title: EBO3_mut_15

city: Zürich

first: Youjin

last: Teo

address: Gloriastrasse 30

department: Institut für Medizinische Mikrobiologie

country: Switzerland

institute: Universität Zürich

data_processing:
Basecalls performed using CASAVA 1.8 and convered into fastq files with bcl2fastq-1.8.4
RNA-Seq reads were aligned to Ensembl GRCh37 genome assembly using STAR_2.4.2a with following parameters: --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Counts were generated with the function featureCounts in the Rsubreads package.
Genome_build: GRCh37
Supplementary_files_format_and_content: count file was generated with the function featureCounts in the Rsubreads package. The numbers are raw counts.

source_name: cell culture

growth_protocol: HEK293 cells stably transfected with RPS2 wild-type or RPS2 A226Y mutant expressing constructs were cultured in Dulbecco's MEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA from cell culture samples was isolated using RNeasy Mini Kit (Qiagen). Total RNA from muscle samples was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: RPS2 A226Y


title: EBO3_mut_14

status: Public on Sep 24 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: EBO3_mut_25


title: in vitro biofilm, 86-5_RNA_S3

city: Columbus

first: Alistair

last: Harrison

state: OH

address: 700 Children's Drive

department: Center for Microbial Pathogenesis

country: USA

institute: The Research Institute at Nationwide Children's Hospital

description: nontypeable Haemophilus influenzae

data_processing:
Image analysis and base calling were performed with XXSequence Analysis Viewer tool
Each sample was aligned to the 86-028NP  reference genome (NCBI; GCA_000012185.1) using the BWA-MEM aligner
Feature coverage counts were calculated using HTSeq and differentially expressed features were calculated using DESeq2
Genome_build: NCBI; GCA_000012185.1
Supplementary_files_format_and_content: Raw and normalized abundance measurements

organism: Haemophilus influenzae

source_name: in vitro biofilm

growth_protocol: Suspensions of bacteria in iron chelated defined iron source (DIS) medium were adjusted to an OD490 of ~0.65 , diluted 10-fold and subcultured into nitric acid-washed 15 ml round bottom glass tubes containing pre- warmed DIS medium with 2 mg/ml of  heme. After static growth for 24 hours at 37˚C in 5% CO2 . Cultures were then equilibrated to an OD490 of ~0.37 and diluted to a concentration of ~ 1E+07 CFU/ml in DIS containing 2 mg /ml of heme . Fifty microliters were then added to each well of a Nunc Lab-Tek 8- well chamber slide containing 200 µl of DIS supplemented with 2mg/ml of  heme. The chamber slide was then incubated at 37˚C with 5% CO2 for 48  with a medium change at 24 hours.

extract_protocol:
Biofilms were scrapped form the chamber suraces and added directly to hot phenol. RNA was purified as described in Santana et al (2014; PMID:25157846)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 86-028NP (parental)

tag: sample type

value: in vitro biofilm


title: in vitro biofilm, 86-6_RNA_S4

description: nontypeable Haemophilus influenzae


title: 6057841100_R04C01

type: genomic

city: Vancouver

first: Michael

middle: S.

last: Kobor

state: BC

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: Centre for Molecular Medicine and Therapeutics / University of British Columbia

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

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

data_processing:
GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)
Average Beta (after background-subtraction and colour-correction in GenomeStudio software according to standard Illumina protocol)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: buccal swab genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: Buccal epithelial cells were collected with using Isohelix Buccal Swabs (Cell Projects, Harrietsham, Kent, England) and stabilized per manufacturer’s instructions for storage at room temperature. Genomic DNA was isolated using Isohelix Buccal DNA Isolation Kits (Cell Projects, Harrietsham, Kent, England), and then purified and concentrated using DNA Clean & Concentrator (Zymo Research, Irvine, CA)

tag: age

tag: gender

value: M


title: 6057841100_R03C01


title: EBO3_WT-23

value: RPS2 WT


title: EBO3_WT-21


title: MeDIP_seq_3B3_serum

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: mapped reads (mm10) were binned across 200bp windows.

library_source: genomic

data_processing:
Reads mapped to mm10 mouse build in the cloud using TMAP software
Data binned into 200bp windows across the genome
Data converted into mm9 build and into a wiggle (.wig) file
data normalised by read count
enriched (5mC) datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph file

organism: Mus musculus

source_name: DNMT 3B3/3L mutant mouse J1 ESCs

growth_protocol: J1 mESCs were cultured in Dulbecco's Modified Eagle's medium (DMEM) high-glucose (Life Technologies™) supplemented with 15% FCS (Sigma), 1x Non-essential amino acids (Sigma), 1mM Sodium Pyruvate (Sigma), 2mM L-glutamine (Life Technologies™), 50µg/ml Penicillin/Streptomycin, 100μM beta-mercaptoethanol (Gibco) and 500U/ml ESGRO LIF ESG1107 (Millipore). J1 mESCs were grown on Mitomycin C inactivated SNLP feeder cells, 2i cells were grown feeder free on 0.2% gelatin-coated plates or flasks following culturing conditions as described in Ying et al 2008.

extract_protocol:
Sheared gDNA was enriched using antibodies of choice. prior to enrichment through magnetic IgG beads . Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 18 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

tag: culture condition

value: Serum

tag: strain/cell type

value: J1 - Dnmt3b & 3l hyperactive

tag: cell type

value: mESC

tag: antibody

value: Anti 5mc - Eurogentec BI-MECY-0101


title: EBO3_WT-20


title: in vitro biofilm, 86-2_RNA_S2

description: nontypeable Haemophilus influenzae


title: 6057841100_R02C01


title: hMeDIP_seq_J1_serum

source_name: mouse J1 ESCs

value: Anti 5-hmC - Active Motif (cat# 39769)


title: Retina: Sample 21

city: Iowa City

first: Matthew

last: Harper

state: IA

address: Bldg 42 VAMC

institute: University of Iowa

data_processing:
Enriched RNA pool was fragmented, converted to cDNA and ligated to sequencing adaptors containing indexes using the Illumina TruSeq stranded mRNA sample prep kit (Cat. #RS-122-2101)
Libraries were sequenced on the Illumina HiSeq 4000 genome sequencer using 150 bp paried-end SBS chemistry, then mapped to mm10 whole genome using STAR (v2.5.3a)
We used featureCounts from the subreads package (v1.5.2) to quantify transcripts at the gene level.
Downstream analyses used the R (v3.3.2) packages DESeq2 for differential expression.
Genome_build: mm10

source_name: Retina

extract_protocol:
RNA extraction using Qiagen RNEasy Mini Kit per manufacturers instruction. Illumina TruSeq stranded mRNA Sample Prep Kit (Cat#RS-122-2101) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each mouse was subjected to a specific blast condition mentioned in SAMPLES section

tag: tissue

value: retina

tag: injury

value: sham (5 PSI then 5 PSI)


title: EBO3_WT-19


title: 6057841098_R06C02

value: F


title: TEPA+Hypoxia_Input DNA

city: Chengdu

first: Zhijuan

last: Wu

state: Sichuan

address: Keyuan Road 4, Gaopeng avenue

department: Sichuan University West China Hospital

country: China

institute: Regenerative Medicine Research Center

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
ChIP-seq reads were aligned to the GRCh38 genome assembly using Bowtie aligner version 2.0 with default parameters.
Data were filtered using the following specifications
MACS2 peak finding algorithm (version 2.1.0) was used to identify regions of ChIP-seq enrichment over background (qvalue < 0.05).
Genome_build: GRCh38
Supplementary_files_format_and_content: bw files were generated using deeptools.

growth_protocol: EA.Hy926 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen, USA) supplemented with 10% fetal bovine serum (FBS, Natocor, ARG). Cells were routinely cultured in a standard culture incubator with humidified air containing 5% CO2 at 37℃. Hypoxic conditions were introduced by incubating cells in a tri-gas incubator for 8 h with oxygen concentration in 1%. For treatment with reagents, cells were seeded in 6-well plates or 150 mm petri dishes and grown overnight. Thereafter, a final concentration of 50 μM TEPA (Sigma, USA) in the culture was added to the cultures for 16 h, followed by further incubation in normoxia or hypoxia for additional 8 h.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The purified DNA fragments were blunt-ended, ligated to the Solexa paired-end adaptors by using NEBNext Ultra II DNA Library Prep kit and NEBNext Multiplex Oligos kit (NEB, USA) to build the libraries and tested by Agilent 2200.

value: Human umbilical vein endothelial cell line

tag: chip antibody


title: MeDIP_seq_J1_14d_2i_IP

data_processing:
Reads mapped to mm10 mouse build in the cloud using TMAP software
Data binned into 200bp windows across the genome
Data converted into mm9 build and into a wiggle (.wig) file
data normalised by read count
enriched (5mC) datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph file of input-normalized signal

source_name: mouse J1 ESCs converted in 2i

extract_protocol:
Sheared gDNA was enriched using Anti 5mc - Eurogentec BI-MECY-0100. prior to enrichment through magnetic IgG beads (Dynabeads M-280 sheep anti-mouse IgG. Dynal Biotech #112.01). Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 18 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

value: 14 day 2i media

value: Anti 5mc - Eurogentec BI-MECY-0100


title: MeDIP_seq_J1_14d_2i_input

value: none (input)


title: PDS DRIP-seq + RnaseH

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

country: Italy

institute: University of Bologna

description: This library serves as a negative control of DRIP-seq experiments. The substantial absence of enriched regions is an expected result, therefore the processed peakdataset contains only few peaks.

data_processing:
Adapters trimming performed with Trimmomatic version 0.35
Reads mapping on human genome (hg19) performed with BWA version 0.7.12 with parameters -n 2 -t 8
Reads filtering by Merged Consensus blacklist fron ENCODE (ftp://encodeftp.cse.ucsc.edu/users/akundaje/rawdata/blacklists/hg19/wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz) and duplicates removal with Samtools version 1.3.1
Peak calling performed with MACS2 version 2.1.1.20160309 with parameters -q 0.05 -m 5 50 -g hs -f BAMPE
Genome_build: hg19
Supplementary_files_format_and_content: Bed files produced by macs2

source_name: U2OS cells

growth_protocol: U2OS cells were grown in Dulbecco's modified Eagle's medium (DMEM, Carlo Erba Reagents) supplemented with 10% fetal bovine serum (FBS, Carlo Erba Reagents) and 2 mM L-glutamine (Carlo Erba Reagents). Cell lines were maintained by trypsinization and splitting 2-3 times a week, and incubated at 37°C in 5% CO2.

