title: Ythdf1-CLIP-seq_input_repl.2

description:
A2
RNA crosslinked with proteins with the same size of Ythdf1
A_Ythdf1_CLIP_seq_peak_list.xlsx


title: spinal_cord_anterior_rep2

status: Public on Aug 17 2018

type: RNA

city: Suita

first: Hiroki

middle: R

last: Ueda

state: Osaka

address: 1-3 Yamadaoka

department: QBiC

country: Japan

institute: RIKEN

description: Pooled samples collected at every 4 hours over 1 day.

hyb_protocol: cRNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: spinal cord anterior

label_protocol: cDNA samples were subjected to the one-cycle target labeling procedure for biotin labeling by in vitro transcription (Affymetrix).

growth_protocol: Balb/c mice (male) purchased 5 weeks postpartum, were adapted under standard 12 h light/dark cycles (LD) for 2 weeks, before samples were obtained under LD or constant darkness (DD) conditions, every 4 h over 1 day, starting at ZT0.

extract_protocol: The total RNA was prepared from the pooled samples for each region taken at all time points using Trizol reagent (GIBCO BRL).

treatment_protocol: Slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix (Neuroscience, Tokyo), frozen, and the specific regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope.

tag: gender

value: male

tag: strain

value: Balb/c

tag: age

value: 7-8 weeks

tag: tissue

value: spinal cord anterior


title: Retina_rep2

source_name: retina

value: retina


title: Retina_rep1


title: Cb_vermis_rep1

source_name: cerebellar cortex vermis

value: cerebellar cortex vermis


title: Cb_vermis_rep2


title: Cb_lobe_rep2

source_name: cerebellar cortex lobe

value: cerebellar cortex lobe


title: Pn_rep2

source_name: pontine nucleus

value: pontine nucleus


title: SC_rep2

source_name: superior colliculus

value: superior colliculus


title: spinal_cord_posterior_rep2

source_name: spinal cord posterior

value: spinal cord posterior


title: Cb_lobe_rep1


title: Tg_rep1

source_name: dorsal tegmental nucleus

value: dorsal tegmental nucleus


title: spinal_cord_anterior_rep1


title: SN_rep2

source_name: substantia nigra

value: substantia nigra


title: Pn_rep1


title: Cb_nucleus_rep1

source_name: cerebellar nucleus

value: cerebellar nucleus


title: spinal_cord_posterior_rep1


title: VTA_rep1

source_name: ventral tegmental area

value: ventral tegmental area


title: MVe_rep2

source_name: medial vestibular nucleus

value: medial vestibular nucleus


title: IC_rep2

source_name: inferior colliculus

value: inferior colliculus


title: SC_rep1


title: IC_rep1


title: PAG_rep1

source_name: periaqueductal gray

value: periaqueductal gray


title: LH_rep1

source_name: lateral hypothalamus

value: male

value: lateral hypothalamus


title: Tg_rep2

value: Balb/c

value: 7-8 weeks


title: SN_rep1


title: LH_rep2


title: PAG_rep2


title: MVe_rep1


title: VTA_rep2


title: Cb_nucleus_rep2


title: Arc_rep2

source_name: arcuate hypothalamic nucleus

value: arcuate hypothalamic nucleus


title: Arc_rep1


title: VMH_rep2

source_name: ventromedial hypothalamic nucleus

value: ventromedial hypothalamic nucleus


title: SPa_dorsal_rep2

source_name: subparaventricular zone dorsal

value: subparaventricular zone dorsal


title: SPa_ventral_rep1

source_name: subparaventricular zone ventral

value: subparaventricular zone ventral


title: SPa_dorsal_rep1


title: VMH_rep1


title: DM_rep1

source_name: dorsomedial hypothalamic nucleus

value: dorsomedial hypothalamic nucleus


title: SO_rep2

source_name: supraoptic nucleus

value: supraoptic nucleus


title: Pituitary_rep1

source_name: pituitary

value: pituitary


title: SPa_ventral_rep2


title: M_rep2

source_name: mammillary body

value: mammillary body


title: DM_rep2


title: M_rep1


title: Pineal_rep2

source_name: corpus pineal

value: corpus pineal


title: ME_rep1

source_name: median eminence

value: median eminence


title: ME_rep2


title: SCN_rep1

source_name: suprachiasmatic nucleus

value: suprachiasmatic nucleus


title: MPA_rep2

source_name: medial preoptic area

value: medial preoptic area


