).

treatment_protocol: To obtain PGCs and male and female germ cells, ICR female mice were mated with Dppa3-EGFP male mice or Ddx4-RFP male mice, d4PGCLCs as BV(+) cells, and cultured PGCLCs as SC(+) cells.

value: germ cells derived from ESCs

tag: Stage

value: culture day0

tag: genotype


title: GFP_microglia_3

status: Public on Feb 21 2020

type: SRA

city: Stanford

first: Sean

middle: K

last: Wang

state: CA

address: 269 Campus Drive

department: Genetics

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Smart-Seq2 libraries were constructed and sequenced by the Broad Institute Genomics Platform on an Illumina NextSeq 500
Reads were aligned using STAR and quantified using featureCounts
Analysis of differential gene expression was performed using DESeq2
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: normalized abundance measurements

molecule: polyA RNA

organism: Mus musculus

source_name: Retinal microglia

extract_protocol:
Retinas were dissected, dissociated with papain, and subjected to cell sorting. Microglia and non-microglia cells were isolated in Buffer TCL by antibody staining.
Libraries were constructed by the Broad Institute Genomics Platform using a modified Smart-Seq2 protocol

treatment_protocol: Mice were subretinally injected with either AAV8-GFP or AAV8-GFP + AAV8-TGFB1.

tag: cell type

value: Retinal microglia

tag: strain

value: rd1 (FVB)

tag: age

value: postnatal day 30

tag: treatment


title: TGFB1_microglia_2

value: AAV8-GFP + AAV8-TGFB1


title: Zglp1KO_cloneE5_c0_n1

city: Kyoto

country: Japan

description: 3'-RNAseq amplified from 1ng RNA

molecule: total RNA

tag: tissue


title: HEME_28d_scATAC-seq

city: Utrecht

first: Cristian

last: Ruiz-Moreno

state: Utrecht

address: 25 Heidelberglaan

country: Netherlands

institute: Prinses Máxima Centrum

library_source: genomic

data_processing:
library strategy: scATAC-seq
CellRanger v1.1.0 was used to demultiplex NextSeq500 data.
CellRanger v1.1.0 was used for aligment and generation of filtered peaks.
Genome_build: mm10
Supplementary_files_format_and_content: scATAC-seq profiles are in bigWig format.

molecule: genomic DNA

growth_protocol: LSK cells were purified from bone marrow of mice treated with 2 mg/kg Heme or equivalent vehicle dose (NaOH pH 7.4). Purification was done negative selection with MACS columns and subsequent sorting. Cells were frozen in 90% FCS and 10% DMSO until Nuclei preperation

extract_protocol:
Nuclei were isolated with a mix of detergents (Digitonin, Tween and NP40). Up-front tagmentation and single-nuclei partition into GEMs were performed using the Chromium Controller and 10x Genomics reagents.
Libraries were generated using the scATAC-seq reagent kit from 10x Genomics

value: 2 mg/kg Heme (pH 7.4) i.p.

value: Bone Marrow (BM)

tag: bm sampling/sorting time point

value: 28 days later

value: LSK cells


title: CTR_28d_scATAC-seq

value: NaOH (pH 7.4) i.p.


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c9_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day9

value: Prdm1-mVenusTg/0; Dppa3-ECFPTg/0; Tg(piggyBac-D4Z4-tetO/mCMV-Zglp1CDS-IRES-mCherry-EF1a-Pac); Tg(piggyBac-D4Z4-EF1a-rtTA-IRES-Neo); Stra8-/-


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c7_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day7


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c5_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day5


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c4_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day4


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c9_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: TGFB1_microglia_3


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c9_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c7_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c7_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: HEME_7d_scATAC-seq

value: one week later


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c5_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA

value: germ cells derived from ESCs


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c9_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c4_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c7_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c9_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c5_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE;Stra8KO_cloneA11_c7_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c7_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c9_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c4_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c9_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c5_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c7_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c7_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c9_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c4_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c9_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c7_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c9_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c7_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c9_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c7_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c5_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c9_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c5_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c7_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c7_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c4_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c4_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c9_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneB6_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c9_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c4_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c5_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c9_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c9_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c7_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c7_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c7_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c5_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Stra8KO_cloneF6_c4_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c4_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c5_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c9_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c5_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c7_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c9_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c4_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c7_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c7_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c5_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c4_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c9_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c9_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c9_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c7_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c4_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c7_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneG10_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c7_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c7_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c5_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c9_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c4_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c5_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c7_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c9_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c4_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c9_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_BMSDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c5_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_BMSDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c5_BMSDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c5_BMS_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_BMSDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_BMS_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_BMS_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_BMS_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1KO_cloneE5_c5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_SerumMinusWINDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_SerumMinusWINDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.54.02

city: Chapel Hill

first: Xianlu

middle: Laura

last: Peng

state: NC

address: 450 West Dr.

institute: The University of North Carolina at Chapel Hill

data_processing:
BCL files were converted to FASTQ with bcltofastq software (v2.19.0).
Individual lane files were combined into one FASTQ for each sample
FASTQ of PDX samples were split into human and mouse reads using bbmap v37.90
The total expected read counts per gene were quantified by Salmon 0.9.1
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Homo sapiens

source_name: PDAC

extract_protocol:
RNA was isolated from matched patient tumor biopsies collected at baseline and post-treatment cycle two.
RNA expression libraries were generated with TruSeq Stranded mRNA kits according to the manufacturer’s instructions.

treatment_protocol: Patients were treated with FOLFIRINOX or PF-04136309 in combination with FOLFIRINOX as previously described (Nywening et al, Lancet oncol, 2016).

tag: sample type

value: tumor biopsies

value: pancreatic ductal adenocarcinoma


title: S1124.51.02


title: S1124.57.02


title: S1124.53.02


title: S1124.54.01


title: S1124.53.01


title: S1124.57.01


title: S1124.51.01


title: S1124.48.01


title: S1124.46.02


title: PGCLC_Zglp1OE_cloneA2_c5_SerumMinusWINDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.46.01


title: S1124.43.02


title: PGCLC_Zglp1OE_cloneA2_c9_SerumMinusWIN_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_SerumMinusWINDox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.43.01


title: S1124.52.01


title: S1124.42.02


title: Tamo

type: RNA

city: Izumo

first: Yoshio

last: Honma

address: 89-1 Enya

department: Biochemistry

institute: Shimane University

description: Gene expression data from MOLT-4 cells treated with tamoxifen

hyb_protocol: cRNA was hybridized for 16 hours at 45oC on GeneChip Human Genome U133 Plus 2.0 Array.

scan_protocol: GeneChip array was scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Thermo Fisher Scientific default setting and global scaling as normalization method.The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

source_name: T-cell leukemia

label_protocol: Biotinylated cRNA was synthesized by GeneChip 3' IVT PLUS Reagent Kit from 100 ng total RNA.

growth_protocol: MOLT-4 cells were cultured in RPMI1640 medium with 10% fetal bovine serum at 37oC.

extract_protocol: Total RNA was extracted using TRI reagent.

treatment_protocol: MOLT-4 cells were treated with romidepsin and/or tamoxifen for 24 hours.

value: T-cell leukemia cell

tag: cell line

value: tamoxifen


title: PGCLC_Zglp1OE_cloneA2_c5_SerumMinusWIN_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.41.02


title: PGCLC_Zglp1OE_cloneA2_c7_SerumMinusWIN_n2

description: 3'-RNAseq amplified from 1ng RNA


title: Comb

description: Gene expression data from MOLT-4 cells treated with romidepsin plus tamoxifen

value: romidepsin plus tamoxifen


title: Romi

description: Gene expression data from MOLT-4 cells treated with romidepsin

value: romidepsin


title: PGCLC_Zglp1OE_cloneA2_c7_BMSDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_BMSDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_SerumMinusWIN_n2

description: 3'-RNAseq amplified from 1ng RNA


description: Gene expression data from untreated MOLT-4 cells

value: untreated


title: S1124.41.01


title: PGCLC_Zglp1OE_cloneA2_c9_BMS_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_BMSDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.38.01


title: S1124.37.02


title: S1124.40.01


title: S1124.38.02


title: PGCLC_Zglp1OE_cloneA2_c5_BMS_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_BMS_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.37.01


title: S1124.35.02


title: S1124.35.01


title: S1124.42.01


title: S1124.34.02


title: PGCLC_Zglp1OE_cloneA2_c9_SerumMinusWINDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.34.01


title: PGCLC_Zglp1OE_cloneA2_c5_SerumMinusWINDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.48.02


title: PGCLC_Zglp1OE_cloneA2_c5_BMSDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_SerumMinusWINDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_SerumMinusWIN_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.33.01


title: S1124.32.02


title: S1124.31.02


title: S1124.32.01


title: S1124.30.02


title: PGCLC_Zglp1OE_cloneA2_c5_SerumMinusWIN_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_SerumMinusWIN_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_BMS_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.31.01


title: PGCLC_Zglp1OE_cloneA2_c9_SerumMinus_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.28.02


title: PGCLC_Zglp1OE_cloneA2_c7_SerumMinus_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_SerumMinusWIN_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c5_SerumMinus_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c4_SerumMinus_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.28.01


title: S1124.25.02


title: PGCLC_Zglp1OE_cloneA2_c7_SerumMinusWINDox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.33.02


title: PGCLC_Zglp1OE_cloneA2_c9_Dox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c9_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.25.01


title: PGCLC_Zglp1OE_cloneA2_c7_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.24.01


title: S1124.24.02


title: S1124.23.01


title: PGCLC_Zglp1OE_cloneA2_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.21.01


title: S1124.30.01


title: PGCLC_Zglp1OE_cloneA2_c9_Dox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.16.02


title: PGCLC_Zglp1OE_cloneA2_c9_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c7_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.17.01


title: S1124.16.01


title: S1124.14.02


title: PGCLC_Zglp1OE_cloneA2_c5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.15.01


title: S1124.14.01


title: S1124.13.02


title: PGCLC_Zglp1OE_cloneA2_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c7_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day3.5

value: Prdm1-mVenusTg/0; Dppa3-ECFPTg/0


title: PGCLC_cloneH18_c9_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c5_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.12.01


title: S1124.13.01


title: PGCLC_cloneH18_c3.5_B2RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_Zglp1OE_cloneA2_c5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c3.5_RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c4_RA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.11.01


title: PGCLC_cloneH18_c9_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.15.02


title: S1124.09.01


title: PGCLC_Zglp1OE_cloneA2_c9_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.17.02


title: S1124.08.02


title: PGCLC_cloneH18_c7_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c5_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c3.5_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c4_BMP2_n2