extract_protocol:
gDNA was extracted from lysated cells, digested using a restriction enzyme cocktail , incubated with S9.6 antibody and immunoprecipitated
genomic DNA were sonicated. Ligation of Illumina Truseq adapters was performed according to manufacturer’s instructions.

value: bone

tag: disease

value: osteosarcoma

tag: treatment

value: RnaseH


title: 6057841098_R05C02


title: MeDIP_seq_J1_serum_input


title: 6057841098_R04C02

value: M


title: MeDIP_seq_3B3_14d_2i

source_name: DNMT 3B3/3L mutant mouse J1 ESCs converted in 2i


title: MeDIP_seq_J1_serum_IP


title: 6057841098_R03C02


title: Control DRIP-seq + RnaseH


title: Liver_adult_2

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Whole cell RNA from tissue

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Genome_build: Human rDNA (18S, 28S, 5.8S, 5S). The reference sequences are in Supplementary_Data_1.fasta
Supplementary_files_format_and_content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.

source_name: Liver

extract_protocol:
Tissues were homogenized and whole cell RNA was extracted using Tri-Reagent (Euromedex) according to the manufacturers instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: Liver

tag: developmental stage

value: adult


title: Hypoxia_Input DNA


title: TEPA+Hypoxia_HIF1A_ChIPSeq

value: HIF-1alpha (Novus, NB100-134)


title: control_peripheral blood_00032

city: Ji'nan

first: Huang

last: Guangyong

address: Cultural West Road,No.44

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were mapped to human genome (ucsc hg19) by hisat2 (v2.04) software with default parameters.
Cuffdiff2 software (v2.2.1) was used to perform differentially expressed gene analysis.
Genome_build: hg19
Supplementary_files_format_and_content: excel format; raw and normalized counts

source_name: control_peripheral blood

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA)

tag: subject status

value: healthy control

value: male

tag: age (yrs)

value: peripheral blood


title: pXEN_vesicle_CHIR_Serum_free, 2

city: Ansan

first: Yixiang

last: Zhong

state: Gyeonggi-do

address: 55 Hanyangdeahak-ro, Sangnok-gu

country: South Korea

institute: Hanyang University

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
To avoid low-quality data , we clipped and trimmed the reads using Trimmomatic (v0.38)
For the analysis of differentially expressed genes, the data of quality-checked reads for each condition were processed with the STAR (version 2.6.1) software based on reference genome sequence (Rattus norvegicus UCSC rn6) and the gene annotation was depended on Ensembl Release 94.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Rattus norvegicus UCSC rn6
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

organism: Rattus norvegicus

source_name: blastocyst

growth_protocol:
Normal cells were cultured essentially as previously described (Lo Nigro et al., 2012).
Vacuolated cells were culture with 14% BCS or 0.5μM Chir99021 in routine culture condition as previously described (Lo Nigro et al., 2012).
Vesicles were cultured with 10ng/ml murine LIF and 3μM Chir99021 in N2B27 medium as previously described but without MEF, PD0325901, Y-27632 (Yaoyao Chen et al., 2017).

extract_protocol:
RNA was extracted using RNAiso Plus (Takara, Shiga, Japan) and QIAGEN RNeasy® Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext® Ultra™ Directional RNA Library preparation kit from Illumina® (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMius™ Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ‘A’ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2500 (101 cycles PE lane).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: rat XENP

value: WKY

tag: passages

value: Female


title: TEPA+Hypoxia_Pol II_ChIPSeq

tag: cell line

value: Human umbilical vein endothelial cell line

value: Pol II (Abcam, ab5408)


title: FG DRIP-seq + RnaseH


title: pXEN_vesicle_CHIR_Serum_free, 3

tag: strain


title: in vitro biofilm, 86-1_RNA_S1

description: nontypeable Haemophilus influenzae

value: 86-028NP (parental)

tag: sample type

value: in vitro biofilm


title: pXEN_vesicle_CHIR_Serum_free, 1

tag: gender


title: Hypoxia_H3K27ac_ChIPSeq

value: H3K27ac (Abcam, ab4729)


title: 6057841100_R01C01

tag: age


title: control_peripheral blood_00030


title: TEPA+Hypoxia_H3K27ac_ChIPSeq


title: Hypoxia_Pol II_ChIPSeq


title: 6057841098_R01C02


title: control_peripheral blood_00029

value: female


title: pXEN_vesicle_CHIR_Serum, 3


title: 6057841098_R05C01


title: pXEN_vesicle_CHIR_Serum, 2


title: Hypoxia_HIF1A_ChIPSeq


title: 6057841098_R04C01

value: F


title: TEPA+Hypoxia_rep3_RNA-seq

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the human reference genome (GRCh38) using HISAT2 (version 2.1.0) .
Read counts were calculated, and then DESeq (Log2FC > 1 or < -1, FDR < 0.05) was used for differential analysis of gene expression.
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for all samples.

extract_protocol:
Cells were cllected on ice and RNA was extracted from each sample using TRIzol reagent (Invitrogen, 15596-026, USA) according to the manufacturer’s instruction. The concentration and quality of each sample was measured by Agilent Technologies 2200 TapeStation (Life Technologies, USA).
NEBNext ultra directional RNA Library Prep kit, NEBNext Poly (A) mRNA magnetic isolation module and NEBNext multiplex oligos (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.


title: control_peripheral blood_00028


title: pXEN_vesicle_CHIR_Serum, 1


title: control_peripheral blood_00025


title: control_peripheral blood_00031


title: TEPA+Hypoxia_rep2_RNA-seq


title: control_peripheral blood_00020


title: pXEN_vacuole_CHIR_sorted, 2


title: 6057841098_R01C01

value: M


title: TEPA_rep3_RNA-seq


title: pXEN_vacuole_CHIR_sorted, 3


title: 6057841093_R06C02


title: 6057841098_R06C01


title: control_peripheral blood_00018


title: pXEN_vacuole_CHIR_sorted, 1


title: pXEN_vacuole_BCS_unsorted, 3


title: control_peripheral blood_00016


title: TEPA_rep2_RNA-seq


title: 6057841093_R05C02


title: pXEN_vacuole_BCS_unsorted, 2


title: 6057841093_R04C02


title: DCM_peripheral blood_00037

source_name: DCM_peripheral blood

value: dilated cardiomyopathy (DCM)  patient


title: TEPA_rep1_RNA-seq


title: 6057841098_R03C01


title: Hypoxia_rep3_RNA-seq


title: 6057841098_R02C01


title: DCM_peripheral blood_00035


title: pXEN_vacuole_BCS_unsorted, 1


title: Hypoxia_rep2_RNA-seq


title: 6057841093_R02C02


title: 6057841093_R03C02


title: DCM_peripheral blood_00034


title: pXEN_vacuole_CHIR_unsorted, 3


title: control_peripheral blood_00019


title: TEPA+Hypoxia_rep1_RNA-seq


title: DCM_peripheral blood_00033


title: pXEN_vacuole_CHIR_unsorted, 2


title: Hypoxia_rep1_RNA-seq


title: DCM_peripheral blood_00027


title: pXEN_vacuole_CHIR_unsorted, 1


title: Control_rep2_RNA-seq


title: 6057841093_R06C01


title: 6057841093_R01C02


title: pXEN_normal, 3


title: 6057841093_R05C01


title: DCM_peripheral blood_00013


title: Control_rep1_RNA-seq


title: pXEN_normal, 2


title: 6057841093_R04C01


title: DCM_peripheral blood_00005


title: 6057841093_R03C01


title: B73 WT 54 R10

city: College Station

last: Kolomiets

state: Texas

address: 496 Olsen Blvd.2132 TAMU

department: Plant Pathology and Microbiology

institute: Texas A&M University

description: Sample 38

data_processing:
fastq files were aligned to B73 maize genome (AGPv4 release 38) using TopHat2 v2.1.0 pipeline
Uniquely aligned reads were counted with the HT-Seq 0.6.1 pipeline
FPKM values were determined using the Ballgown (v2.10.0) pipeline
Genome_build: AGPv4 release 38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Zea mays

source_name: maize roots

growth_protocol: Maize seedlings were germinatedon LB plates, then transferred to hydroponic growth conditions (half-strength Murashige and Skoog liquid media with mesh to only allow roots access to the media)

extract_protocol:
Roots were removed, flash frozen in liquid nitrogen, and RNA harvested using Trizol reagent. cDNA libraries were created with the NEXTflex® Rapid Illumina Directional RNA-Seq Library Prep Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1g Wild-type Trichoderma virens mycelia was added to the MS media in the jars

tag: cultivar

tag: agent

value: WT T. virens treated

tag: time point


title: DCM_peripheral blood_00004

tag: tissue


title: B73 WT 54 R9

description: Sample 37


title: 6057841093_R02C01


title: DCM_peripheral blood_00003


title: B73 WT 54 R8

description: Sample 36


title: 6057841093_R01C01


title: hrpk1_tm5522_L4_rep2

city: Beer-Sheva

first: Isana

last: Veksler-Lublinsky

address: P.O.B. 653 Beer-Sheva

country: Israel

institute: Ben-Gurion university of the Negev

data_processing:
Sequencing files in FastQ format were processed using cutadapt (1.15) to remove the 3' adapter sequences (ATCTCGTATGCCGTCTTCTGCTTG).
Fastx toolkit was used to split the reads according to the 3' 6 nt barcode sequences.
Additional round of 3' dapater sequence (TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC) trimming was performed with cutadapt.
The last and the first 4 nts from each read were trimmed and reads in the size of 17-25 were kept.
Reads with identical sequences were combined.
Reads were than aligned to the Caenorhabditis elegans genome (WormBase release WS215) using bowtie with arguments, -v 3 -f -B 1 -a–best –strata
Alignments were then filtered based on the length of the read and the number of mismatches as follows: for sequence lengths 17, 18–19, 20–24, or >24: zero, one, two, or three mismatches were allowed, respectively.
Genome_build: WS215
Supplementary_files_format_and_content: miRNA raw counts are supplied in matrix table (tab-delimited)

organism: Caenorhabditis elegans

growth_protocol: C. elegans strains were grown in standard conditions on NGM plates using OP50 as a food source. Strains were maintained at 20oC.

extract_protocol:
RNA from embryos and L4 animals was prepared as previously described ( Zinovyeva et al 2014, PLOS Genetics https://doi.org/10.1371/journal.pgen.1004286) with the following modifications. Mixed stages animals resuspended in 250μL water were mixed with 1ml of Trizol (Fisher Scientific) and RNAse free Rhino beads (MIDSCI) and homogenized using a Bullet blender (MIDSCI) at the highest setting for 4 minutes. Homogenate was then moved into a fresh tube, mixed with 212μL of chloroform, and spun down to separate the phases. All remaining steps of the RNA purification were performed as previously described
Small RNA libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq Kit v3.