title: MPA_rep1


title: Pa_rep1

source_name: paraventricular hypothalamic nucleus

value: paraventricular hypothalamic nucleus


title: SCN_rep2

value: male


title: SO_rep1


title: Pa_rep2


title: Pineal_rep1


title: LG_rep2

source_name: lateral geniculate body

value: lateral geniculate body


title: MG_rep1

source_name: medial geniculate nucleus

value: Balb/c

value: medial geniculate nucleus


title: Hb_rep2

source_name: habenular nucleus

value: 7-8 weeks

value: habenular nucleus


title: LG_rep1


title: Pituitary_rep2


title: Hb_rep1


title: MG_rep2


title: VPM_VPL_rep2

source_name: ventral posterolateral thalamic nucleus / ventral posteromedial thalamic nucleus


title: VA_VL_rep2

source_name: ventral anterior thalamic nucleus / ventrolateral thalamic nucleus


title: VPM_VPL_rep1

value: ventral posterolateral thalamic nucleus / ventral posteromedial thalamic nucleus


title: VA_VL_rep1

value: ventral anterior thalamic nucleus / ventrolateral thalamic nucleus


title: CPu_lateral_rep1

source_name: caudate putamen lateral

value: caudate putamen lateral


title: MD_rep2

source_name: mediodorsal thalamic nucleus

value: mediodorsal thalamic nucleus


title: A_anterior_rep1

source_name: amygdala anterior

value: amygdala anterior


title: DG_rep1

source_name: dentate gyrus (hippocampus)

value: dentate gyrus (hippocampus)


title: GP_rep1

source_name: globus pallidus

value: globus pallidus


title: CA2_CA3_rep1

source_name: CA2 / CA3 (hippocampus)

value: CA2 / CA3 (hippocampus)


title: DG_rep2


title: A_posterior_rep1

source_name: amygdaloid complex (posterior)

value: amygdaloid complex (posterior)


title: A_posterior_rep2


title: MD_rep1


title: Tu_rep1

source_name: olfactory tubercle

value: olfactory tubercle


title: ventral_S_rep2

source_name: ventral subiculum

value: ventral subiculum


title: ventral_S_rep1

value: male


title: Pir_rep2

source_name: piriform cortex

value: piriform cortex


title: A_anterior_rep2

value: Balb/c


title: CPu_medial_rep2

source_name: caudate putamen medial

value: caudate putamen medial


title: CPu_medial_rep1

value: 7-8 weeks


title: Pir_rep1


title: GP_rep2


title: CA2_CA3_rep2


title: OB_anterior_rep2

source_name: olfactory bulb anterior

value: olfactory bulb anterior


title: OB_posterior_rep1

source_name: olfactory bulb posterior

value: olfactory bulb posterior


title: Tu_rep2


title: CA1_rep1

source_name: CA1 (hippocampus)

value: CA1 (hippocampus)


title: OB_posterior_rep2


title: CA1_rep2


title: Cx_cingulate_rep2

source_name: cerebral cortex cingulate

value: cerebral cortex cingulate


title: CPu_lateral_rep2

value: caudate putamen lateral


title: Cx_motor_rep2

source_name: cerebral cortex motor

value: cerebral cortex motor


title: Cx_cingulate_rep1


title: Cx_motor_rep1


title: RS_rep2

source_name: retrosplenial cortex

value: retrosplenial cortex


title: RS_rep1


title: ZAPKO11_uIFN_genomic DNA

type: SRA

city: Seattle

first: Molly

last: Ohainle

state: WA

address: 1100 Fairview Ave N, C2-023

country: USA

institute: Fred Hutchinson Cancer Research Center

description: genomic DNA

library_source: genomic

data_processing:
Library strategy: CRISPR screen
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to demultiplexing  using FASTX-Toolkit v0.0.13
Reads were trimmed and aligned to the PIKA HIV guide library using Bowtie v1.0.0, allowing 0 mismatches in the guide sequence, followed by tabulation of read counts using R
Genome_build: PIKA HIV sgRNA Library.  FASTA is available on series record. More information on the library is also available on bioRxiv:
https://www.biorxiv.org/content/early/2018/07/20/363432
Supplementary_files_format_and_content: tab delimited files with read counts for each guide sequence

molecule: genomic DNA

organism: Homo sapiens

source_name: THP-1 monocytic cell line

growth_protocol: THP-1 monocytic cells are grown in RPMI with 10% FBS and Pen/Strep (supplemented to 10mM HEPES, 4.5 g/L D-Glucose, 0.11 g/L Sodium Pyruvate + Glutamax), passaging between 2e5 cells/mL and 1e6 cells/mL.