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.08.01


title: S1124.07.02


title: S1124.07.01


title: S1124.04.01


title: S1124.03.02


title: S1124.03.01


title: PGCLC_cloneH18_c5_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c4_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: S1124.02.01


title: S1124.02.02


title: PGCLC_cloneH18_c3.5_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c4_RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: MS2RPRET_O_read2

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
ks110
mRNA: ribosome footprints
MS2RPRET_O_minus.wig
MS2RPRET_O_plus.wig

data_processing:
Library strategy: Ribo-seq
Perfectly matching reads (including 5’-end and 3’-end UMI) were converted to a single read. The linker sequence was trimmed and reads mapping to rRNA, tRNA, ssrA, ssrS, lacI, or ffs sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cell cultures

growth_protocol: Unless specified, cells were cultured at 37 °C in 500 mL of LB + ampicillin (50 mg/L). IPTG was added (0.3 mM final concentration) when the culture reached OD600 = 0.3 and cells were harvested by filtration at OD600 = 0.5. To induce cold shock, cells were cultured at 37 °C in 175 mL of LB + ampicillin to OD600 = 0.65, induced with IPTG for 20 min at 37 °C, then mixed with 325 mL of ice-cold LB + ampicillin (50 mg/L) + IPTG (0.3 mM) and cultured at 10 °C for 30 min. To prepare samples in stationary phase, cells were cultured at 37 °C in 500 mL of LB + ampicillin to OD600 = 2.0, then further cultured at 37 °C for 4 h. IPTG was added to the culture and cells were further incubated for 1 h. For profiling with retapamulin, cells were grown at 37 °C in 500 mL of LB + ampicillin to OD600 = 0.3, induced with IPTG, grown to OD600 = 0.45, and then harvested by filtration 5 min after the addition of retapamulin (100 µg/mL final concentration).

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. Cell lysates were clarified by centrifugation. For standard ribosome profiling (StRP),  lysates were digested with nucleases, and monosomes were purified over a sucrose gradient. For MS2 ribosome profiling (MS2RP), monosomes were purified by pulldown with MS2 coat protein.
For StRP and MS2RP, ribosome footprints were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified. For RNAseq, libraries were constructed by TruSeq Stranded Total RNA Gold

tag: rna purified from

value: MS2 pulldown

tag: growth conditions

value: 100 ug/mL retapamulin, 5 min


title: MS2RPRET_A

description:
ks172
mRNA: ribosome footprints
MS2RPRET_A_minus.wig
MS2RPRET_A_plus.wig


title: MS2RPRET_S

description:
ks171
mRNA: ribosome footprints
MS2RPRET_S_minus.wig
MS2RPRET_S_plus.wig


title: MS2RPRET_O_read3

description:
ks182
mRNA: ribosome footprints
MS2RPRET_O_minus.wig
MS2RPRET_O_plus.wig


title: PGCLC_cloneH18_c9_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c5_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: MS2RPRET_C

description:
ks170
mRNA: ribosome footprints
MS2RPRET_C_minus.wig
MS2RPRET_C_plus.wig


title: PGCLC_cloneH18_c4_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c3.5_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c3.5_RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: PGCLC_cloneH18_c3.5_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA


title: StRP_A_stationary_lysate2

description:
ks174
mRNA: ribosome footprints
StRP_A_stationary_lysate2_minus.wig
StRP_A_stationary_lysate2_plus.wig

value: monosome fraction

value: stationary phase


title: PGCLC_cloneH18_c3.5_control_n1

description: 3'-RNAseq amplified from 1ng RNA


title: MS2RP_A_stationary_lysate1_read2

description:
ks181
mRNA: ribosome footprints
MS2RP_A_stationary_lysate1_minus.wig
MS2RP_A_stationary_lysate1_plus.wig


title: PGCLC_cloneH18_c7_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: MS2RPRET_O_read1

description:
ks83
mRNA: ribosome footprints
MS2RPRET_O_minus.wig
MS2RPRET_O_plus.wig


title: PGCLC_cloneH18_c9_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: MS2RP_A_stationary_lysate1_read1

description:
ks160
mRNA: ribosome footprints
MS2RP_A_stationary_lysate1_minus.wig
MS2RP_A_stationary_lysate1_plus.wig


title: StRP_A_stationary_lysate1_read2

description:
ks180
mRNA: ribosome footprints
StRP_A_stationary_lysate1_minus.wig
StRP_A_stationary_lysate1_plus.wig


title: MS2RP_A_stationary_lysate2

description:
ks173
mRNA: ribosome footprints
MS2RP_A_stationary_lysate2_minus.wig
MS2RP_A_stationary_lysate2_plus.wig


title: CRB_SCR_32w_2

city: La Jolla

first: Shane

middle: Gary

last: Poplawski

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.

tag: genotype/variation

value: SCRAMBLE ASO

tag: time point

value: 32 weeks

value: cerebellum


title: CRB_SCR_32w_1


title: CRB_SCR_32w_3


title: CRB_ASO_32w_2

value: HDAC2 ASO


title: CRB_ASO_32w_3


title: PGCLC_cloneH18_c7_BMP2_n1

description: 3'-RNAseq amplified from 1ng RNA

value: germ cells derived from ESCs


title: MS2RP_A_cold_lysate2_read1

description:
ks159
mRNA: ribosome footprints
MS2RP_A_cold_lysate2_minus.wig
MS2RP_A_cold_lysate2_plus.wig

value: 10 C for 30 min


title: MS2RP_A_cold_lysate2_read2

description:
ks176
mRNA: ribosome footprints
MS2RP_A_cold_lysate2_minus.wig
MS2RP_A_cold_lysate2_plus.wig


title: CRB_ASO_32w_1


title: HPC_SCR_32w_3

source_name: Mouse hippocampus

value: hippocampus


title: HPC_SCR_32w_2


title: RNAseq_A_cold_lysate1

description:
ks108
mRNA
RNAseq_A_cold_lysate1_minus.wig
RNAseq_A_cold_lysate1_plus.wig

data_processing:
Perfectly matching reads (including 5’-end and 3’-end UMI) were converted to a single read. The linker sequence was trimmed and reads mapping to rRNA, tRNA, ssrA, ssrS, lacI, or ffs sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

value: whole cell lysate


title: HPC_SCR_32w_1


title: MS2RP_A_cold_lysate1_read3

description:
ks179
mRNA: ribosome footprints
MS2RP_A_cold_lysate1_minus.wig
MS2RP_A_cold_lysate1_plus.wig


title: HPC_ASO_32w_3


title: MS2RP_A_cold_lysate1_read2

description:
ks116
mRNA: ribosome footprints
MS2RP_A_cold_lysate1_minus.wig
MS2RP_A_cold_lysate1_plus.wig


title: MS2RP_A_cold_lysate1_read1

description:
ks90
mRNA: ribosome footprints
MS2RP_A_cold_lysate1_minus.wig
MS2RP_A_cold_lysate1_plus.wig


title: CTX_SCR_32w_3

source_name: Mouse cortex

value: cortex


title: HPC_ASO_32w_2


title: StRP_A_cold_lysate1_read2

description:
ks119
mRNA: ribosome footprints
StRP_A_cold_lysate1_minus.wig
StRP_A_cold_lysate1_plus.wig


title: MS2RP_A_lysate3

description:
ks151
mRNA: ribosome footprints
MS2RP_A_lysate3_minus.wig
MS2RP_A_lysate3_plus.wig


title: StRP_A_lysate3

description:
ks175
mRNA: ribosome footprints
StRP_A_lysate3_minus.wig
StRP_A_lysate3_plus.wig


title: CTX_SCR_32w_1


title: StRP_A_cold_lysate1_read1

description:
ks99
mRNA: ribosome footprints
StRP_A_cold_lysate1_minus.wig
StRP_A_cold_lysate1_plus.wig


title: RNAseq_A_lysate2

description:
ks68
mRNA
RNAseq_A_lysate2_minus.wig
RNAseq_A_lysate2_plus.wig


title: CTX_ASO_32w_3


title: CTX_ASO_32w_2


title: RNAseq_S_lysate2

description:
ks67
mRNA
RNAseq_S_lysate2_minus.wig
RNAseq_S_lysate2_plus.wig


title: RNAseq_O_lysate2

description:
ks66
mRNA
RNAseq_O_lysate2_minus.wig
RNAseq_O_lysate2_plus.wig


title: CTX_ASO_32w_1


title: StRP_A_stationary_lysate1_read1

description:
ks169
mRNA: ribosome footprints
StRP_A_stationary_lysate1_minus.wig
StRP_A_stationary_lysate1_plus.wig


title: CRB_SCR_16w_3

value: 16 weeks


title: StRP_A_cold_lysate2

description:
ks168
mRNA: ribosome footprints
StRP_A_cold_lysate2_minus.wig
StRP_A_cold_lysate2_plus.wig