tag: strain background

tag: genotype/variation

tag: molecule subtype

value: small RNA


title: B73 WT 54 R7

description: Sample 35


title: 6057833060_R06C02


title: hrpk1_zen17_L4_rep3


title: hrpk1_tm5522_L4_rep1


title: B73 WT 54 R6

description: Sample 34


title: hrpk1_zen17_L4_rep2


title: 6057833060_R04C02


title: DCM_peripheral blood_00002


title: hrpk1_zen17_L4_rep1


title: B73 WT 54 R5

description: Sample 33


title: hrpk1_zen17_Embryo_rep3

value: Embryo


title: 6057833060_R05C02


title: pXEN_normal, 1

tag: cell type


title: 6057833060_R03C02


title: B73 WT 54 R4

description: Sample 32


title: 6057833060_R01C02


title: 6057833060_R02C02


title: B73 WT 54 R2

description: Sample 30


title: B73 WT 54 R1

description: Sample 29


title: WT_N2_L4_rep3

value: Wild type

tag: developmental stage


title: B73 WT30 R10

description: Sample 28


title: 6057833060_R05C01


title: 6057833060_R06C01


title: 6057833060_R04C01


title: B73 WT30 R9

description: Sample 27


title: WT_N2_L4_rep2


title: WT_N2_L4_rep1


title: Control_rep3_RNA-seq


title: B73 WT30 R8

description: Sample 26


title: WT_N2_Embryo_rep3


title: 6057833060_R03C01


title: B73 WT 54 R3

description: Sample 31


title: hrpk1_zen17_Embryo_rep2


title: FN3T: Bone metastatic primary tumour 3

type: RNA

city: Sheffield

first: Penelope

last: Ottewell

state: England

address: Medical School, Beech Hill Road

department: Oncology and Metabolism

institute: University of Sheffield

hyb_protocol: pooled samples (n=3/pool) were hybridised to whole genome Affymetrix arrays (Prime View Gene Expression Arrays, Applied Biosystems)

scan_protocol: Three sets of 3 pooled samples were analysed separately.

data_processing: Qluocore analysis

label: biotin

source_name: Metastatic breast cancer

label_protocol: not provided

growth_protocol: MDA-MB-231 cells were injected orthotopically into mammary glands 4 in female NOD SCID mice 4-weeks after implantation of human femoral bone discs. Femoral bone discs from the same patient were also implanted into NOD SCID mice that did not receive tumour cells as a control.

extract_protocol: RNA was extracted using an Rneasy kit (Qiagen) and manufacturers instructions

value: Metastatic breast cancer


title: FN7B: Naïve (patient matched) bone

source_name: Naïve bone

value: Naïve bone


title: FN6T: Non-metastatic primary tumour 3

source_name: Non-metastatic breast cancer

value: Non-metastatic breast cancer


title: FN5T: Non-metastatic primary tumour 2


title: FN1T: Bone metastatic primary tumour 1


title: B73 WT30 R7

description: Sample 25


title: FN2T: Bone metastatic primary tumour 2


title: WT_N2_Embryo_rep2


title: FN2B: Bone with metastases 2

source_name: Bone metastases

value: Bone metastases


title: WT_N2_Embryo_rep1


title: I16F-BNST

city: Boston

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

data_processing:
All samples were processed using a small RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Quality control of the raw reads was performed as above for the RNA-seq data using FastQC and atropos.
Trimmed reads were aligned to miRBase v21 to the specific species with seqbuster (*mirna files). In addition, the trimmed reads were aligned to the Rat genome (version rno6) using STAR.
The aligned reads were analyzed with seqcluster to characterize the whole small RNA transcriptome and classify reads into rRNA, miRNA, repeats, genes, tRNAs and others from the UCSCannotation.
Data were loaded into R using the bcbioSmallRna R package (https://github.com/lpantano/bcbioSmallRna) and isomiRs Bioconductor package to get normalized expression values
Genome_build: Rnor6

source_name: anterodorsal BNST

extract_protocol:
The anterodorsal BNST (adBNST) was punched from frozen brains, total RNA was extracted using Trizol reagent (Ambion, Life Technologies) and was treated with a DNA-free kit (Ambion, Life Technologies). Total RNA (215ng) was used for the library construction as described below.
MiRNA Libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq kit v3. Total RNA (215ng) was denatured and NEXTflex adapters were ligated to the 3' and 5' ends of the RNA. After adapter ligations and cleanups, the adapter-ligated RNA entered reverse transcription, resulting in a cDNA first strand synthesis product. The reverse transcription products were then isolated and amplified by PCR (22 cycles). Successful library production and isolation was confirmed by the Agilent High-Sensitivity Screentape assay. Quantification of libraries was performed using Qubit Picogreen and KAPA quantitative real-time polymerase chain reaction (qRT-PCR) assays. Libraries were normalized, pooled, denatured and sequenced on the HiSeq 2500 using Rapid v2 sequencing reagents and flowcell.
All samples were processed using the small RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).

treatment_protocol: Male and female pups were weaned on postnatal day 21 and housed either singly (socially isolated; SI) or in groups of three same-sex littermates (group housed; GH; controls). SI and GH rats were maintained under these housing conditions for 6 weeks and were tested for anxiety-like behavior using the Elevated Plus Maze (EPM) when they reached adulthood (9 weeks old). Following EPM test, rats were killed, brains were collected and the adBNST was punched from frozen brains.

tag: housing condition

value: Socially Isolated (SI)

tag: Sex

value: Female

value: Sprague-Dawley


title: B73 WT30 R6

description: Sample 24


title: I12F-BNST


title: FN1B: Bone with metastases 1


title: FN4T: Non-metastatic primary tumour 1


title: hrpk1_zen17_Embryo_rep1


title: B73 WT30 R4

description: Sample 22


title: I10F-BNST


title: Control_2

city: Santiago de Compostela

first: Diego

last: Robledo

address: Rúa Lope Gómez de Marzoa s/n CIBUS building

department: Genetics

country: Spain

institute: University of Santiago de Compostela

description: RNA-Seq of Petromyzon marinus: control-treated brainstem after spinal injury

data_processing:
Raw paired-end FASTQ files were quality filtered using Fastp to remove leading or trailing bases with Phred quality scores < 15 (-q 15), reads with length < 30 base pairs (-l 30), polyG tails (--trim_poly_g) and trim adaptor sequences (detected by per-read overlap, default).
Genome alignment: The resulting trimmed FASTQ files were aligned against the latest lamprey genome assembly (Pmar_germline 1.0) using STAR in 2-pass mapping mode (--twopassMode Basic) with the following parameters: 10 maximum multiple alignments allowed per read (--outFilterMultimapNmax 10), 10 maximum mismatches per read pair (--outFilterMismatchNmax 10), minimum and maximum intron lengths of 20 and 1M bp respectively (--alignIntronMin 20; --alignIntronMax 1000000), maximum distance of 1 Mb between mate reads (--alignMatesGapMax 1000000) and detection of chimerica sequences with a minimum mapped length of 20 bp (--chimSegmentMin 20; --chimScoreMin 1).
Transcriptome reconstruction: StringTie with default parameters (fr-firststrand, --rf) was used to construct the lamprey transcriptome for our samples using the genome alignment files.
Generation of read counts per gene: FeatureCounts was used to quantify gene expression at the gene level with the following parameters: fragments (paired-end reads) were counted instead of individual reads ('-p'), only fragments with both ends mapper were considered ('-B'), chimeric fragments were not considered ('-C'), and strand specified as reversely stranded ('-s 2').
Genome_build: Pmar_germline 1.0
Supplementary_files_format_and_content: Tab delimited text with raw read counts for each gene in the genome-guided de novo transcriptome (TSA submission GHVE00000000). The first six columns of the file correspond to gene ID, chromosome, start and end positions, strand and length of the gene

molecule: polyA RNA

organism: Petromyzon marinus

source_name: Brainstem

extract_protocol:
The brainstems of control and treated larvae were dissected out and immediately put in RNAlater (Ambion Inc., TX, USA). RNA extraction was performed using the RNeasy mini kit (Qiagen) with DNase treatment following the manufacturer’s instructions. Isolated RNAs were eluted in nuclease free water.
mRNA sequencing libraries were prepared from poly dT selected mRNA using the Illumina TrueSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol.

tag: treatment

value: Control

tag: ecotype

value: Spain:river Ulla

value: 5-7 years


title: Control_1


title: I14F-BNST

tag: strain


title: GABA_3

description: RNA-Seq of Petromyzon marinus: GABA-treated brainstem after spinal injury

value: GABA


title: B73 WT30 R2

description: Sample 20


title: B73 WT30 R1

description: Sample 19


title: G17F-BNST

value: Group Housed (GH)


title: B73 WT30 R5

description: Sample 23


title: FN3B: Bone with metastases 3


title: I17F-BNST


title: G13F-BNST


title: B73 WT30 R3

description: Sample 21


title: G16F-BNST


title: GABA_1


title: B73 WT 6 R9

description: Sample 17

value: 6 h


title: Primary_tumor_02

city: SHANGHAI

first: wei

last: li

address: Yanchang RD.

institute: WFIRM

description: circRNA expression  in metastatic tumor tissue

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

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 6 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 1.5 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: case2 metastatic renal cell carcinoma tissue

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

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: All fresh tumor tissues are collected from the RCC patients and immediately frozen in liquid nitrogen, and then placed in a -80 refrigerator for long-term storage.