extract_protocol:
Genomic DNA was extracted using a QIAamp DNA Blood Midi kit (Qiagen)
Genomic DNA or reverse-transcribed viral RNA were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All Viral RNA was amplified for each sample where appropriate. For Genomic DNA samples a total of 500-fold coverage of the 15,414 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For viral RNA, all PCR1 was amplified in the second round. For gDNA, 5uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided SPRI (AMPureXP, Beckman Coulter), quantified with a Qubit HS dsDNA assay and pooled for sequencing.

treatment_protocol: 8e6 cells (>500X coverage) were transduced with the PIKAHIV library (MOI of 0.75) and selected in 1ug/mL puromycin for 10-14 days. For each replicate, 8e6 cells were infected with or without overnight IFNα treatment with HIV. Cells and viral supernatants were harvested 3 days post-infection.

tag: cell type

tag: genotype

value: ZAP-KO

tag: ifn treatment

value: yes

tag: hiv strain

value: HIV-1 LAI


title: ZAPKO46_noIFN_genomic DNA

description: genomic DNA

value: no


title: ZAPKO46_uIFN_genomic DNA

description: genomic DNA


title: ZAPKO11_noIFN_genomic DNA

description: genomic DNA


title: wt_noIFN_genomic DNA

description: genomic DNA

value: wildtype


title: wt_uIFN_genomic DNA

description: genomic DNA


title: OB_anterior_rep1

value: male


title: LS_rep1

source_name: lateral septal nucleus

value: lateral septal nucleus


title: 10days Lp(a)_OSM rep1

city: Montreal

first: Adel

last: Schwertani

state: Quebec

address: 1001 Decarie Blvd

department: Cardiology

country: Canada

institute: RI-MUHC

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol with  Illumina HumanHT-12 V4.0 expression beadchip.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with FlexArray 1.6.3 developed by Genoquebec Innovation Center, McGill University.

source_name: HAVICs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HAVICs were isolated from non stenotic human aortic valve excised surgically, and cultured in DMEM medium (high glucose, ThermoFishers) plus 10% FBS and 1xAntibiotic Antimycotic Solution. Cells of passage 3-5 were used for Lp(a) treatment. For calcification inducing, HAVICs were cultured in osteogenic medium (OSM: full DMEM medium plus 2mM phosphate buffer, pH7.4).

extract_protocol: Total RNA were extracted using Trizol reagent and QIAGEN RNeasy mini kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: HAVICs were treated with or without purified human Lp(a) at 50µg/ml for 3 days, 10 days and 20 days in DMEM medium or osteogenenic medium.

tag: cells

value: Aortic Valve Interstitial Cells

tag: medium

value: Osteogenic Medium

tag: lp(a)

value: 50 µg/ml

tag: time

value: 10 days


title: 20days OSM Ct rep1

description: replicate 1

value: 20 days


title: 3days Lp(a)_OSM rep1

description: replicate 1

value: 3 days


title: m6A-RIP-seq_ECT_RIP_repl.3

city: Chicago

first: Chuan

last: He

state: ILLINOIS

address: 929 E 57th St., GCIS E319

department: Department of Chemistry

institute: The University of Chicago

description:
D12
polyA RNA, anti-m6A-antibody enriched
D_m6A_RIP_seq_ECT_processed.xlsx

library_source: transcriptomic

data_processing:
Sequencing data were mapped to mouse genome version mm10 downloaded from UCSC using Tophat v2.0.14.
For RNA-seq analysis, RPKM were calculated by Cuffnorm. For CLIP-seq experiments, after removing the adapter by Cutadapt, the reads were aligned to the mouse genome (mm10) by Bowtie2.
Peaking calling in Ythdf1-CLIP-seq. All mapped reads were treated as background and mutations were treated as signals for peak calling. PARalyzer was use for peak calling in CLIP-seq sample with a few modifications: (1) mutations in both "CLIP" and “Input” are removed in "CLIP"; (2) sites with 100% mutations rate were also removed. The remaining mutations were used for peak calling. At least two mutation sites are need in each peak (MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER =2).
Peak calling in m6A-CLIP-seq. We followed the same peak calling method as reported in Nature volume 542, pages 475–478 (23 February 2017)
For m6A-RIP-seq: Low-quality bases and adaptor sequences from original reads were removed using Trimmomatic. The remaining reads were then mapped to the mouse genome (mm10) using STAR aligner. Mapped reads between samples were normalized using DESeq2. The “Input” and “RIP” libraries were normalized respectively.
Genome_build: mm10
Supplementary_files_format_and_content: CLIP-seq: peak list including gene name, genome coordinates, strand, and number of muations under the peak; RNA-seq: rpkm; m6A-RIP-seq: readcounts and rpkm.