title: MS2RP_A_lysate2_read1

description:
ks64
mRNA: ribosome footprints
MS2RP_A_lysate2_minus.wig
MS2RP_A_lysate2_plus.wig


title: MS2RP_A_lysate2_read2

description:
ks178
mRNA: ribosome footprints
MS2RP_A_lysate2_minus.wig
MS2RP_A_lysate2_plus.wig


title: CRB_SCR_16w_2


title: MS2RP_S_lysate2_read2

description:
ks177
mRNA: ribosome footprints
MS2RP_S_lysate2_minus.wig
MS2RP_S_lysate2_plus.wig


title: CRB_ASO_16w_3


title: MS2RP_S_lysate2_read1

description:
ks63
mRNA: ribosome footprints
MS2RP_S_lysate2_minus.wig
MS2RP_S_lysate2_plus.wig


title: CRB_ASO_16w_2


title: CRB_SCR_16w_1


title: HPC_ASO_32w_1


title: CTX_SCR_32w_2


title: CRB_ASO_16w_1


title: MS2RP_C_lysate2

description:
ks61
mRNA: ribosome footprints
MS2RP_C_lysate2_minus.wig
MS2RP_C_lysate2_plus.wig


title: MS2RP_O_lysate2

description:
ks62
mRNA: ribosome footprints
MS2RP_O_lysate2_minus.wig
MS2RP_O_lysate2_plus.wig


title: StRP_A_lysate2

description:
ks60
mRNA: ribosome footprints
StRP_A_lysate2_minus.wig
StRP_A_lysate2_plus.wig


title: HPC_SCR_16w_2


title: HPC_SCR_16w_3


title: StRP_C_lysate2

description:
ks57
mRNA: ribosome footprints
StRP_C_lysate2_minus.wig
StRP_C_lysate2_plus.wig


title: HPC_SCR_16w_1


title: HPC_ASO_16w_3


title: StRP_S_lysate2

description:
ks59
mRNA: ribosome footprints
StRP_S_lysate2_minus.wig
StRP_S_lysate2_plus.wig


title: HPC_ASO_16w_2


title: StRP_O_lysate2

description:
ks58
mRNA: ribosome footprints
StRP_O_lysate2_minus.wig
StRP_O_lysate2_plus.wig


title: RNAseq_C_lysate2

description:
ks65
mRNA
RNAseq_C_lysate2_minus.wig
RNAseq_C_lysate2_plus.wig


title: MS2RP_S_lysate1

description:
ks25
mRNA: ribosome footprints
MS2RP_S_lysate1_minus.wig
MS2RP_S_lysate1_plus.wig


title: CTX_SCR_16w_3


title: CTX_SCR_16w_2


title: MS2RP_O_lysate1

description:
ks24
mRNA: ribosome footprints
MS2RP_O_lysate1_minus.wig
MS2RP_O_lysate1_plus.wig


title: HPC_ASO_16w_1


title: MS2RP_C_lysate1

description:
ks23
mRNA: ribosome footprints
MS2RP_C_lysate1_minus.wig
MS2RP_C_lysate1_plus.wig


title: MS2RP_A_lysate1

description:
ks26
mRNA: ribosome footprints
MS2RP_A_lysate1_minus.wig
MS2RP_A_lysate1_plus.wig


title: CTX_SCR_16w_1


title: CTX_ASO_16w_2


title: CTX_ASO_16w_3


title: CTX_ASO_16w_1


title: CRB_SCR_8w_3

value: 8 weeks


title: CRB_SCR_8w_1


title: CRB_SCR_8w_2


title: CRB_ASO_8w_3


title: CRB_ASO_8w_1


title: CRB_ASO_8w_2


title: HPC_SCR_8w_2


title: HPC_SCR_8w_1


title: HPC_ASO_8w_2


title: HPC_ASO_8w_3


title: Karpas299

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
NEBNext small RNA adapter sequence (AGATCGGAAGAGCACACGTCT) was removed and reads with 30 Phred average quality and not aligned to known or predicted miRNA precursors were mapped with Bowtie (v1.1.2) to the reference genome.
The alignments were analyzed with derfinder software tool (Collado-Torres et al. 2017, Nucleic Acids Res) to identify expressed RNAs and the corresponding genomic regions.
Among regions supported by at least 10 reads we selected those with 13-50 contiguous bases and in the top 5% of expression for further characterization.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw read count matrix to putative non miRNA-derived small RNAs, tab separated values.

growth_protocol: Tumor biopsies were sent to out lab in culture medium; peripheral blood samples from patients and healthy donors were sent in Na-citrate anticoagulant; ALCL cell lines were maintained in standard culture conditions with 15% FBS, then FBS was removed 48 hrs before exosomes collection.

extract_protocol:
Exosomal RNA was extracted by using exoRNeasy Midi kit (Qiagen). Biopsy RNA was extracted by Trizol reagent (Invitrogen).
RNA-seq libraries were prepared with NEBNext Multiplex Small RNA Library Prep Kit for Illumina (New England Biolabs), and sequenced on an Illumina HiSeq 4000 platform.

treatment_protocol: All patients were at diagnosis.

value: ALCL cell line

value: Exosomes


title: CTR11

value: Healthy donor


title: HPC_ASO_8w_1


title: EXO16

value: ALCL patient


title: SR786


title: EXO20


title: EXO17


title: SUDHL1


title: CTR21


title: CTR4


title: MAC2A


title: EXO18


title: CTR12


title: CTR16


title: EXO19


title: SUPM2


title: EXO15


title: CTX_SCR_8w_3


title: EXO14


title: CTX_SCR_8w_2


title: CTX_SCR_8w_1


title: EXO12


title: CTX_ASO_8w_3


title: CTX_ASO_8w_2


title: EXO10


title: CTX_ASO_8w_1


title: HPC_SCR_8w_3


title: EXO9


title: EXO8


title: Zglp1OE_cloneA2_c5_Dox_n2

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
For transcriptome analysis, total RNAs of ESCs, EpiLCs, day 4 (c0) PGCLCs (BV-sorted), c3, c4, c5, c7, and c9 cultured PGCLCs (SC-sorted) were extracted and purified using an RNeasy Micro Kit.  For each sample, 3' ends of mRNAs were enriched/amplified from 1 ng of total RNAs as the starting material as previously reported ( Nakamura, 2015, GSE63266).
The cDNA library preparation for Nextseq500 (Illumina) was performed as previously reported (Nakamura, 2015, GSE63266, Ishikura, 2016, GSM2328360).

value: culture day5


title: Zglp1KO_cloneG10_c0_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day0


title: Zglp1OE_cloneA2_c4_Dox_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day4


title: EXO4


title: EXO3


title: Zglp1OE_cloneA2_c5_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: Zglp1OE_cloneA2_c4_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA


title: BIO20

value: Biopsy


title: EXO13


title: Zglp1OE_cloneA2_c0_n2

description: 3'-RNAseq amplified from 1ng RNA


title: EXO1


title: BIO19


title: EXO2


title: EXO7


title: Zglp1OE_cloneA2_c7_Dox_n1

description: 3'-RNAseq amplified from 1ng RNA

value: culture day7


title: Zglp1OE_cloneA2_c7_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: EXO5


title: Zglp1OE_cloneA2_c7_Dox_n2

description: 3'-RNAseq amplified from 1ng RNA


title: EXO11


title: EXO6


title: Zglp1KO_cloneG10_c0_n1

description: 3'-RNAseq amplified from 1ng RNA


title: BIO18


title: Zglp1OE_cloneA2_c3_n2

description: 3'-RNAseq amplified from 1ng RNA

value: culture day3


title: Zglp1OE_cloneA2_c7_DoxRA_n2

description: 3'-RNAseq amplified from 1ng RNA

value: germ cells derived from ESCs


title: BIO17


title: BIO16


title: BIO15


title: BIO14


title: Zglp1OE_cloneA2_c4_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: BIO13


title: Zglp1OE_cloneA2_c4_Dox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: Zglp1OE_cloneA2_c3_n1

description: 3'-RNAseq amplified from 1ng RNA


title: BIO8


title: Parental clone (H18)_c4_control_n1

description: 3'-RNAseq amplified from 1ng RNA

value: Prdm1-mVenusTg/0; Dppa3-ECFPTg/0


title: BIO10


title: E15.5_oocytes_n3

description: 3'-RNAseq amplified from 1ng RNA

source_name: fetal oocytes

value: germ cells


title: BIO12


title: Zglp1OE_cloneA2_c0_n1

description: 3'-RNAseq amplified from 1ng RNA


title: BIO9


title: Parental clone (H18)_c4_B2RA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: Parental clone (H18)_c4_control_n2