tag: disease

value: Renal cell carcinoma

value: Primary tumor tissue

value: male


title: G12F-BNST


title: G15F-BNST


title: metastatic_tumor_01

description: circRNA expression  in primary tumor tissue

source_name: case1 primary renal cell carcinoma tissue

value: metastatic tumor tissue


title: B73 WT 6 R8

description: Sample 16

value: WT T. virens treated


title: Primary_tumor_03

source_name: case3 metastatic renal cell carcinoma tissue


title: metastatic_tumor_02

source_name: case2 primary renal cell carcinoma tissue


title: metastatic_tumor_03

source_name: case3 primary renal cell carcinoma tissue


title: m1A-IP-seq, "+AlkB", replicate3

city: Chicago

first: Huiqing

last: Zhou

state: Illinois

address: LOADING DOCK BEHIND 5741 S DREXEL AVE  929 E 57TH ST

institute: University of chicago

data_processing:
PCR dupilcates were removed by the Raw data (R2 reads of the pair-end data) were first processed with the “clumpify.sh” program in the BBMap package (BBMap-Bushnell B.-sourceforge.net/projects/bbmap/) with the option “dedupe subs=0” to remove PCR duplicates.
Adaptors were trimmed by the “cutadapt” program while reads were filtered by quality and length with options “-a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 20 -m 30”
Reads were aligned to the hg19 genome file downloaded from the UCSC database as well as the known splicing sites via the hisat2 aligner with the option “--trim5 11 ” removing the unique molecular identifier (UMI) sequence and not performing the soft-clipping at the end of reads, with the script “run_cut_alignment_R2_hg19.sh”.
Single base reads counting were performed with bam-readcount.
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing mutation counts at base resolution

source_name: HEK-293T cells

extract_protocol:
RNA samples were extracted from HEK-293T cells using the TRIzol reagent and standard protocol; mRNA were enriched by the Dyna-Oligo(dT)25 beads and m1A IP was performed with the m1A antibody.
Libraries were constructed using ligation-based library construction approach incoporating the newly developed RT in the current work.

tag: cell line

value: HEK-293T cells

tag: passages

tag: experimental

value: m1A-IP-seq, "+AlkB"


title: m1A-IP-seq, "+AlkB", replicate2


title: GABA_2

tag: age


title: Control_5

value: Brainstem


title: B73 WT 6 R7

description: Sample 15

tag: cultivar

tag: agent

tag: time point


title: m1A-IP-seq, "+AlkB", replicate1


title: B73 WT 6 R10

description: Sample 18


title: B73 WT 6 R6

description: Sample 14


title: I20M-BNST

value: Socially Isolated (SI)

value: Male


title: I17M-BNST

value: Sprague-Dawley


title: Control_4

tag: tissue

value: Control


title: MCF-7_siTMPO-AS1_#2

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

description: Gene expression data from MCF-7 cells treated with siRNA targeting TMPO-AS1 (siTMPO-AS1 #2)

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Clariom D Assay, human). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

source_name: MCF-7 cells treated with siTMPO-AS1 #2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Human breast cancer MCF-7cells were maintained in Dulbecco's modified Eagle's medium (DMEM).

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: MCF-7 cells were transfected with siRNAs targeting TMPO-AS1 (siTMPO-AS1 #1 and #2) or control siRNA (siControl) for 48 hours.

tag: sirna


title: m1A-IP-seq, "-AlkB", replicate3

value: m1A-IP-seq, "-AlkB"


title: m1A-IP-seq, "-AlkB", replicate2


title: Control__3

value: Spain:river Ulla

value: 5-7 years


title: Primary_tumor_01

source_name: case1 metastatic renal cell carcinoma tissue


title: MCF-7_siControl

description: Gene expression data from MCF-7 cells treated with control siRNA

source_name: MCF-7 cells treated with siControl

value: siControl


title: Control__2


title: B73 WT 6 R3

description: Sample 11

value: 6 h


title: m1A-quant-seq, "+AlkB", replicate3

value: m1A-quant-seq, "+AlkB"


title: B73 WT 6 R5

description: Sample 13


title: B73 WT 6 R4

description: Sample 12


title: m1A-quant-seq, "+AlkB", replicate2


title: I15M-BNST


title: m1A-IP-seq, "-AlkB", replicate1


title: B73 WT 6 R2

description: Sample 10


title: MCF-7_siTMPO-AS1_#1

description: Gene expression data from MCF-7 cells treated with siRNA targeting TMPO-AS1 (siTMPO-AS1 #1)

source_name: MCF-7 cells treated with siTMPO-AS1 #1


title: I19M-BNST


title: B73 WT 6 R1

description: Sample 9

source_name: maize roots


title: 6057833060_R01C01

data_processing:
GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)
Average Beta (after background-subtraction and colour-correction in GenomeStudio software according to standard Illumina protocol)

source_name: buccal swab genomic DNA

extract_protocol: Buccal epithelial cells were collected with using Isohelix Buccal Swabs (Cell Projects, Harrietsham, Kent, England) and stabilized per manufacturer’s instructions for storage at room temperature. Genomic DNA was isolated using Isohelix Buccal DNA Isolation Kits (Cell Projects, Harrietsham, Kent, England), and then purified and concentrated using DNA Clean & Concentrator (Zymo Research, Irvine, CA)

tag: gender

value: M


title: G21M-BNST

value: Group Housed (GH)


title: Baclofen_5

description: RNA-Seq of Petromyzon marinus: baclofen-treated brainstem after spinal injury

value: Baclofen


title: m1A-quant-seq, "+AlkB", replicate1


title: G20M-BNST


title: Baclofen_4


title: Control__1


title: B73 M6 R4

description: Sample 4

value: Untreated


title: m1A-quant-seq, "-AlkB", replicate3

value: HEK-293T cells

value: m1A-quant-seq, "-AlkB"


title: G18M-BNST


title: Baclofen_3

value: Brainstem


title: B73 M6 R2

description: Sample 2


title: m1A-quant-seq, "-AlkB", replicate2


title: Baclofen_2


title: Baclofen_1


title: G16M-BNST


title: G19M-BNST


title: siXAB2-2-Rep2

status: Public on Sep 23 2019

city: Dalian

first: Shuai

last: Hou

state: Liaoning

address: lvshun south road no.9

department: cancer stem cell institute

institute: Dalian Medical University

data_processing:
RNASeq reads were aligned to the hg19 genome assembly using STAR version 2.6.0c.
Alternative splicing events were detected using junction usage model(JUM version 2.0.2).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_pvalue_0.05_final_simplified.txt: Tab-delimited text files include intron retention, A5SS, A3SS, cassette, MXE, composite events and their corresponding deltaPSI, pvalue, qvalue.

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS.

extract_protocol:
Total RNA was purified using TRIzol, treated with DNase I and Ribo-Zero rRNA Removal kit to generate sequencing libraries.
Strand-specific, rRNA-depleted sequencing libraries were prepared using the dUTP second-strand approach.

treatment_protocol: HeLa cells were transfected with control or XAB2 siRNA for 48 h.

value: HeLa

value: XAB2 siRNA-2


title: siXAB2-2-Rep1


title: siNC-Rep2

value: non-target siRNA


title: siXAB2-1-Rep2

value: XAB2 siRNA-1


title: B73 M6 R1

description: Sample 1


title: siNC-Rep1


title: siXAB2-1-Rep1


title: Input_HCT116

city: Shanghai

first: Yun

last: Tan

state: Shanghai

address: Room 1109, Building 11, 197 Ruijin Er Rd

department: Shanghai Institute of Hematology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
All ChIP-seq reads were aligned to the hg38 reference human genome by Bowtie 2 (version 2.2.9)
Enriched p53 occupancies relative to a background input were called using MACS (version 1.4)6 with default settings.
Genomic regions with a P value < 1 × 10−10 were retained and these enriched regions were annotated using the annotatePeaks package from the HOMER suite
The bedgraph files were generated by MACS2 with the -B -trackline settings.
Genome_build: hg38
Supplementary_files_format_and_content: Genomic binding signal of p53 were illustrated as bedGraph files

growth_protocol: HCT116 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco), L-glutamine, and appropriate antibiotics. Cell cultures were maintained in a 5% CO2 humidified incubator at 37℃.

extract_protocol:
ChIP was performed using the ChIP-IT High Sensitivity (HS) Kit (Active Motif 53040) according to the manufacturer’s recommended protocol with the following modifications as briefly described. Cells were cross-linked with 1% formaldehyde in DMEM culture medium for 10 min at room temperature, and quenched in 0.125 M glycine for 5 min. Cells were then washed twice with phosphate-buffered saline (PBS) followed by 3 times with lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40, 1 mM PMSF), and resuspended in ChIP Buffer (Active Motif 37516) supplemented with 1 mM PMSF and a proteinase inhibitor cocktail (Sigma-Aldrich P2714-1BTL). Chromatin was sheared by sonication (30 s alternated with 30-s cooling for 25 cycles) using a Bioruptor Pico ultrasonicator (Diagenode). Solubilised chromatin was used for immunoprecipitation by incubation overnight at 4 °C with 5 μg of the polyclonal antibody FL-393 against human p53 (Santa Cruz Biotechnology sc-6243). The immunoprecipitation reactions were transferred to Protein G Agarose Columns (Active Motif 53039) and incubated for 2 h at 4 °C. Then, each column was washed 4 times with 900 μl Wash Buffer AM1. The ChIPed samples were eluted using 100 μl Elution Buffer AM4 at 37 °C. Cross-linking was reversed by adding 5 μl Proteinase K (New England Biolabs P8107S) and incubated overnight at 65 °C. Input and ChIPed DNA were purified using the DNA purification columns.
ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode C05010014) and the Agencourt AMPure XP system (Beckman Coulter A63880) was used to select 350–550 bp libraries. Sequencing was carried out on the Illumina MiSeq and HiSeq platforms.

treatment_protocol: HCT116 cells were treated with siRNA against iASPP, none-targeting siRNA for 3 days. And HCT116 cells were treated with Nutlin for 12 hours.

tag: chip antibody


title: Nutlin_p53_HCT116

value: Nutlin treatment


title: ctrl_p53_HCT116


title: ChIP-seq Pol2 Chaserr-/- mEFs 1

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

institute: Weizmann Institute of Science

data_processing:
Quantification using RSEM
Alignment to the mm9 mouse genome using STAR2 for RNA-seq and RIP-seq data and using bowtie2 for ChIP-seq, ATAC-seq, and Pol2 data
For ATAC-seq and ChIP-seq data, processing using MACS2 with default parameters
Preparation of bigWig files using wigToBigWIg
Genome_build: mm9
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage, macs2 output for Pol2 input files

source_name: mEF

growth_protocol: The study was conducted in accordance with the guidelines of the Weizmann Institutional Animal Care and Use Committee (IACUC). C57black6 Ola HSD male mice were purchased from Harlan Laboratories (Rehovot, Israel). All other mouse strains were bred and maintained at the Veterinary Resources Department of the Weizmann Institute. Cell lines were routinely cultured in DMEM containing 10% fetal bovine serum and 100 U penicillin/0.1 mg ml-1 streptomycin at 37˚ C in a humidified incubator with 5% CO2.