molecule: polyA RNA

source_name: Dentate gyrus (DG) of the Hippocampus

growth_protocol: All animals were maintained under a 12/12 h light/dark cycle with lights on at 7:00 AM, and temperature and humidity were kept at 22 ± 1 °C, 55% ± 5%, with ad libitum access to food and water.

extract_protocol:
Total RNA from adult mouse DG was isolated using the TRIzol reagent according to the manufacturer's instructions (Invitrogen). mRNA purification was performed with poly(A)+ RNA selection twice using Dynabeads Oligo (dT)25 (Thermo Fisher; 61006).
Customerized protocol as reported in Nature Protocols volume 9, pages 171–181 (2014)

value: Dentate gyrus (DG) of the Hippocampus

value: 8-16 weeks (adult)

tag: ip antibody

value: Rabbit anti-m6A (202 003, SYSY)


title: LS_rep2

value: Balb/c

value: 7-8 weeks


title: ZNF207 KD rep2

city: Bozeman

first: Fang

last: Fang

state: Montana

address: CBB Room 103

department: Cell Biology

institute: Montana State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: all.gene.RPKM.txt file includes RPKM values of differential expressed genes of each Sample …

source_name: H9 ESCs

extract_protocol:
total RNA extracted using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ZNF207 knock down with siRNAs

value: ESCs

value: ZNF207 knock down


title: POA_rep1

source_name: preoptic area

growth_protocol: 5-week Balb/c male mice were adapted under a standard 12-h light/dark cycle (LD) for 2 weeks, and samples were obtained under LD or constant darkness (DD) conditions.

treatment_protocol: Slices (0.5-mm thick) of mouse brain were cut on a Mouse Brain Matrix, frozen, and the BF/POA regions were punched out bilaterally with a microdissecting needle (gauge 0.5 mm) under a stereomicroscope.

value: preoptic area


title: 3days Lp(a)_OSM rep2

description: replicate 2


title: m6A-RIP-seq_ECT_RIP_repl.2

description:
D11
polyA RNA, anti-m6A-antibody enriched
D_m6A_RIP_seq_ECT_processed.xlsx

value: wildtype


title: m6A-RIP-seq_ECT_RIP_repl.1

description:
D10
polyA RNA, anti-m6A-antibody enriched
D_m6A_RIP_seq_ECT_processed.xlsx


title: 20days Lp(a)_OSM rep1

description: replicate 1


title: 10days OSM Ct rep1

description: replicate 1


title: ZNF207 KD rep1


title: ZNF207 ChIP-seq rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie
Mapped reads were then used to call peaks with MACS
Wig to bigwig convertion
Genome_build: hg19
Supplementary_files_format_and_content: BIGWIG files

growth_protocol: H9 ESCs grown on matrigel using mTESR1 media

extract_protocol:
Phenol/choloroform
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) 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. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: no treatment

tag: chip antibody

value: anti-ZNF207 (Santa Cruz Biotechnology, Inc.,  sc-271942)


title: Control Rep1

value: control


title: 3days OSM Ct rep2

description: replicate 2

value: Aortic Valve Interstitial Cells


title: POA_rep2

value: male


title: ZNF207 ChIP-seq rep1


title: 3days OSM Ct rep1

description: replicate 1

value: Osteogenic Medium


title: 3days Lp(a)_DMEM rep2

description: replicate 2

value: DMEM

value: 50 µg/ml


title: 3days DMEM Ct rep2

description: replicate 2

value: 3 days


title: Ovarian CA-MSC 10

city: Melbourne

first: Elizabeth

middle: Louise

last: Christie

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava software v1.17 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37 whole genome and transcriptome using Bowtie2 v2.2.3  and TopHat2 v2.0.13
Gene abundance was estimated using HTSeq, values were log normalised then differential expression was calculated with the R package Limma
Genome_build: GRCh37
Supplementary_files_format_and_content: log2 normalised expression values

source_name: Ovarian tumour tissue

growth_protocol: grown in supplemented MEBM media under adherent tissue culture conditions, harvested at < passage 8