description: 3'-RNAseq amplified from 1ng RNA


title: BIO7


title: E14.5_oocytes_n3

description: 3'-RNAseq amplified from 1ng RNA


title: BIO6


title: BIO3


title: BIO5


title: BIO4


title: Zglp1OE_cloneA2_c5_DoxRA_n1

description: 3'-RNAseq amplified from 1ng RNA


title: Zglp1OE_cloneA2_c5_Dox_n1

description: 3'-RNAseq amplified from 1ng RNA


title: BIO2


title: V5Zglp1OE_c8PGCLCs_DoxRA_Input

data_processing:
All reads were processed with the trim_galore program (Trim Galore! version 0.4.1 and cutadapt 1.9.1) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the “-a ATCACCGACTGCCACGCCTTGGCCGTACAGCA GCCT” and “-q 20” options to remove the Barcode Internal+12 mer adaptor sequences {Mitani, 2017, Nucleic Acids Res} and low quality reads, respectively.  The processed reads of 20 bases and longer were mapped on the mouse genome mm10 by Bowtie v1.1.2 (Langmead, 2009, Genome Biol) with the “-n 3"  and “–m 1” options.  The mapped reads in Sequence Alignment/Map (SAM) format were sorted by chromosome by Picard-tools v2.1.0 (http://piard.sourceforge.net), then processed with SAMtools v1.3 ("-s" option (Li, 2009, Bioinformatics)) and bedtools v2-2.25.0 (Quinlan, 2010, Bioinformatics) (command line: bamToBed) to remove duplicate reads and converted to bed format, respectively.
Peak calling for V5-ZGLP1 was performed using MACS v2.1.1.20160309 with the default settings (Zhang, 2008, Genome Biol).  For MACS peak calling, samples were processed against the respective input read data for each cell type and treatment.  Following peak calling for each sample, we consolidated peaks detected in close proximity (within 500 bp) across different samples as a single peak as follows. 1) We first listed peak summits from all samples, and two neighboring peak summits located within 100 bp were joined as a single summit (i.e., a new summit was created at the center between the two original summits. 2) Newly called summits within a distance of 200 bp were subsequently processed in the same way. 3) The process was repeated for the distances of 300, 400, and 500 bp.
Following the peak summit-bundling process, 32,927 genomic loci (i.e., 32,927 peak summits) were considered as potential ZGLP1-binding sites. All the sequenced reads and their genomic coordinates were listed in a MySQL database table (version 4.6.35).  The database was then queried for the coordinates of genomic loci, and hit counts were identified as read counts when the center of a read, which is extended for 250 bp from the first base of the sequenced read (i.e., the center is located at the 125th base from the first base), was overwrapped with a genomic coordinate of interest by a single base.  For ChIP samples, reads within 500 bp of the peak summits were counted and then normalized as reads per million (RPM).  For input samples, reads within 5,000 bp of the peak summits were counted and then normalized in RPM. The following steps were taken for the selection of ZGLP1-binding sites. 1) We first averaged the read tag density (in RPM) from three input samples (i.e., ESC, c8 Dox only, and c8 Dox+RA) at each potential ZGLP1-binding site and selected 32,725 sites with (0.1 < averaged input RPM < 0.7) for subsequent analysis. 2) RPM values across ChIP’d samples were normalized so that the mean of each sample matched the mean of the c8 Dox+RA sample. 3) The ZGLP1 IP level (IP/input) at each binding site was defined as the ratio between the normalized RPM value of a ChIP’d sample and the averaged RPM value from the three input samples. 4) The IP/input values in PGCLCs for Dox only and Dox+RA samples were averaged between c7 and c8 and log2-converted [i.e., log2((IP/input) + 0.1)]. 5) Lastly, ZGLP1-binding sites in PGCLCs were defined as sites with [averaged log2((IP/Input) + 0.1) > 1 and log2((IP/Input) + 0.1) differences between c7 and c8 samples < 0.585]. The selection process yielded 16,576 ZGLP1-binding sites for the Dox only treatment and 14,662 binding sites for Dox+RA treatment in PGCLCs.  Association of ZGLP1-binding sites with nearby genes was performed using Homer v 4.9.1 {Heinz, 2010, Mol Cell} (command line: annotatePeaks.pl) with the default settings.  For annotation of the binding sites, we focused our analysis on binding sites that were associated with genes included in our RNA-seq analysis (25,315 genes) and binding sites that were within 15 kb of the transcription start sites (TSSs) of the associated genes (10,269 sites for Dox only treatment, 13,379 sites for Dox+RA treatment).
Genome_build: mm10
Supplementary_files_format_and_content: Combined peak summits in bed format. Wig files were generated by IGVTools with default setting and each read count was divided by total mapped reads and multiplied by 1 million (RPM).

source_name: c8 PGCLCs DoxRA input

growth_protocol: The ESC culture, EpiLC induction, and PGCLC induction were performed as described previously (Hayashi, 2011, Cell;Hayashi, 2012, Science;Ohta, 2017, EMBOJ) with a few modifications.  H18 BVSC and BDF1-2-1 BVSC ESCs were cultured in N2B27 medium (prepared based on previous reports {Ying, 2008, Nature ;Hayashi, 2013, Nat Protocol}) with 2 chemical inhibitors: 0.4 µM PD0325901 (Stemgent, 04-0006) and 3 µM CHIR99021 (BioVision, 1677-5) and 1,000 U/ml LIF (Merck Millipore, ESG1107) on a dish coated with 0.01% poly-L-ornithine (Sigma-Aldrich, P3655) and Laminin (300 ng/ml for H18 and 100 ng/ml for BDF1-2-1, respectively; BD Biosciences, 354232).  EpiLCs were induced by plating ESCs on a dish coated with 16.7 µg/ml human plasma fibronectin (Merck Millipore, FC010) in N2B27 medium containing 20 ng/ml activin A (Peprotech, 120-14), 12 ng/ml bFGF (Thermo Fisher Scientific, 13256-029) and 1% KSR (Thermo Fisher Scientific, 10828-028).  At 42–46 hrs of EpiLC culture, PGCLCs were induced under a floating condition by plating 4000 EpiLCs in the wells of a low-cell-binding U-bottom 96-well Lipidure-coat plate (Thermo Fisher Scientific, 81100525) in GMEM (Thermo Fisher Scientific, 11710-035) with 500 ng/ml BMP4 (R&D Systems, 314-BP), 100 ng/ml SCF (R&D Systems, 455-MC), 1000 U/ml LIF, 50 ng/ml EGF (R&D Systems, 2028-EG), 15% KSR, 0.1 mM nonessential amino acids (NEAA) (Thermo Fisher Scientific, 11140), 1 mM sodium pyruvate (Thermo Fisher Scientific, 11360), 2 mM L-glutamine (Thermo Fisher Scientific, 25030), 0.1 mM 2-mecaptoethanol (2-ME) (Thermo Fisher Scientific, 21985-023), and 100 U/ml penicillin and 0.1 mg/ml streptomycin (Thermo Fisher Scientific, 15140). PGCLC mitotic expansion culture was performed as previously described {Ohta, 2017, EMBOJ}.  Briefly, four days after PGCLC induction, BV+ PGCLCs were sorted by a flow cytometer (BD, FACSAriaIII) onto m220 feeder cells, which express a membrane-bound form of SCF {Dolci, 1991, Nature;Majumdar, 1994 J Biol Chem}, in a 0.1% gelatin (Sigma-Aldrich, G1890)-coated well.  The expansion culture was maintained in GMEM containing 100 ng/ml SCF, 10 µM Forskolin (Sigma-Aldrich, F3917), 10 µM Rolipram (Abcam, ab120029), 2.5% FBS (Thermo Fisher Scientific, 10437-028), 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 2 mM L-glutamine, 0.1 mM 2-ME, 100 U/ml penicillin and 0.1 mg/ml streptomycin.

extract_protocol:
The harvested cells were centrifuged at 220×g for 3 min, suspended in 1 mL of PBS and fixed by the addition of 27 µL of 36.5% formalin (Sigma-Aldrich, F8775) for 12 min at room temperature with constant mixing on a tube rotator.  Fixation was terminated by the addition of 110 µL of 1.5 M glycine (Wako, 077-00735).  The fixed cells were washed twice in PBS (Thermo Fisher Scientific, 20012-027) containing 0.1% BSA fraction V and were lysed in 400 µL of SDS-lysis buffer [50 mM Tris-HCl (pH 8.0) (Nacalai Tesque, 35435-11), 1% SDS, 10 mM EDTA, and 1 mM PMSF] on ice for 10 min.  The lysate was split amongst 4 tubes (Diagenode, 315-81401) at 100 µL/tube, and chromatins were sonicated using Picoruptor (Diagenode, 316-81311) at 4 °C for 19 cycles, yielding DNA fragments of 100–300 bp.  The sonicated products from 4 tubes were combined and centrifuged at 16,000×g for 5 min.  The supernatants were diluted in 1 mL ChIP dilution buffer [16.7 mM Tris-HCl (pH 8.0), 0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA (Nacalai Tesque, 14347-21) and 167 mM NaCl (Nacalai Tesque, 31334-51)] and divided into 0.1 mL aliquots as input DNA and 1.3 mL aliquots as ChIP samples. For ChIP samples, 15 µg of rabbit polyclonal anti-V5 antibody was reacted with 40 µL of M280 Dynabeads Protein G (Thermo Fisher Scientific, 10003D) at room temperature for 40 min.  ChIP samples were then mixed with the antibody-Dynabeads complexes and incubated at 4 °C for 22 hrs with gentle mixing on a tube rotator.  The chromatin-antibody-Dynabeads complexes were recovered using a DynaMag-2 magnet (Thermo Fisher Scientific, 123.21D) and washed with 200 µL of a low salt buffer [20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 150 mM NaCl], a high salt buffer [20 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% Triton X-100, 2 mM EDTA, and 500 mM NaCl], RIPA buffer [10 mM Tris-HCl (pH 8.0), 1% sodium deoxycholate (Nacalai Tesque, 10712-96), 1% NP40 (Nacalai Tesque, 23640-94), 250 mM LiCl (Wako, 244-00461), and 1 mM EDTA], and TE buffer [10 mM Tris-HCl (pH 8.0), and 1 mM EDTA].  After transferring to a new tube, the chromatin was then incubated in 50 µL of elution buffer [0.1 M NaHCO3 (Nacalai Tesque, 31213-15), 1% SDS, 10 mM DTT Nacalai Tesque, 14128-91], and 60 ng/µL tRNA (Roche, 10109517001)] for 15 min at room temperature.  The eluted chromatins were separated from the Dynabeads using DynaMag-2, then reverse-crosslinked by the addition of 8 µL of 2.5 M NaCl and incubated at 65 °C for 16 hrs. Then 2 µL of 0.5 M EDTA, 4 µL of 1 M Tris-HCl (pH 6.5), and 0.2 µL of 20 mg/mL proteinase K (Sigma-Aldrich, P2308) were added to the reaction mix, and the reaction mix was further incubated at 45 °C for 1 hr. The ChIP’d DNAs were purified with Qiaquick PCR purification columns (Qiagen, 28104) using buffer EB (Qiagen, 19086) containing 4 ng/µL of tRNA.  Input chromatins were reverse-crosslinked, treated with proteinase K, and purified in the same way as the ChIP’d samples.
Library preparations for the next-generation sequencing were performed as previously described (Mitani, 2017, GSE91038), except that ChIP’d DNAs were not sonicated further by Covaris.  The libraries were sequenced on NextSeq (Illumina) to generate 86 bp single-end reads using a custom read primer (Mitani, 2017, GSE91038).  A total of 8 samples [ESC Dox+RA (ChIP’d), ESC Dox+RA (input), c7 Dox only (ChIP’d), c8 Dox only (ChIP’d), c8 Dox only (input), c7 Dox+RA (ChIP’d), c8 Dox+RA (ChIP’d), and c8 Dox+RA (input)] were sequenced.