extract_protocol:
1x107mEFs were crosslinked with formaldehyde at 1% final concentration, 10 min at room temperature, and then quenched with 125mM glycine for 5 min at room temperature. Cells were centrifuged at 5min, 2000rpm at 4˚, and washed twice with PBS supplemented with PIC (protease inhibitors cocktail). Each pellet was then lysed in 1mL lysis buffer (5 mM PIPES pH 8.0 85 mM KCl, Igepal (10 µl/ml), and PIC) and incubated 15min at 4˚, then centrifuged for 5min at 15000rpm at 4˚.
Pellets were resuspended in 200µl nuclei lysis buffer (50 mM Tris-Cl pH 8.1, 10 mM EDTA, 1% SDS, and PIC) for 30min at 4˚. Lysates were then sonicated (Bioruptor, #B01020001) for 12 cycles of 30s ON, 30s OFF. Pol2 antibody (5µg, anti-Rbp1 NTD (D8L4Y), #14958) was bound to A/G magnetic beads in 1mL binding/washing buffer (PBS supplemented with 0.5% TWEEN and 0.5% BSA) for 1 h at room temperature. Chromatin lysate was then diluted x9 volume with IP dilution buffer (50mM Tris-HCl pH 7.4, 150mM NaCl, 1% Igepal, 0.25% Deoxycholic acid, 1mM EDTA pH 8.0), then washed coupled beads were added to the chromatin lysate and left for slow rotation O.N at 4˚. Beads were handled as described68 .Briefly, beads were washed 5 times with RIPA buffer(10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS and 0.1% Na-DOC), twice with RIPA-500 buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS and 0.1% Na-DOC), twice with LiCl buffer(10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5% NP-40 and 0.5% Na-DOC), once with TE buffer (10 mM Tris-HCl pH 8.0 with 1 mM EDTA pH 8.0). Beads were eluted with  direct elution buffer (10 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8.0, 300 mM NaCl and 0.5% SDS) at room temperature. Eluate was incubated with RNaseA (Homemade) for 30 min at 37˚,next with proteinase K for 2 h in 37°C and lastly O.N at 65˚. DNA was purified with The Agencourt AMPure XP system (Beckman Coulter Genomics, A63881). Libraries were constructed as previously described68, sequenced with paired-end sequencing on Illumina NextSeq 500.

tag: cell type

value: mEF


title: 4C using Chd2 promoter as a viewpoint in Chaserrb/b mESCs

data_processing:
Library strategy: 4C-Seq
Quantification using RSEM
Alignment to the mm9 mouse genome using STAR2 for RNA-seq and RIP-seq data and using bowtie2 for ChIP-seq, ATAC-seq, and Pol2 data
For ATAC-seq and ChIP-seq data, processing using MACS2 with default parameters
Preparation of bigWig files using wigToBigWIg
Genome_build: mm9
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage, macs2 output for Pol2 input files

source_name: mouse embryonic stem cells

extract_protocol: Following depletion from mEFs by 20 min incubation on gelatin-coated plates, 3C was carried out on 5x106 mESCs essentially as described66, with the following slight modification: permeabilization buffer constitution was 10mM Tris-HCl pH8, 10mM NaCl, 0.5% NP-40, supplemented with protease inhibitors.

value: mouse embryonic stem cells


title: 4C using Chd2 promoter as a viewpoint in Chaserrp/p mESCs

extract_protocol:
Following depletion from mEFs by 20 min incubation on gelatin-coated plates, 3C was carried out on 5x106 mESCs essentially as described66, with the following slight modification: permeabilization buffer constitution was 10mM Tris-HCl pH8, 10mM NaCl, 0.5% NP-40, supplemented with protease inhibitors.
4C libraries were prepared as described67, with primers directed to the promoter region of Chd2 (upstream primer sequence: GCTCAAGCACCCTTTTTAAGCCAG, downstream primer sequence: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTGAAATGTAATTTGTTCCTTTTGTC). Libraries were sequenced on Illumina NextSeq 500, and analyzed as described67.


title: 4C using Chd2 promoter as a viewpoint in WT mESCs (PP)


title: ChIP-seq Input Chaserr-/- mEFs 1


title: ChIP-seq Pol2 Chaserr-/- mEFs 2


title: 4C using Chd2 promoter as a viewpoint in WT mESCs (BB)


title: ChIP-seq Input WT mEFs 2


title: ChIP-seq Input Chaserr-/- mEFs 2


title: Chip-seq Pol2 in Chaserrb/b mESCs


title: Chip-seq Input in Chaserrb/b mESCs


title: ChIP-seq Input in WT mESCs


title: ChIP-seq Pol2 in WT mESCs


title: m1A-quant-seq, "-AlkB", replicate1


title: ChIP-seq Input WT mEFs 1


title: ChIP-seq Pol2 WT mEFs 1


title: Input for RIP 2

description: Input

source_name: Neuro2a cells

extract_protocol:
Total RNA was extracted from different cell lines and mice tissues, using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
Lexogen RiboCop kit

value: Neuro2a cells


title: ChIP-seq Pol2 WT mEFs 2


title: Input for RIP 1

description: Input


title: E13.5 Chaserr-/ Chd2m/m mEF matched from Chd2+/m cross 1

extract_protocol:
Total RNA was extracted from different cell lines and mice tissues, using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
Lexogen SENSE mRNA-seq kit


title: IgG RIP 1

description: IgG


title: CHD2 RIP 2


title: IgG RIP 2

description: IgG


title: E13.5 WT mEF matched from Chaserr+/- Chd2+/m cross 3


title: CHD2 RIP 1


title: E13.5 Chaserr-/ Chd2m/m mEF matched from Chd2+/m cross 2


title: E13.5 Chd2m/m mEF matched from Chd2+/m cross 2


title: E13.5 WT mEF matched from Chaserr+/- Chd2+/m cross 1


title: 2TS22C YPet-SOX2 ChIP

city: Lausanne

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

institute: École polytechnique fédérale de Lausanne

description:
Immunoprecipitated genomic DNA
2TS22C cells overexpressing YPet-SOX2 treated with doxycycline

data_processing:
Reads were aligned to the mouse reference genome mm10 using STAR 2.5.3a with settings ‘-- alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd -- outFilterMultimapNmax 1’
Duplicate reads were removed with Picard and reads not mapping to chromosomes 1-19, X, or Y were removed
Peaks were called with MACS 2.1.1.20160309 with settings ‘-f BAMPE -g mm -q 0.01’ and merged for all samples. Peaks overlapping peaks called for ChIP-seq Input data from asynchronous mouse ES cells (GSE89599) were discarded.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated with deepTools 2.4.2 with settings '--normalizeUsingRPKM' on merged triplicates

source_name: 2TS22C mouse ES cells

growth_protocol: Cells were routinely cultured on dishes coated with 0.1% gelatin type B in GMEM supplemented with 10% ES-cell qualified fetal bovine serum, nonessential amino acids, 2mM L-glutamine, sodium pyruvate, 100μM 2-mercaptoethanol, penicillin and streptomycin, homemade leukemia inhibitory factor (LIF), CHIR99021 at 3μM and PD184352 at 0.8μM.

extract_protocol: At least 10^7 cells were fixed with 1% formaldehyde for 10 minutes at room temperature, subsequently quenched with 200 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at  80°C. The cell pellet was then resuspended in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100), incubated 10 min at 4°C, spun down, resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min at 4°C. The pellet was spun down and rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and resuspended in 0.9 ml SDS shearing buffer. All buffers contained Protease Inhibitor Cocktail in DMSO diluted at 1:100. The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken. Sonicated chromatin was incubated with 5ug/10^7 cells of the anti-SOX2 Y-17 or 5ul of antibody/4x10^6 cells of the anti-OCT4A C30A3C1 at 4°C overnight. 0.5% BSA-blocked Protein G Dynabeads were added to the chromatin and incubated for 3 hours at 4°C. The chromatin was washed several times at 4°C with 5 min incubation between each wash and 2 min magnetization to collect beads; twice with Low Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with High Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with LiCl Wash Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM PMSF), and with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were subsequently resuspended in Elution buffer (TE buffer with 1% SDS and 150 mM NaCl), treated with 400 ng/ml Proteinase K and reverse crosslinked at 65°C overnight. Samples were purified using MinElute PCR purification kit. One replicate of each ChIP-seq library was prepared with NEBNext ChIP-seq Library Prep Master Mix Set using insert size selection of 250 bp.

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 40-48 hours before fixation to ensure complete depletion of endogenous SOX2

tag: background cell line


title: ZHBTc4 YPet-OCT4 ChIP

description:
Immunoprecipitated genomic DNA
ZHBTc4 cells overexpressing YPet-OCT4 treated with doxycycline

source_name: ZHBTc4 mouse ES cells

extract_protocol: At least 10^7 cells were first fixed with 2 mM Disuccinimidyl glutarate (DSG) for 50 minutes in PBS at room temperature, washed and then fixed with 1% formaldehyde for 10 minutes at room temperature, subsequently quenched with 200 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at  80°C. The cell pellet was then resuspended in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100), incubated 10 min at 4°C, spun down, resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min at 4°C. The pellet was spun down and rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and resuspended in 0.9 ml SDS shearing buffer. All buffers contained Protease Inhibitor Cocktail in DMSO diluted at 1:100. The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken. Sonicated chromatin was incubated with 5ug/10^7 cells of the anti-SOX2 Y-17 or 5ul of antibody/4x10^6 cells of the anti-OCT4A C30A3C1 at 4°C overnight. 0.5% BSA-blocked Protein G Dynabeads were added to the chromatin and incubated for 3 hours at 4°C. The chromatin was washed several times at 4°C with 5 min incubation between each wash and 2 min magnetization to collect beads; twice with Low Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with High Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with LiCl Wash Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM PMSF), and with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were subsequently resuspended in Elution buffer (TE buffer with 1% SDS and 150 mM NaCl), treated with 400 ng/ml Proteinase K and reverse crosslinked at 65°C overnight. Samples were purified using MinElute PCR purification kit. One replicate of each ChIP-seq library was prepared with NEBNext ChIP-seq Library Prep Master Mix Set using insert size selection of 250 bp.

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 40-48 hours before fixation to ensure complete depletion of endogenous OCT4


title: E13.5 WT mEF matched from Chd2+/m cross 3


title: SLOL rep3 ATAC

description:
Tn5-transposed genomic DNA
SBROS cells sorted for SOX2-SNAP low and OCT4-HALO low signal
SLOL.bw
ATAC_SBROS_merged.bed

source_name: SBROS knock-in mouse ES cells

extract_protocol:
Cells were pelleted and washed with 1X ice cold PBS at 800g for 5 min. Cells were gently resuspended in 50 μl of ice-cold ATAC lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and immediately pelleted at 800g for 10 min at 4°C. To transpose open chromatin regions, cells were resuspended in 50 μl of transposition reaction mix containing 0.5 μM of Tn5 transposase (in-house prepared) in TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. The transposed DNA was purified using a DNA purification kit and eluted in 12 μl of water.
A 65 μl PCR reaction was setup with 10 μl of transposed DNA, 0.5 μM of forward primer Ad1_noMX, 0.5 μM of multiplexing reverse primer Ad2.x (Buenrostro et al. 2013), 0.6x SYBR Green I, and 1x PCR Master Mix. The samples were thermocycled at 72°C for 5 minutes, 98°C for 30 s, followed by 12 cycles of 98°C for 10 s, 63°C for 30 s and 72°C for 1 min. The amplified ATAC libraries were purified using a DNA purification kit and size selected using Agencourt AMPure beads (0.55X unbound fraction followed by 1.2X bound fraction).

treatment_protocol: SBROS cells were stained with the HaloTag TMR Ligand and the SNAP-SiR647 dye at a concentration of 100nM or 12nM, respectively, for one hour. Subsequently, cells were incubated in with Hoechst 33342 at a concentration of 1.62µM for 15 minutes. Cells were then trypsinised, washed in PBS and resuspended in PBS/1% FBS for sorting on a BD FACSAria II.


title: E13.5 WT mEF matched from Chd2+/m cross 1


title: E13.5 WT mEF matched from Chd2+/m cross 2


title: E13.5 Chd2m/m mEF matched from Chd2+/m cross 1


title: SLOL rep2 ATAC


title: SBR OCT4 ChIP

description:
Immunoprecipitated genomic DNA
SBR cells

source_name: SBR knock-in mouse ES cells

extract_protocol: At least 10^7 cells were first fixed with 2 mM Disuccinimidyl glutarate (DSG) for 50 minutes in PBS at room temperature, washed and then fixed with 1% formaldehyde for 10 minutes at room temperature, subsequently quenched with 200 mM Tris-HCl pH 8.0, washed with PBS, spun down, and stored at 80°C. The cell pellet was then resuspended in 1.5 ml LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100), incubated 10 min at 4°C, spun down, resuspended in 1.5 ml LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and incubated 10 min at 4°C. The pellet was spun down and rinsed twice with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS), and resuspended in 0.9 ml SDS shearing buffer. All buffers contained Protease Inhibitor Cocktail in DMSO diluted at 1:100. The suspension was transferred to a milliTUBE 1 ml AFA fiber and sonicated on a E220 focused ultrasonicator (Covaris) using the following settings: 20 min, 200 cycles, 5% duty, 140W, and input sample aliquots were taken. Sonicated chromatin was incubated with 5ug/10^7 cells of the anti-SOX2 Y-17 or 5ul of antibody/4x10^6 cells of the anti-OCT4A C30A3C1 at 4°C overnight. 0.5% BSA-blocked Protein G Dynabeads were added to the chromatin and incubated for 3 hours at 4°C. The chromatin was washed several times at 4°C with 5 min incubation between each wash and 2 min magnetization to collect beads; twice with Low Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with High Salt Wash Buffer (10 mM Tris-HCl pH 8.0, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.15% SDS, 1 mM PMSF), once with LiCl Wash Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 250 mM LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM PMSF), and with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Beads were subsequently resuspended in Elution buffer (TE buffer with 1% SDS and 150 mM NaCl), treated with 400 ng/ml Proteinase K and reverse crosslinked at 65°C overnight. Samples were purified using MinElute PCR purification kit. One replicate of each ChIP-seq library was prepared with NEBNext ChIP-seq Library Prep Master Mix Set using insert size selection of 250 bp.


title: SLOH rep3 ATAC

description:
Tn5-transposed genomic DNA
SBROS cells sorted for SOX2-SNAP low and OCT4-HALO high signal
SLOH.bw
ATAC_SBROS_merged.bed


title: ZHBTc4 OCT4-HALO ChIP

description:
Immunoprecipitated genomic DNA
ZHBTc4 cells overexpressing OCT4-HALO treated with doxycycline


title: E13.5 Chaserr-/ Chd2m/m mEF matched from Chd2+/m cross 3


title: SHOL rep2 ATAC

description:
Tn5-transposed genomic DNA
SBROS cells sorted for SOX2-SNAP high and OCT4-HALO low signal
SHOL.bw
ATAC_SBROS_merged.bed


title: SLOH rep1 ATAC


title: E13.5 WT mEF matched from Chaserr+/- Chd2+/m cross 2


title: SHOL rep3 ATAC


title: SHOH rep2 ATAC

description:
Tn5-transposed genomic DNA
SBROS cells sorted for SOX2-SNAP high and OCT4-HALO high signal
SHOH.bw
ATAC_SBROS_merged.bed


title: ATAC_MEF_KO_3, Chaser-/- mEFs

data_processing:
Quantification using RSEM
Alignment to the mm9 mouse genome using STAR2
Preparation of bigWig files using wigToBigWIg
Genome_build: mm10
Supplementary_files_format_and_content: RSEM quantification files and bigWig read coverage

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor adjustment for application to tissue material. Six fresh L4-L6 DRGs were extracted in 100 µl ice cold cell lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% IGEPAL CA-630) for 5 minutes on ice, then a 21g needle on a 1 mL syringe was used to shear the tissue through the needle 5 times.
As in Buenrstro et al. 2013


title: SHOL rep1 ATAC


title: SHOH rep1 ATAC


title: ATAC_MEF_KO_2, Chaser-/- mEFs


title: SHOH rep3 ATAC


title: ATAC_MEF_KO_1, Chaser-/- mEFs


title: SLOL rep1 ATAC


title: ATAC_MEF_WT_6, same pregnancy as Chaser-/- mEFs


title: SLOH rep2 ATAC


title: ATAC_MEF_WT_5, same pregnancy as Chaser-/- mEFs


title: ATAC_MEF_DKO_1, Chaser-/- Chd2m/m mEFs


title: ATAC_MEF_WT_1, same pregnancy as Chaser-/- Chd2m/m mEFs


title: ATAC_MEF_WT_2, same pregnancy as Chaser-/- Chd2m/m mEFs


title: ATAC_MEF_WT_4, same pregnancy as Chaser-/- mEFs


title: ATAC_MEF_WT_3, same pregnancy as Chaser-/- Chd2m/m mEFs


title: MEF_KO_3


title: MEF_WT_6, same pregnancy as MEF KO


title: MEF_KO_2


title: MEF_WT_4, same pregnancy as MEF KO


title: MEF_Het_1


title: ATAC_MEF_DKO_3, Chaser-/- Chd2m/m mEFs


title: MEF_WT_3, same pregnancy as MEF Het


title: MEF_KO_1


title: MEF_WT_1, same pregnancy as MEF Het


title: Brain_WT_3

source_name: Adult brain

extract_protocol:
Total RNA was extracted from different cell lines and mice tissues, using the TRIREAGENT (MRC) according to the manufacturer’s protocol.
TruSeq stranded mRNA kit

value: Adult brain


title: MEF_WT_5, same pregnancy as MEF KO


title: Brain_WT_1


title: Brain_Het_1


title: Brain_Het_3


title: Brain_WT_2


title: E13.5_Het_3

source_name: E13.5 embryo

value: E13.5 embryo


title: ATAC_MEF_DKO_2, Chaser-/- Chd2m/m mEFs


title: Control_3

source_name: Brainstem

extract_protocol:
The brainstems of control and treated larvae were dissected out and immediately put in RNAlater (Ambion Inc., TX, USA). RNA extraction was performed using the RNeasy mini kit (Qiagen) with DNase treatment following the manufacturer’s instructions. Isolated RNAs were eluted in nuclease free water.
mRNA sequencing libraries were prepared from poly dT selected mRNA using the Illumina TrueSeq Stranded mRNA Library Preparation kit according to the manufacturer’s protocol.

tag: treatment

value: Control

value: Spain:river Ulla

value: 5-7 years


title: E13.5_Het_2


title: MEF_WT_2, same pregnancy as MEF Het


title: E13.5_WT_2


title: MEF_Het_3


title: E13.5_Het_1


title: E9.5_Het_3

source_name: E9.5 embryo

value: E9.5 embryo


title: E13.5_WT_3


title: E9.5_Het_2


title: E9.5_WT_3


title: LN_FRC_TG-_4

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE vM19 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are one tab delimited text file per sample indicating the raw counts for each gene in the GENCODE vM19 GTF file with --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand. STAR outputs read counts per gene into ReadsPerGene.out.tab.txt file with 4 columns which correspond to different strandedness options: column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA, column 4: counts for the 2nd read strand aligned with RNA. The TruSeq RNA libraries are 2nd stranded so column 4 is the most appropriate for gene expression analysis, though other counts may be useful for other analyses.

source_name: Skin Draining Lymph Nodes

growth_protocol: Cells were isolated from either lymph nodes or pancreatic islets harvested from freshly euthanized mice.

extract_protocol:
Total RNA was extracted and purified using QIAgen RNAeasy columns.
Total RNA was prepped for sequencing with the KAPA RNA HyperPrep Kits with RiboErase (HMR) according to manufacturer's protocols

treatment_protocol: Tissues were processed until a single cell suspension was obtained. Cell suspensions were stained using fluorescently-labeled antibodies and sorted directly on TRIzol.

value: Lymph Node Fibroblastic Reticular cells (FRCs)

tag: strain/genotype

value: NOD/ShiLtJ

value: Skin Draining Lymph Nodes

value: 12 weeks


title: LN_FRC_TG+_2

value: Ins2-CCL21 NOD


title: E9.5_WT_1


title: LN_FRC_TG+_3


title: E9.5_WT_2


title: input DNA

first: Lin

last: Liangyu

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Science

data_processing:
The sequence reads generated by Illumina sequencing (using NextSeq  500) are mapped to mm10 genome using the BWA algorithm with default settings.
Peaks were called using the MACS 2.1.0 algorithms with the following setting: band width = 200, model fold = [5, 50], pvalue cutoff = 1.00e-07, Broad region calling is off.
The tag number of all samples (within a comparison group) is reduced by random sampling to the number of tags present in the smallest sample.
To compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Active Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals; “merged peaks”). In locations where only one sample has an Interval, this Interval defines the Active Region.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using Active Motive software; Scores represent density of fragments  along the genome,

source_name: peritoneal macrophages

growth_protocol: Macrophages were cultured in 1640 complete medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using a Active Motive ChIP-IT ChIP-Seq kit (Cat# 53041). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, dNTP mix, DNA polymerase I Klenow and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Ligate adapter to DNA fragments in a cocktail containing DNA, quick ligation buffer, adapter oligo mix and T4 DNA ligase for 20 minutes at room temperature. After adapter ligation DNA was PCR amplified with PCR primers mix for 18 cycles and library fragments of 200-300 bp were band isolated from an agarose gel.