treatment_protocol: Cultured PGCLCs were treated with Dox only, or Dox and RA from c3 onward. Treated PGCLCs were SC- and mCherry sorted by FACS. ESCs were treated with Dox and RA for 24-hr under 2iLIF culture condition before FACSorted for mCherry signals.

value: C57BL/6 x DBA2

value: PGCLCs

tag: chip antibody

value: anti-V5, Rb polyclonal, AB3792

tag: cell sorting

value: FACS (SC+, mCherry+)


title: V5Zglp1OE_ESCs_DoxRA_ChIP

description: ChIP from 4.0 x 10^6 cells

source_name: ES DoxRA

value: ESCs

value: FACS (mCherry+)


title: V5Zglp1OE_ESCs_DoxRA_Input

source_name: ES DoxRA input


title: BIO11


title: V5Zglp1OE_c8PGCLCs_DoxRA_ChIP

description: ChIP from 4.0 x 10^6 cells

source_name: c8 PGCLCs DoxRA


title: BIO1


title: V5Zglp1OE_c7PGCLCs_DoxRA_ChIP

description: ChIP from 4.0 x 10^6 cells

source_name: c7 PGCLCs DoxRA


title: E9.5_PGC_n3

description: 3'-RNAseq amplified from 1ng RNA

source_name: primordial germ cells


title: V5Zglp1OE_c8PGCLCs_DoxOnly_Input

source_name: c8 PGCLCs Dox only input


title: Whole blood, ZT12

type: genomic

city: Ji'nan

first: Yaran

last: Zhang

address: North industrial road

country: China

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: Zhaotong cattle

tag: altitude (m)

tag: longitude

tag: latitude

value: Whole blood


title: Whole blood, ZT07

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


title: Whole blood, ZT13


title: Whole blood, ZT10


title: Whole blood, ZT09


title: V5Zglp1OE_c7PGCLCs_DoxOnly_ChIP

description: ChIP from 4.0 x 10^6 cells

source_name: c7 PGCLCs Dox only

tag: strain

tag: cell type


title: V5Zglp1OE_c8PGCLCs_DoxOnly_ChIP

description: ChIP from 4.0 x 10^6 cells

source_name: c8 PGCLCs Dox only


title: Whole blood, ZT04

tag: tissue


title: Whole blood, ZT05


title: Whole blood, ZT03


title: NPC PJ-B PROX1 Dkk1 klón2 p12

city: Budapest

first: János

middle: Miklós

last: Réthelyi

address: Balassa utca 6.

country: Hungary

institute: Semmelweis University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for short or low-quality sequence using Trimgalore! With parameters: s -5, -q 20, -l 50, then mapped to hg19 reference genome using hisat2 v.2.1.0
Mapped reads were annotated to genes using featureCounts
After exclusion of all X and Y chromosome genes, differential expression analysis (SZ-HU-PROB compare to SZ-HU-MO and SZ-HU-PROB compare to SZ-HUFA) was performed by using DESeq2 program
Rlog normalization was performed by DESeq2 analysing all the sample
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts of sequencing reads for the genes

source_name: Neuronal progenitor cell

growth_protocol: We used the dentate gyrus differentiation protocol (Yu et al, Stem Cell Reports, 2014)

extract_protocol:
Total RNA was isolated from NPCs using TRIzol™ reagent.
RNA libraries were prepared for sequencing using standard Illumina NextSeq 500 protocols
Sequencing was performed after library preparation on the NextSeq500 platform using 75 bp reads.

treatment_protocol: NO specific treatment was applied.

value: IPSC-derived neural progenitor cells

tag: passage

value: SZ-HU-PROB

tag: phenotype

value: schizophrenia


title: NPC PJ-B PROX1 Dkk1 klón2 p13

tag: cell line


title: NPC FJ-A PROX1 Dkk1 klón1 p18

value: SZ-HU-FA

value: control


title: NPC MA-A PROX1 Dkk1 klón1 p16

value: SZ-HU-MO


title: NPC MA-A PROX1 Dkk1 klón1 p19


title: NPC FJ-A PROX1 Dkk1 klón1 p14


title: Whole blood, ZT02


title: NPC MA-A PROX1 Dkk1 klón1 p15


title: NPC FJ-A PROX1 Dkk1 klón1 p15


title: NPC PJ-B PROX1 Dkk1 klón2 p16


title: NPC PJ-B PROX1 Dkk1 klón2 p11


title: Whole blood, ZT11


title: Whole blood, XJB08

value: Xinjiang Brown cattle


title: NPC FJ-A PROX1 Dkk1 klón1 p13


title: Whole blood, ZT08


title: Whole blood, ZT06


title: NPC MA-A PROX1 Dkk1 klón1 p14


title: Whole blood, XJB03


title: HD58_Hemin_24h

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15, followed by fragment size modeling (http://code.google.com/p/phantompeakqual-tools/). The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the binding sites for the histone marks at p-value of 10-10. H3K27ac peaks were called using the default (narrow) setting.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq files are in bigWig format, DownSampled to make all files the same read depth.

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were negatively selected from peripheral blood and immediately fixed for ChIP.

extract_protocol:
Purified cells were fixed with 1% formaldehyde (ThermoFisher Scientific) at a concentration of approximately 5 million cells/ml. Fixed cell preparations were sonicated using a Diagenode Bioruptor UCD-300 for 3x 10 minutes (30 seconds on; 30 seconds off). 33 µl of chromatin (1 ug) was used for immunoprecipitation.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Monocytes were cultured for 24 hours in media with or without Hemin and B-glucan.

value: Monocyte

tag: treatment protocol

value: 24 hours in media with Hemin

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)

tag: donor


title: Whole blood, XJB04


title: HD58_BG_24h

value: 24 hours in media with B-glucan


title: HD58_T0

value: attached for 1 hour


title: HD58_RPMI_24h

value: 24 hours in media


title: Whole blood, XJB02


title: HD57_BG_24h


title: Whole blood, ZT01


title: Whole blood, XJB01


title: Whole blood, WZ05

organism: Bos indicus

value: Weizhou cattle


title: HD57_RPMI_24h


title: HD57_Hemin_24h


title: Whole blood, WZ02

value: Female


title: Whole blood, WZ04


title: Whole blood, WZ03


title: HD56_Hemin_24h


title: Whole blood, WZ01


title: Whole blood, XJB06


title: Whole blood, WN20

value: Weining cattle


title: Whole blood, WN19

value: Whole blood


title: Whole blood, XJB05


title: HD51_Hemin_24h


title: HD56_T0


title: HD51_BG_24h


title: HD56_RPMI_24h


title: Whole blood, WN18


title: Whole blood, WN17


title: HD51_T0


title: HD51_RPMI_24h


title: HD57_T0


title: HD56_BG_24h


title: Whole blood, WN15


title: Whole blood, WN12


title: Whole blood, WN13


title: Whole blood, XJB07


title: Whole blood, WN11


title: HD50_RPMI_24h


title: HD50_T0


title: HD50_Hemin_24h


title: Whole blood, WN10


title: Whole blood, WN07


title: HD51_Hemin_d6_LPS_4h_RNA-seq

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 data.
Library strategy: RNA-seq. MMSEQ package was used to infer gene expression levels. Reads were mapped to human gene annotation using Bowtie1 (Ensemble release 68).
Genome_build: hg19
Supplementary_files_format_and_content: RNA files are in a .gene.mmseq format, containing counts per gene.

growth_protocol: Monocytes were negatively selected from adult peripheral blood.

extract_protocol:
RNA was extracted using the RNEasy mini kit.
Libraries were prepared using the KAPA hyperprep kit.

treatment_protocol: Monocytes were cultured in media with or without Hemin or B-glucan. Then differentiated to macrophages. Cells were collected at baseline (after attachment), 4 hours, 24 hours, and 6 days after culture, and 6 days plus 4 hours LPS exposure.

value: blood

value: 24 hours in media with Hemin, then 5 days in media, then LPS for 4 hours


title: Whole blood, WN08


title: Whole blood, WN06


title: Whole blood, WN09


title: HD51_BG_d6_RNA-seq

value: 24 hours in media with B-glucan, then 5 days in media


title: HD51_RPMI_d6_RNA-seq

value: 6 days in media


title: Whole blood, WN05


title: HD51_Hemin_d6_RNA-seq

value: 24 hours in media with Hemin, then 5 days in media


title: HD51_BG_24h_RNA-seq


title: Whole blood, WN14


title: Whole blood, WN03


title: HD51_Hemin_24h_RNA-seq


title: HD51_RPMI_d6_4h_RNA-seq

value: 6 days and 4 hours in media


title: Whole blood, WN04


title: Whole blood, WN02


title: Whole blood, WN01


title: Whole blood, THMY18

organism: Bos grunniens

value: Tibetan High Mountain yak


title: HD51_BG_4h_RNA-seq

value: Monocyte

value: 4 hours in media with B-glucan


title: Whole blood, THMY19


title: HD51_RPMI_24h_RNA-seq


title: HD51_BG_d6_LPS_4h_RNA-seq

value: 24 hours in media with B-glucan, then 5 days in media, then LPS for 4 hours


title: Whole blood, THMY16


title: HD51_Hemin_4h_RNA-seq

value: 4 hours in media with Hemin


title: HD51_RPMI_4h_RNA-seq

value: 4 hours in media


title: Whole blood, THMY17


title: HD49_BG_d6_LPS_4h_RNA-seq


title: HD51_RPMI_d6_LPS_4h_RNA-seq

value: 6 days in media and then LPS for 4 hours


title: Whole blood, THMY14


title: Whole blood, THMY13


title: Whole blood, THMY15


title: Whole blood, THMY12


title: HD49_RPMI_d6_LPS_4h_RNA-seq


title: HD49_Hemin_d6_LPS_4h_RNA-seq


title: HD49_RPMI_d6_RNA-seq


title: HD49_BG_d6_RNA-seq


title: HD49_RPMI_d6_4h_RNA-seq


title: Whole blood, THMY11


title: Whole blood, THMY10


title: Whole blood, THMY09


title: HD49_Hemin_d6_RNA-seq


title: HD49_Hemin_24h_RNA-seq

value: 24 hours in media with Hemin


title: HD49_BG_4h_RNA-seq


title: HD51_T0_RNA-seq

value: attached for 1 hour


title: Whole blood, THMY08

value: Female


title: Whole blood, THMY06

value: Whole blood


title: Whole blood, THMY04


title: Whole blood, THMY07


title: Whole blood, THMY03


title: Whole blood, THMY05


title: Whole blood, THMY02


title: HD49_Hemin_4h_RNA-seq

value: blood


title: HD48_Hemin_d6_LPS_4h_RNA-seq

value: 24 hours in media with Hemin, then 5 days in media, then LPS for 4 hours


title: HD49_RPMI_4h_RNA-seq


title: HD48_RPMI_d6_LPS_4h_RNA-seq


title: HD48_BG_d6_LPS_4h_RNA-seq


title: Whole blood, THMY01


title: Whole blood, TB10

value: Tibetan cattle


title: HD49_BG_24h_RNA-seq

value: 24 hours in media with B-glucan


title: HD49_RPMI_24h_RNA-seq

value: 24 hours in media


title: Whole blood, TB07


title: Whole blood, TB09


title: Whole blood, TB08


title: HD48_BG_d6_RNA-seq

value: 24 hours in media with B-glucan, then 5 days in media


title: HD48_Hemin_d6_RNA-seq

value: 24 hours in media with Hemin, then 5 days in media


title: Whole blood, TB06


title: Whole blood, TB03


title: Whole blood, TB02


title: HD48_RPMI_d6_RNA-seq

value: Monocyte

value: 6 days in media


title: HD48_BG_24h_RNA-seq


title: Whole blood, SJ09

value: Sanjiang cattle


title: HD48_RPMI_d6_4h_RNA-seq

value: 6 days and 4 hours in media


title: Whole blood, TB04


title: HD48_RPMI_24h_RNA-seq


title: HD48_Hemin_24h_RNA-seq


title: HD48_RPMI_4h_RNA-seq

value: 4 hours in media


title: HD48_Hemin_4h_RNA-seq

value: 4 hours in media with Hemin


title: HD37_Hemin_d6_LPS_4h_RNA-seq


title: Whole blood, TB01


title: Whole blood, SJ06


title: HD37_BG_d6_RNA-seq


title: Whole blood, SJ10


title: HD48_T0_RNA-seq


title: HD48_BG_4h_RNA-seq

value: 4 hours in media with B-glucan


title: Whole blood, SJ07


title: Whole blood, SJ08


title: HD37_BG_d6_LPS_4h_RNA-seq

value: 24 hours in media with B-glucan, then 5 days in media, then LPS for 4 hours


title: HD37_Hemin_d6_RNA-seq


title: Whole blood, TB05

value: Female


title: Whole blood, SGH12

value: Shigatse Humped cattle

value: Whole blood


title: HD37_Hemin_24h_RNA-seq

value: blood

value: 24 hours in media with Hemin


title: HD37_RPMI_24h_RNA-seq


title: Whole blood, SJ05


title: Whole blood, SJ02


title: Whole blood, SJ03


title: HD37_RPMI_d6_4h_RNA-seq


title: HD37_BG_4h_RNA-seq


title: Whole blood, SJ04


title: HD37_RPMI_d6_RNA-seq


title: Whole blood, SGH06


title: Whole blood, SJ01


title: Whole blood, SGH07


title: HD37_T0_RNA-seq

value: attached for 1 hour


title: HD37_BG_24h_RNA-seq

value: 24 hours in media with B-glucan


title: Whole blood, SGH11


title: HD49_T0_RNA-seq


title: Whole blood, SGH09


title: HD34_BG_d6_RNA-seq

value: 24 hours in media with B-glucan, then 5 days in media


title: Whole blood, SGH02


title: HD37_RPMI_d6_LPS_4h_RNA-seq

value: 6 days in media and then LPS for 4 hours


title: Whole blood, SGH01


title: HD37_RPMI_4h_RNA-seq

value: Monocyte


title: HD37_Hemin_4h_RNA-seq


title: Whole blood, SGH08


title: Whole blood, QC29

value: Qinchuan cattle


title: HD34_BG_d6_LPS_4h_RNA-seq


title: Whole blood, SGH05


title: HD34_Hemin_d6_LPS_4h_RNA-seq

value: 24 hours in media with Hemin, then 5 days in media, then LPS for 4 hours


title: Whole blood, SGH04


title: HD34_RPMI_d6_LPS_4h_RNA-seq


title: HD34_Hemin_24h_RNA-seq


title: HD34_BG_4h_RNA-seq


title: Whole blood, QC26


title: Whole blood, SGH03


title: Whole blood, SGH10


title: HD34_Hemin_d6_RNA-seq

value: 24 hours in media with Hemin, then 5 days in media


title: Whole blood, QC30


title: HD34_Hemin_4h_RNA-seq


title: HD34_RPMI_d6_4h_RNA-seq

value: 6 days and 4 hours in media


title: Whole blood, QC23


title: Whole blood, WN16

value: Weining cattle


title: HD34_RPMI_d6_RNA-seq

value: 6 days in media


title: Whole blood, QC20


title: HD34_BG_24h_RNA-seq


title: Whole blood, QC19


title: Whole blood, QC28


title: Whole blood, QC27


title: Whole blood, QC24


title: Whole blood, QC18


title: Whole blood, QC21


title: HD34_RPMI_4h_RNA-seq

value: 4 hours in media


title: HD34_T0_RNA-seq


title: HD34_RPMI_24h_RNA-seq

value: 24 hours in media


title: Whole blood, QC22

value: Female


title: Whole blood, QC25

value: Whole blood


title: Whole blood, QC14


title: Whole blood, QC15


title: 4434_+dox_day20_2

city: Heidelberg

first: Jochen

last: Utikal

address: Im Neuenheimer Feld 280

department: Clinical Cooperation Unit Dermato-Oncology

country: Germany

institute: German Cancer Research Center

description: Gene expression data from cells reprogrammed partially at day 20 a

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were analyzed with Chispter using Affymetrix default analysis settings

source_name: melanoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: All cells were culture under standar conditions of CO2 and temperature.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed.

treatment_protocol: Cells were treated with doxycycline to induce expression of Sox2, Oct4 and Klf4 murine genes

tag: dox

value: plus


title: 4434_-dox_day20_3

description: Gene expression data from control cells (non induced with doxycycline) at day 20

value: neg


title: Whole blood, QC12


title: 4434_+dox_day20_3


title: Whole blood, QC13


title: Whole blood, QC17


title: Whole blood, QC16


title: Whole blood, QC11


title: Whole blood, QC10


title: Whole blood, QC08


title: 4434_-dox_day20_2


title: Whole blood, QC06


title: C790_+dox_DMSO_day20_3

description: Gene expression data from reprogrammed cells

treatment_protocol: Cells were treated with DMSO and trametinib for 72 hours.