treatment_protocol: Thioglycollate-induced peritoneal macrophages were matured in the presenc or absenc of IGF2

tag: strain


title: LN_FRC_TG+_4


title: H3K27ac_IGF2

value: H3K27Ac(Cat# 39133 Active Motif)

tag: teatment


title: LN_FRC_TG-_2


title: Brain_Het_2


title: H3K27ac_PBS

value: PBS


title: LN_FRC_TG-_1


title: LN_FRC_TG-_3


title: H3K4me1_IGF2

value: H3K4me1(Cat#39297 Active Motif)


title: islet_gp38_low_TG+_4

source_name: Pancreatic Islets

value: FRC like cell from islet tertiary lymphoid organs (TLO)

value: Pancreatic Islets


title: islet_gp38_low_TG+_3


title: H3K4me1_PBS


title: H3K4me3_IGF2

value: H3K4me3(Cat# 39159 Active Motif)


title: E13.5_WT_1


title: islet_gp38_low_TG+_2


title: H3K4me3_PBS


title: islet_gp38_low_TG+_1


title: NPC_shTet3_oxBS-1

city: London

first: Miguel

middle: R

last: Branco

address: 4 Newark Street

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using trim_galore! with --rrbs option.
Trimmed reads were mapped to mm9 using bismark.
Methylation calls from both strands of each CpG were pooled and only CpGs with 5 or more reads in all samples were kept for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files contain methylation calls in the format required for the methylKit R package.

source_name: neural precursor cells (from ES)

growth_protocol: A2lox.cre ES cells (Iacovino et al., Stem Cells, 2011) containing inducible shRNAs for Tet3 or a non-targetting control were expanded on feeder cells in complete ES medium containing serum and LIF. Neural differentiation of ES cells was performed following a protocol previously described (Bibel et al., Nature Protocols, 2007).

extract_protocol:
Genomic DNA was isolated using the Qiagen AllPrep DNA/RNA Mini kit (Qiagen).
Oxidative reduced representation bisulfite sequencing (oxRRBS) libraries were generated from 100 ng of genomic DNA. After MspI digestion and size selection with AMPure XP beads, methylated adaptors were ligated using NEBNext reagents. Half of each sample was oxidised with potassium perruthenate, followed by bisulfite conversion (oxBS; detects 5mC). The remaining half was just bisulfite converted (BS; detects 5mC+5hmC).

treatment_protocol: For shRNA expression, doxycycline (2 µg/ml) was added to the medium during 5 days to achieve knockdown of the gene of interest.

tag: cell line

tag: shRNA

tag: oxbs/bs

value: oxBS


title: islet_gp38_low_TG-_3

tag: age


title: NPC_shTet3_oxBS-2


title: islet_gp38_low_TG-_4


title: islet_gp38_high_TG+_2


title: NPC_shScr_oxBS-2

value: Non-targeting


title: islet_gp38_low_TG-_2


title: NPC_shTet3_BS-1

value: BS


title: NPC_shScr_oxBS-1


title: islet_gp38_high_TG+_1


title: islet_gp38_low_TG-_1


title: NPC_shScr_BS-1


title: DGDE492-X

city: Roanoke

first: Shannon

last: Farris

state: VA

address: 2 Riverside Circle

department: Fralin Biomedical Research Institute

institute: Virginia Tech

description:
RNA-Seq replicate
DGDE492-X

data_processing:
All sequence data was evaluated for quality using FASTQC. From each RNA-Seq library, reads were trimmed using Sickle (v1.33), adapters were trimmed using cutadapt, and only paired reads with a quality score >20 and a minimum length of 20 bp were aligned to the GENCODE (vM12) gene models and the mm10 mouse genome assembly index using STAR (v2.5.1b) or Salmon (v0.9.1, indexed with kmer size 31) with the recommended ENCODE RNA-Seq parameters.
For STAR alignments, strand-specific gene counts were produced using featureCounts (v1.5.1) with transcripts flattened per gene from GENCODE (vM12) gene models. The four duplicate samples were merged as technical replicates during Salmon quantitation. Differential gene expression was evaluated in R (v3.4.2) using limma (v3.32.2) and/or DESeq2 (v1.18.1), using median normalized Salmon counts for detected genes only. Differential isoform expression was evaluated in R (v3.4.2) using limma (v3.32.2) using median normalized Salmon TPMs for genes with two or more detected isoforms.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include median normalized gene-level counts and median normalized transcript-level TPMs for each RNA-Seq sample.
Supplementary_files_format_and_content: farris_gene-normalized_log2counts_26jun2018.xlsx: log 2 gene-level abundance
Supplementary_files_format_and_content: farris_detectedTx-log2counts_19mar2018.xlsx, farris_detectedTx-log2counts_19mar2018.xlsx: log2 transcript-level abundance
Supplementary_files_format_and_content: ArrayRMA-genesDetected-sharedRNAseq_03apr2018.xlsx: log2 abundance correlation with microarray

source_name: hippocampal DG dendritic layer

extract_protocol:
Total RNA was extracted using the QIAGEN micro RNeasy RNA extraction kit (cat #74004). Approximated 20 LCM caps (5 sections/cap) were acquired per region (8 regions per brain) and immediately lysed with 10ul of lysis buffer incubated at room temperature for 5min. Lysates were stored at -80C until further processing. For RNA extraction, lysates from each subregion were pooled and RNA was isolated one at a time to minimize degradation. All samples were subjected to on-column DNase-treatment (Qiagen, cat#79254). We obtained 2-30ng of high quality total RNA (RIN >8.7) from each subregion and compartment, measured using the Agilent RNA 6000 Pico kit and 2100 Bioanalyzer.
cDNA libraries were made using the Ovation Universal RNA-Seq system for mouse (NuGEN, part # 0348) according to the manufacturer’s instructions, including the shearing step to 200bp with a Covaris S-series Sonication System, using 1ng total RNA input for dendrite samples and 5ng total RNA input for cell body samples. Samples from each mouse (8 samples/mouse, cell body and dendrite samples from each subregion, CA1, CA2, CA3 and DG) were processed together without the experimenter blind to sample IDs. The resulting cDNA libraries were amplified using 16 cycles of PCR prior to quantification using the High Sensitivity DNA kit (Agilent, Cat # 5067-4626) and a 2100 Agilent Bioanalyzer, as well as fluorometrically using Qubit dsDNA HS Assay kit and a Qubit 2.0 Fluorometer (Invitrogen, Thermo Fisher Scientific). Libraries from one animal were eight-plexed and sequenced on one high throughput lane on an Illumina NextSeq 500 instrument acquiring 100 bp paired-ends reads to a depth of 50 million reads per sample (+/- 10 mil). Four samples (out of 24 samples total) had fewer than 60% of paired-end reads mapped, therefore their libraries were remade and four-plexed on an additional mid-throughput lane as described above.

treatment_protocol: Three 6-8-week-old male Amigo2-EGFP mice from separate litters were used for the main study. Tissue was harvested within a 2-hour time window near the end of the light cycle (3-5pm, lights off 6pm). Mice were deeply anesthetized with Fatal Plus (50mg/kg) before swift removal of the brain (<2 min). Brains were bisected in the sagittal plane and individually flash frozen by being placed in a 22 x 22mm disposable cryomold (Polysciences, Inc.) filled with Optimal Cutting Temperature compound and submerged in isopentane cooled to -20C on a dry ice and ethanol slurry. Samples were stored at -80C until laser capture microdissection (LCM). Mouse hippocampal subregions (CA1, CA2, CA3 and DG) cell body and dendrite samples were separately captured using IR-based laser capture microdissection from eight micron fresh frozen brain sections as described in detail in Farris et al., 2017, Frontiers in Molecular Neuroscience.

value: Amigo2-GFP C57BL/6J

value: brain/hippocampus

value: 6-8 weeks

tag: Sex

value: male

tag: animal id


title: NPC_shTet3_BS-2


title: NPC_shScr_BS-2


title: islet_gp38_high_TG-_2

value: NOD/ShiLtJ


title: islet_gp38_high_TG-_1


title: DGDE502-X

description:
RNA-Seq replicate
DGDE502-X


title: islet_CD45_TG+_4

value: Lymphocytes from islet infiltrates


title: CA2DE502-X

description:
RNA-Seq replicate
CA2DE502-X

source_name: hippocampal CA2 dendritic layer


title: CA2DE492-X

description:
RNA-Seq replicate
CA2DE492-X


title: islet_CD45_TG+_2

value: 12 weeks


title: DGDE492

description:
RNA-Seq
DGDE492


title: DGCB492

description:
RNA-Seq
DGCB492

source_name: hippocampal DG cell body layer


title: islet_CD45_TG+_1

value: Ins2-CCL21 NOD


title: islet_CD45_TG+_3


title: I22M-BNST

source_name: anterodorsal BNST

extract_protocol:
The anterodorsal BNST (adBNST) was punched from frozen brains, total RNA was extracted using Trizol reagent (Ambion, Life Technologies) and was treated with a DNA-free kit (Ambion, Life Technologies). Total RNA (215ng) was used for the library construction as described below.
MiRNA Libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq kit v3. Total RNA (215ng) was denatured and NEXTflex adapters were ligated to the 3' and 5' ends of the RNA. After adapter ligations and cleanups, the adapter-ligated RNA entered reverse transcription, resulting in a cDNA first strand synthesis product. The reverse transcription products were then isolated and amplified by PCR (22 cycles). Successful library production and isolation was confirmed by the Agilent High-Sensitivity Screentape assay. Quantification of libraries was performed using Qubit Picogreen and KAPA quantitative real-time polymerase chain reaction (qRT-PCR) assays. Libraries were normalized, pooled, denatured and sequenced on the HiSeq 2500 using Rapid v2 sequencing reagents and flowcell.
All samples were processed using the small RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).