tag: treatment

value: DMSO day 20


title: D10

city: Harbin

first: Shuli

last: Tang

state: Heilongjiang Province

address: Haping Road No.150, Nangang District

institute: Harbin Medical University Cancer Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include readcount values for each Sample

source_name: Serum exosomal miRNA_healthy

extract_protocol:
Exosomes were isolated using the ExoQuick exosome precipitation solution (System Biosciences, Mountain View, CA, USA) according to the manufacturer’s instructions with slight modifications.RNA of exosomes was isolated using miRNeasy micro kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s protocol. The extracted RNA was eluted with 14 μL of RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy individual

tag: age

tag: tumor stage

value: control

tag: sample

value: serum exosome


title: D11


title: 4434_-dox_day20_1


title: C790_+dox_Trametinib_day20_3

value: trametinib day 20


title: 4434_+dox_day20_1


title: Whole blood, QC01

tag: gender

tag: breed

value: Qinchuan cattle

tag: altitude (m)


title: Whole blood, NY14

value: Nanyang cattle

tag: longitude

tag: latitude


title: C790_-dox_Trametinib_day20_ 3

description: Gene expression data from control

tag: cell type


title: C790_+dox_Trametinib_day20_2


title: C790_+dox_DMSO_day20_2


title: C790_-dox_DMSO_day20_3

description: Gene expression data from control


title: C790_-dox_Trametinib_day20_ 2

description: Gene expression data from control


title: C790_-dox_Trametinib_day20_ 1

description: Gene expression data from control


title: Whole blood, QC09

tag: tissue


title: D07


title: HD50_BG_24h

value: Monocyte

value: 24 hours in media with B-glucan

tag: chip antibody

value: Rabbit polyclonal anti-H3K27ac (Diagenode, cat. # pAb-196-050)


title: D06


title: Whole blood, QC05


title: Whole blood, NY11


title: Whole blood, QC07


title: Whole blood, NY09


title: Whole blood, QC04


title: Whole blood, NY08


title: D12


title: Whole blood, QC03


title: C12

source_name: Serum exosomal miRNA_patient

value: gastric cancer patient

value: IIB


title: C790_+dox_Trametinib_day20_1


title: C790_-dox_DMSO_day20_2

description: Gene expression data from control


title: Whole blood, NY05


title: Whole blood, QC02


title: C790_-dox_DMSO_day20_1

description: Gene expression data from control


title: D09


title: Whole blood, NY03


title: D08


title: Whole blood, NY13


title: Whole blood, NY12


title: D05


title: C790_+dox_DMSO_day20_1


title: Whole blood, MWY18

value: Maiwa yak


title: Whole blood, NY10

value: Female


title: C06

value: IB


title: C05


title: C03


title: Whole blood, NY02

value: Whole blood


title: D04


title: Whole blood, NY07


title: D03


title: D02


title: D01


title: C11


title: Whole blood, NY04


title: Whole blood, MWY14


title: C10


title: C01

value: IA


title: Whole blood, MWY11


title: Whole blood, NY06


title: C08

value: IIA


title: Whole blood, NY01


title: B10


title: B11


title: Whole blood, MWY17


title: C07


title: Whole blood, MWY16


title: B09


title: Whole blood, MWY09


title: C09


title: B06


title: C04


title: Whole blood, MWY13


title: Whole blood, MWY12


title: Whole blood, MWY15


title: Whole blood, MWY05


title: B12


title: C02


title: B08


title: Whole blood, MG07

value: Menggu cattle


title: Whole blood, MWY04


title: Whole blood, MWY01


title: B01


title: B04


title: A12


title: Whole blood, MWY08


title: Whole blood, MWY07


title: B07


title: Whole blood, MWY06


title: B05


title: B03


title: A10


title: Whole blood, MG04


title: Whole blood, MWY03


title: Whole blood, MWY02


title: A08


title: B02


title: Whole blood, MG03


title: Whole blood, MG02


title: Whole blood, MG06


title: A09


title: Whole blood, MG01


title: Whole blood, MG05


title: A05


title: A07


title: Whole blood, LX08

value: Luxi cattle


title: A06

value: serum exosome


title: Whole blood, LX12


title: Whole blood, LX11


title: A01


title: Whole blood, MWY10


title: A04


title: Whole blood, LX07


title: A03


title: A11


title: Whole blood, LX04


title: A02


title: Whole blood, LX03


title: Whole blood, LX10


title: Whole blood, LX09


title: Cold-sensitive rice under low temperature stress (10°C for up to 10 days), biological rep1

city: Lajeado

first: Raul

middle: Antonio

last: Sperotto

address: Av. Avelino Talini, 171

department: Biological Sciences and Health Center

country: Brazil

institute: University of Taquari Valley - Univates

description:
IRGA 959-1-2-2F-4-1-4-D-1-CA-1
Gene expression data from roots of Cold-sensitive rice exposed for ten days under low temperature stress (10°C )

data_processing:
cDNA sequencing by Illumina HiSeq 2000 technology (Fasteris SA, Plan-les-Ouates, Switzerland - http://www.fasteris.com/).
The cDNA libraries were prepared according to Illumina’s protocols. Briefly, RNAseq was performed using the following successive steps: poly-A purification; cDNA synthesis using a poly-T primer, shotgun method to generate inserts of approximately 500 bp; 3p and 5p adapter ligations; pre-amplification; colony generation; and Illumina single-end 50 bp sequencing.
Low quality reads (FASTq value <13) were removed, and 3p and 5p adapter sequences were trimmed using Genome Analyzer Pipeline (Fasteris).
The remaining low quality reads with ‘n’ were removed using Python script. After cleaning the data (low quality reads, adapter sequences), the mRNAseq data from the eight libraries was aligned to the rice genome using the software Bowtie version 0.12.7.
Genome_build: Only sequences with up to two mismatches to the rice reference genome (ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/peudomolecules/version_6.1/all.dir/all.seq) were used.
Supplementary_files_format_and_content: tab-delimited text files include reads for each Sample

organism: Oryza sativa

source_name: Roots

growth_protocol: Seeds from both selected genotypes were germinated for five days in distilled water and then transferred to holders positioned over plastic pots covered with aluminum foil and containing 300 mL of nutrient solution . The pH of the nutrient solution was adjusted to 5.4. Plants were kept at 28°C ± 1°C under photoperiod of 16 h / 8 h light/dark (150 μmol.m-2.s-1). Solutions were replaced every two days.

extract_protocol:
Total RNA was extracted from rice roots using Concert Plant RNA Reagent (Invitrogen®) and treated with DNase I (Invitrogen®).
Approximately 20 µg of total RNA were used in high-throughput cDNA sequencing by Illumina HiSeq 2000 technology (Fasteris SA, Plan-les-Ouates, Switzerland - http://www.fasteris.com/). We constructed two individual single-end cDNA library for each rice genotype (cold tolerant and sensitive), after 24 h of cold or control treatment, totalizing eight libraries (four plants per library). The cDNA libraries were prepared according to Illumina’s protocols. Briefly, RNAseq was performed using the following successive steps: poly-A purification; cDNA synthesis using a poly-T primer, shotgun method to generate inserts of approximately 500 bp; 3p and 5p adapter ligations; pre-amplification; colony generation; and Illumina single-end 50 bp sequencing.

treatment_protocol: At the three-leaf stage (approximately 30 days), plants were transferred to a growth chamber and maintained at 10°C (or control condition at 28°C) for up to 10 days (light intensity of 100 μmol.m-2.s-1).

tag: cultivar

value: indica

value: Seeds from both selected genotypes were germinated for five days in distilled water and then transferred to holders positioned over plastic pots covered with aluminum foil and containing 300 mL of nutrient solution . The pH of the nutrient solution was adjusted to 5.4. Plants were kept at 28degreeC ± 1degreeC under photoperiod of 16 h / 8 h light/dark (150 umol.m-2.s-1). Solutions were replaced every two days.

tag: developmental stage

value: At the three-leaf stage (approximately 30 days), plants were transferred to a growth chamber and maintained at 10degreeC (or control condition at 28degreeC) for up to 10 days (light intensity of 100 umol.m-2.s-1).

tag: group

value: Cold-sensitive

tag: protocol

value: low temperature stress


title: Cold-sensitive rice under control solution, biological rep2

description:
IRGA 959-1-2-2F-4-1-4-D-1-CA-1
Gene expression data from roots of Cold-sensitive rice in control condition at 28°C

value: control condition


title: Cold-tolerant rice under low temperature stress (10°C for up to 10 days), biological rep2

description:
IRGA 959-1-2-2F-4-1-4-A
Gene expression data from roots of Cold-tolerant rice exposed for ten days under low temperature stress (10°C )

value: Cold-tolerant


title: Cold-sensitive rice under control solution, biological rep1


title: Cold-tolerant rice under low temperature stress (10°C for up to 10 days), biological rep1


title: Whole blood, LX01


title: Cold-sensitive rice under low temperature stress (10°C for up to 10 days), biological rep2


title: Whole blood, LS13

value: Liangshan cattle


title: Whole blood, LS12


title: Cold-tolerant rice under control solution, biological rep2

description:
IRGA 959-1-2-2F-4-1-4-A
Gene expression data from roots of Cold-tolerant rice in control condition at 28°C


title: Whole blood, LS11


title: Cold-tolerant rice under control solution, biological rep1


title: Whole blood, LX05


title: Whole blood, LS10


title: Whole blood, LX02


title: Whole blood, LS08


title: Whole blood, LS05


title: Whole blood, LS06


title: Whole blood, LS04


title: AID-4_PP_IgH_GC

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine (PCMM)

institute: Boston Children's Hospital / Harvard Medical School

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).

source_name: Peyer's Patches germinal center 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: AID-deficient mice SPF

value: Peyer's Patches

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

value: IgH


title: AID-1_PP_IgH_GC


title: AID-2_PP_IgH_GC


title: AID-3_PP_IgH_nonGC

source_name: Peyer's Patches naïve B cells


title: AID-4_PP_IgH_nonGC


title: AID-3_PP_IgH_GC


title: AID-2_PP_IgH_nonGC


title: Whole blood, LS02

value: Female

value: Whole blood


title: Whole blood, LS09


title: Whole blood, LS01


title: Whole blood, LS03


title: AID-1_PP_IgH_nonGC


title: WT mouse liver

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

institute: Medical Institute of Bioreguration, Kyushu University

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Mouse Gene Expression Microarray 4x44K v2; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of all samples were normalized by the quantile algorithm with the Bioconductor.

source_name: liver

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

tag: genotype

value: Wild-type

value: liver


title: SRBC8d-4_SP_IgH_GC

source_name: splenic germinal center B cells

value: SRBCs IP immunization 8 day

value: spleen


title: SRBC8d-4_SP_IgH_nonGC

source_name: splenic naïve B cells


title: SRBC8d-3_SP_IgH_GC


title: Whole blood, LQ12

value: Leiqiong cattle


title: Whole blood, LS07


title: Whole blood, LQ11


title: SRBC8d-3_SP_IgH_nonGC


title: Whole blood, LQ10


title: Whole blood, LQ09


title: Alb-Cre;CAG-floxed neo-Snail mouse liver

value: Alb-Cre;CAG-floxed neo-Snail


title: SRBC8d-2_SP_IgH_GC


title: SRBC8d-2_SP_IgH_nonGC


title: Whole blood, LQ07


title: SRBC8d-1_SP_IgH_GC


title: SRBC8d-1_SP_IgH_nonGC


title: Whole blood, LQ05


title: SFB-4_PP_IgL_nonGC

value: GF+SFB

value: IgL


title: Whole blood, LQ04


title: SFB-4_PP_IgL_GC


title: SFB-3_PP_IgL_GC


title: Whole blood, LQ01


title: Whole blood, LQ02


title: SFB-3_PP_IgL_nonGC


title: SFB-2_PP_IgL_GC


title: SFB-1_PP_IgL_GC


title: SFB-2_PP_IgL_nonGC


title: SFB-1_PP_IgL_nonGC


title: GF-5x3_PP_IgL_GC

value: GF


title: GF-5x3_PP_IgL_nonGC


title: Whole blood, LQ08


title: Whole blood, JXR12

value: Jiaxian Red cattle


title: Whole blood, JXR09


title: Whole blood, JXR10


title: Whole blood, JXR08


title: Whole blood, LQ06


title: GF-3x3_PP_IgL_GC


title: Whole blood, LX06

value: Luxi cattle


title: Whole blood, JXR06


title: Whole blood, JXR14


title: Whole blood, LQ03


title: Whole blood, JXR04


title: GF-3x3_PP_IgL_nonGC


title: GF-2x3_PP_IgL_GC


title: Whole blood, JXR11


title: Whole blood, JXR03


title: SPF-16_PP_IgL_nonGC

value: GF+SPF


title: Whole blood, JXR01


title: GF-2x3_PP_IgL_nonGC


title: SPF-15_PP_IgL_nonGC


title: GF-4x3_PP_IgL_GC


title: SPF-14_PP_IgL_GC


title: Whole blood, JN14

value: Jinnan cattle


city: San Francisco

first: Sahar

last: Houshdaran

address: 513 Parnassus Ave HSE1619

department: OB/GYN

institute: UCSF

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

hyb_protocol: Sodium bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Minfi in GenomeStudio.
matrix_processed_*.txt: Average Beta values, Detection Pvals
matrix_signal_intensities_*.txt: Unmethylated and methylated signal intensities, Detection Pvals

label: Cy5 and Cy3

source_name: Endo IV-4 E2+P4

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA of hormone treated eSF cells was extracted using Qiagen DNeasy Blood and Tissue Kit according to manufacturer's recommendations.

value: Eutopic endometrial stromal fibroblasts

tag: disease state

value: Endometriosis Stage IV

tag: treatment

tag: individual

value: Endo IV-4


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

source_name: Endo IV-4 Veh

tag: gender

value: Female

value: vehicle


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

source_name: Endo IV-4 P4


title: SPF-14_PP_IgL_nonGC

value: Peyer's Patches


title: Whole blood, JN13

source_name: Jugular vein

tag: breed

tag: altitude (m)

tag: longitude

value: Whole blood


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

source_name: Endo IV-4 E2

tag: cell type


title: Whole blood, JN12

tag: latitude

tag: tissue


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

source_name: Endo IV-3 E2+P4


title: Whole blood, JXR07


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

source_name: Endo IV-3 P4


title: Whole blood, JXR02


title: SPF-6_PP_IgL_GC


title: SPF-15_PP_IgL_GC


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

source_name: Endo IV-3 E2


title: SPF-6_PP_IgL_nonGC


title: Whole blood, JN10


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

source_name: Endo IV-2 Veh

value: Endo IV-2


title: SPF-16_PP_IgL_GC


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

source_name: Endo IV-2 E2+P4


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

source_name: Endo IV-2 P4


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

source_name: Endo IV-2 E2


title: SPF-5_PP_IgL_GC

source_name: Peyer's Patches germinal center B cells


title: Whole blood, JN09

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


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

source_name: Endo IV-1 Veh

value: Endo IV-1


title: Whole blood, JN08


title: SPF-4_PP_IgL_GC


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

source_name: Endo IV-1 E2+P4


title: Whole blood, JN07


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

source_name: Endo IV-1 P4


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

source_name: Endo IV-1 E2


title: SPF-4_PP_IgL_nonGC

source_name: Peyer's Patches naïve B cells


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

source_name: Endo I-4 Veh

value: Endometriosis Stage I

value: Endo I-4


title: Whole blood, JN06

source_name: Jugular vein


title: Whole blood, JN11


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

source_name: Endo I-4 E2+P4


title: SPF-3_PP_IgL_GC

value: IgL


title: Whole blood, JN05


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

source_name: Endo I-4 E2


title: Whole blood, JN04


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

source_name: Endo I-3 Veh

value: Endo I-3


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

source_name: Endo I-3 E2+P4


title: SPF-3_PP_IgL_nonGC


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

source_name: Endo I-4 P4


title: SPF-2_PP_IgL_GC


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

source_name: Endo I-3 E2


title: SPF-5_PP_IgL_nonGC


title: SPF-2_PP_IgL_nonGC


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

source_name: Endo I-2 Veh

value: Endo I-2


title: Whole blood, JN03


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

source_name: Endo I-2 E2+P4


title: Whole blood, JN02


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

source_name: Endo I-2 P4


title: SPF-1_PP_IgL_GC

source_name: Peyer's Patches germinal center B cells

value: GF+SPF


title: Whole blood, JN01

value: Jinnan cattle


title: Whole blood, JA18

value: Ji'an cattle


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

source_name: Endo I-2 E2

value: Eutopic endometrial stromal fibroblasts


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

source_name: Endo I-1 Veh

value: Endo I-1


title: singlePP-1PP7_IgH_GC

value: SPF

value: IgH


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

source_name: Endo I-1 E2

value: Female


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

source_name: Endo I-1 P4


title: Whole blood, JA17

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

value: Whole blood


title: singlePP-1PP6_IgH_GC

value: Peyer's Patches


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

value: Normal


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

value: vehicle


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

source_name: Endo I-3 P4

value: Endometriosis Stage I


title: singlePP-1PP7_IgH_nonGC

source_name: Peyer's Patches naïve B cells


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


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


title: Whole blood, JA15

source_name: Jugular vein


title: Whole blood, JA14


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


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


title: singlePP-1PP6_IgH_nonGC


title: singlePP-1PP5_IgH_GC


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


title: Whole blood, JXR13

value: Jiaxian Red cattle


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

source_name: Endo I-1 E2+P4


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


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


title: Whole blood, JA12


title: singlePP-1PP5_IgH_nonGC


title: Whole blood, JA13


title: Whole blood, JA16


title: singlePP-1PP4_IgH_GC


title: Whole blood, JA11


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


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


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


title: Whole blood, JA10


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


title: singlePP-1PP4_IgH_nonGC


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


title: singlePP-1PP3_IgH_GC


title: SPF-1_PP_IgL_nonGC

value: IgL


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


title: Whole blood, JA09

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


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


title: Whole blood, JA08


title: singlePP-1PP3_IgH_nonGC


title: method_validation_Vld1,2_bait_rep3

source_name: v-Abl pro-B cell line

value: C57BL/6, 129sve mixed

value: Cer/Sis-deleted

value: bone marrow


title: Whole blood, JA07


title: Whole blood, JA06


title: method_validation_Vk3d_bait_rep3


title: method_validation_mixed_JL_baits_rep3


title: Whole blood, JA05


title: method_validation_Vld1,2_bait_rep2


title: Whole blood, JA04


title: Whole blood, JA03


title: method_validation_mixed_JL_baits_rep2


title: Whole blood, JA02


title: method_validation_Vk3d_bait_rep2


title: Whole blood, JA01


title: method_validation_Vk3d_bait_rep1


title: Whole blood, HSK15

value: Hazake cattle


title: 1244 PXI (05.10.15)

city: Hennigsdorf

first: Martina

last: Schad

address: Neuendorfstrasse 16b

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.

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: skin


title: 200 PXI

value: PXI


title: 200 PXII

value: PXII


title: GF-4x3_PP_IgL_nonGC

value: GF


title: 1214 PVIII

value: PVIII


title: method_validation_mixed_JL_baits_rep1


title: 1117 PXIII

value: PXIII


title: 1244 PXI (02.06.15)


title: 1196 PX

value: PX


title: 1196 PVIII


title: Whole blood, HSK14

value: Female

value: Whole blood


title: method_validation_Vld1,2_bait_rep1


title: 1244 PX


title: 1244 PIX

value: PIX


title: 1196 PXI (08.04.15)


title: 1196 PXI (23.06.15)


title: 1214 PX


title: 1214 PXIII


title: 200 PX


title: 1214 PXI


title: method_validation_mixed_JH_baits_rep3

source_name: splenic naïve B cells

value: SPF

value: spleen

value: IgH


title: 200 PVIII


title: 1117 PXI (07.04.15)


title: Whole blood, HSK13


title: Whole blood, JXR05

value: Jiaxian Red cattle


title: method_validation_hVH1-2_bait_rep3


title: Whole blood, HSK12


title: 1117 PXII


title: 1098 PX


title: 1117 PXI (01.10.15)


title: method_validation_mixed_JH_baits_rep2


title: Whole blood, HSK11


title: Whole blood, HSK10


title: Whole blood, HSK07


title: method_validation_mixed_JH_baits_rep1


title: GF+SPFfeces-10_PP_IgH_GC

value: GF+SPF

value: Peyer's Patches


title: 1098 PVII

value: PVII


title: Whole blood, HSK09

value: Hazake cattle


title: 1098 PVIII

value: skin