tag: housing condition

value: Socially Isolated (SI)

value: Male

value: Sprague-Dawley


title: islet_CD45_TG-_3

tag: tissue


title: islet_CD45_TG-_2


title: CA3CB492

description:
RNA-Seq
CA3CB492

source_name: hippocampal CA3 cell body layer


title: islet_CD45_TG-_1


title: CA2DE492

description:
RNA-Seq
CA2DE492


title: CA3DE492

description:
RNA-Seq
CA3DE492

source_name: hippocampal CA3 dendritic layer


title: CA2CB492

description:
RNA-Seq
CA2CB492

source_name: hippocampal CA2 cell body layer


title: CA1CB492

description:
RNA-Seq
CA1CB492

source_name: hippocampal CA1 cell body layer


title: CA1DE492

description:
RNA-Seq
CA1DE492

source_name: hippocampal CA1 dendritic layer


title: PSPA14_Rep2

city: VALENCIA

first: LOMAS LOPEZ

last: RODRIGO

address: C/ Eduardo Primo Yúfera, 3 (junto Oceanogràfic)

institute: CIPF

data_processing:
Illumina reads were mapped to the Pseudomonas genome PA14 (NCBI reference sequence, NC_008463.1) and PAO1 (GeneBank, version AE004091.2) by TopHat (version TopHat v1.0.12)
Gene expression was done by the Htseq package, after removing rRNA mapping reads
Data was normalized using the RPKM conversion
Differential expression analysis was done using the Bioconductor package NOISeqBIO version 2.6.0.
Genome_build: PA14 (NCBI reference sequence, NC_008463.1) and PAO1 (GeneBank, version AE004091.2)
Supplementary_files_format_and_content: All processed txt data are single text tables with gene coverage (HTSeq-count).

organism: Pseudomonas aeruginosa PAO1

source_name: P. aeruginosa PAO1

growth_protocol: Cultures were inoculated at an optical density at 600 nm (OD600) of 0.1 with overnight cultures, and strains were grown at 37°C with aeration in rich media (LB) to early stationary phase.

extract_protocol:
Total RNA was isolated from cell pellets equivalent to 2 OD600 units of bacterial culture using SV total RNA isolation system (Promega) folowing the manufacturer's instructions. Once isolated and prior to the library preparation, the integrity of RNA samples was assessed with Bioanalyzer system.
Libraries were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit from Illumina. 50 base pair single end sequence reads were generated using the Illumina HiSeq 2000 platform at the Vienna BioCenter Core Facility (http://www.csf.ac.at)

tag: sample type

value: cell pellets


title: DGCB496

description:
RNA-Seq
DGCB496


title: CA3CB496

description:
RNA-Seq
CA3CB496


title: CA2DE496

description:
RNA-Seq
CA2DE496


title: CA3DE496

description:
RNA-Seq
CA3DE496


title: DGDE496

description:
RNA-Seq
DGDE496


title: CA2CB496

description:
RNA-Seq
CA2CB496


title: islet_CD45_TG-_4

value: Pancreatic Islets


title: DGDE502

description:
RNA-Seq
DGDE502


title: CA1DE496

description:
RNA-Seq
CA1DE496


title: DGCB502

description:
RNA-Seq
DGCB502


title: CA3DE502

description:
RNA-Seq
CA3DE502


title: CA1CB496

description:
RNA-Seq
CA1CB496


title: CA2DE502

description:
RNA-Seq
CA2DE502


title: 208_Wang_input_WTPY79

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University at Bloomington

description: ChIP using anti-SMC antibodies

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For Hi-C, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently by Bowtie version 2.1.0 to preserve the order of reads. All the processing steps afterwards were performed using an in-house Perl scripts. For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
For Hi-C, the two resulting SAM files were then merged together. Unaligned reads were discarded.
For Hi-C, the Bacillus subtilis (PY79) genome was divided into restriction fragments (2398 HindIII fragments). Each aligned read was sorted into its corresponding restriction fragment. We inferred that a DNA fragment resulted from non-ligation or self-ligation if reads from both ends were from the same restriction fragment; these reads were discarded. Only DNA fragments for which the reads came from different restriction fragments were retained and used for construction of a Hi-C contact map.
For Hi-C, the genome of Bacillus subtilis (PY79) was then divided into bins 10 kb and the remaining reads were allocated to their corresponding bin. We then counted the number of fragments having reads with in different bins. A raw Hi-C contact map is the matrix of read counts in which each entry, mij, indicates the number of fragments with ends mapping to bins i and j. The raw Hi-C contact map/matrix is biased due to the uneven distribution of restriction enzyme sites and, to a lesser extent, differences in GC content and the mappability of individual reads. We normalized raw contact maps using an iterative normalization procedure (Imakaev et al., 2012 PMID: 22941365). Essentially, we converted the number of interactions, or read counts, into Hi-C scores by applying the following equation and iteratively repeating it for the resulting contact map after each cycle:  mij =mij * (total reads) / (total reads in bin i * total reads in bin j). The iterative procedure was repeated until the maximum relative error of the total number of Hi-C scores in a bin was less than 10-5. Resulting matrices were normalized so that Hi-C scores for each row and column sum to 1. Subsequent analysis and visualization was done using R scripts.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .matrix.txt: tab-delimited text files of the iteratively-corrected Hi-C contact maps/matrices. Files ending with .csv: comma-separated values files of ChIP-seq results.
Supplementary_files_format_and_content: text files contain 10kb bins of B. subtilis genome and normalized Hi-C interaction scores
Supplementary_files_format_and_content: csv files contain genome position and number of reads at each genome position

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.

extract_protocol:
Hi-C experiments were performed using HindIII according to previous publications (Le et al, 2013, PMID: 24158908; Wang et al 2015, PMID: 26253537). ChIP-seq experiments were performed using anti-SMC, anti-ScpA, anti-ScpB, anti-ParB or anti-GFP antibodies according to previous publication (Graham et al 2014, PMID: 24829297).
Standard library construction protocol was used for Illumina Nextseq 500 sequencing platform (Hi-C) or Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
None

tag: developmental stage

value: CH, 37 C

tag: genotype

value: wild-type

tag: restriction enzyme


title: 206_Wang_input_BWX3612_10m_rif

description: ChIP using anti-GFP antibodies

treatment_protocol:
Cells were growing in CH medium at 37˚C, rifampicin was added to 25ug/ml final concentration for 10 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 25 ug/ml rifampicin for 10 min

value: rpoC-gfp (spec), parS-delta-9 no a.b., +26^ring parS (loxP-kan-loxP)


title: 207_Wang_input_BWX3612_30m_rif

description: ChIP using anti-GFP antibodies

treatment_protocol:
Cells were growing in CH medium at 37˚C, rifampicin was added to 25ug/ml final concentration for 30 min, fixed by 3% formaldehyde for 30min at room temperature
None

value: CH, 37 C, 25 ug/ml rifampicin for 30 min


title: PSPA14_Rep1


title: CA1DE502

description:
RNA-Seq
CA1DE502

value: Amigo2-GFP C57BL/6J

value: brain/hippocampus


title: CA2CB502

description:
RNA-Seq
CA2CB502

value: 6-8 weeks

value: male


title: 205_Wang_ChIPSMC_WTPY79

description: ChIP using anti-SMC antibodies


title: GFP LT-HSCs + LT-HSCs for wt [CC6]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

description: GFP cells visualized using the loxP-IRES-GFP-polyA-loxP sequence as reference (sample 1 (2147 cells) and 2 (8662) are two aliquots of the same cells pool)

data_processing:
The raw sequencing reads were processed with the inDrops pipeline (https://github.com/indrops/indrops) using bowtie 1.1.1, samtools 1.3.1 and RSEM 1.3.0. The inDrops pipeline was executed with the parameter -e 100 for bowtie and the default parameters for the other tools.
The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The sequence of loxP-IRES-GFP-polyA-loxP was added in the above reference transcriptome to facilitate the detection of GFP positive cells.
The data were processed and analyzed as previously described in Rodriguez-Fraticelli AE et al, Nature 2018.
Genome_build: GRCm38.81
Supplementary_files_format_and_content: inDrop v3 derived count table

source_name: Bone marrow

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Reverse transcription of single cell lysates was performed at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols 2017

treatment_protocol: After euthanasia, whole bone marrow (excluding the cranium) was isolated in 2% fetal bovine serum (FBS) in phosphate buffered saline (PBS), followed by removal of erythrocytes using RBC lysis buffer. Lineage depletion was performed using Magnetic Assisted Cell Sorting (Miltenyi Biotec) with anti-biotin magnetic beads and the following biotin-conjugated lineage markers: B220, Gr1, Ter119, CD4, CD8. Cell populations from the Lin- BM were sorted using 1.5 sorting mode with a FACSAria II sorter (BD). GFP cells from Mds1-GFP/+ Flt3-Cre mice were sorted solely using DAPI-GFP+. SLAM LT-HSCs from wild type mice were sorted using DAPI-Lin-cKit+Sca+CD48-CD150+. Flow cytometry data were analyzed with FlowJo (Tree Star).

value: Mds1-GFP/+ Flt3-Cre

value: bone marrow

tag: cell type

value: GFP+ long-term hematopoietic stem cells

tag: purification for gfp

value: DAPI-GFP+ purification for LT-HSC from wt:DAPI-Lin-cKit+Sca+CD48-CD150+


title: CA1CB502

description:
RNA-Seq
CA1CB502


title: GFP LT-HSCs + LT-HSCs for wt [CC5]


title: CA3CB502

description:
RNA-Seq
CA3CB502


title: 36-12days-Kainate-technical-replicate-d

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina Bcl2fastq 2.17.1.14 software was used for basecalling.
The analyses were performed using the Eoulsan pipeline version 2.0-beta3, including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis: Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus musculus genome from Ensembl version 81 using STAR (version 2.4.0k). Alignments from reads matching more than once on the reference genome were removed using Java version of samtools. To compute gene expression, Mus musculus GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced genes were counted using HTSeq-count 0.5.3. The sample counts were normalized using DESeq2 1.8.1 [5]. Statistical treatments and differential analyses were also performed using DESeq2 1.8.1.
Genome_build: mm10 (Ensembl 81)
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample

source_name: Hippocampus CA1 area

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA XS kit (Macherey-Nagel). For each sample 10 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech).  Afterwards an average of 180 ng of amplified cDNA was used to prepare libraries.
Libraries were prepared using the Nextera XT DNA kit (Illumina)

tag: genetic background

tag: time

value: 12 days

tag: treatment

value: Kainate


title: 35-12days-Kainate-technical-replicate-c


title: 36-12days-Kainate-technical-replicate-a


title: 36-12days-Kainate-technical-replicate-b


title: 35-12days-Kainate-technical-replicate-d


title: 36-12days-Kainate-technical-replicate-c


title: 35-12days-Kainate-technical-replicate-b


title: 35-12days-Kainate-technical-replicate-a


title: 34-12days-Kainate-technical-replicate-d