extract_protocol:
RNA from cells was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v2 was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: high grade serous ovarian cancer


title: 3days DMEM Ct rep1

description: replicate 1


title: 3days Lp(a)_DMEM rep1

description: replicate 1


title: m6A-RIP-seq_Mock_RIP_repl.1

description:
D7
polyA RNA, anti-m6A-antibody enriched
D_m6A_RIP_seq_ECT_processed.xlsx

value: Dentate gyrus (DG) of the Hippocampus

value: 8-16 weeks (adult)


title: m6A-RIP-seq_ECT_input_repl.3

description:
D6
Quantification of transcritps abundance in mouse DG 1-hour post ECT
D_m6A_RIP_seq_ECT_processed.xlsx

extract_protocol:
Total RNA from WT littermate control and Ythdf1-KO mouse hippocampus was extracted using Trizol (Invitrogen) and isopropanol precipitation.  mRNA extraction was performed by poly(A)+ RNA selection once using Dynabeads  mRNA DIRECT  Purification Kit (Invitrogen)
Customerized protocol as reported in Nature Protocols volume 9, pages 171–181 (2014)


title: m6A-RIP-seq_Mock_RIP_repl.2

description:
D8
polyA RNA, anti-m6A-antibody enriched
D_m6A_RIP_seq_ECT_processed.xlsx

value: Rabbit anti-m6A (202 003, SYSY)


title: m6A-RIP-seq_Mock_RIP_repl.3

description:
D9
polyA RNA, anti-m6A-antibody enriched
D_m6A_RIP_seq_ECT_processed.xlsx


title: Ovarian CA-MSC 9


title: m6A-RIP-seq_ECT_input_repl.1

description:
D4
Quantification of transcripts abundance in mouse DG 1-hour post ECT
D_m6A_RIP_seq_ECT_processed.xlsx


title: m6A-RIP-seq_Mock_input_repl.3

description:
D3
Quantification of transcripts abundance in mouse DG before ECT
D_m6A_RIP_seq_ECT_processed.xlsx


title: Ovarian CA-MSC 5

value: low grade serous ovarian cancer


title: Ovarian CA-MSC 8


title: m6A-RIP-seq_Mock_input_repl.2

description:
D2
Quantification of transcripts abundance in mouse DG before ECT
D_m6A_RIP_seq_ECT_processed.xlsx


title: Ovarian CA-MSC 4


title: m6A-RIP-seq_ECT_input_repl.2

description:
D5
Quantification of transcripts abundance in mouse DG 1-hour post ECT
D_m6A_RIP_seq_ECT_processed.xlsx


title: Ovarian CA-MSC 7

value: endometrioid ovarian cancer


title: Ovarian CA-MSC 1

value: poorly differentiated ovarian adenocarcinoma


title: Normal omental MSC 4

source_name: Normal omentum

value: benign adipose


title: Normal omental MSC 2

description: A-MSC-X

value: benign omental adipose


title: Normal omental MSC 3


title: Ume6 ChIP-exo 4.1 Replicate 2

city: University Park

first: Matthew

middle: John

last: Rossi

state: Pennsylvania

address: 453 N Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description:
PSU10636
Ume6_ChIP-exo4.1_peaks.gff

data_processing:
Library strategy: ChIP-exo
For paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
Reads were aligned to sacCer3 or GRch37(hg19) genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: gff, peak pair calls filtered for significance over background

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

value: Ume6-TAP (Sigma i5006-100MG, Lot#SLBM2617V)

tag: cell description

value: GRF88, MATa his4-38, S288C background


title: Ume6 ChIP-exo 5.0 Replicate 2

description:
PSU11017
Ume6_ChIP-exo5.0_peaks.gff


title: Ume6 ChIP-exo 4.0 Replicate 2

description:
PSU10629
Ume6_ChIP-exo4.0_peaks.gff


title: Ume6 ChIPmentation (alt ChIP-seq)

description:
PSU10249
Ume6_ChIPmentation_peaks.gff

data_processing:
For paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
Reads were aligned to sacCer3 or GRch37(hg19) genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: gff, peak pair calls filtered for significance over background


title: Ovarian CA-MSC 2


title: Ume6 ChIP-exo 5.0 Replicate 1

description:
PSU10858
Ume6_ChIP-exo5.0_peaks.gff


title: m6A-RIP-seq_Mock_input_repl.1

description:
D1
Quantification of transcripts abundance in mouse dentate gyrus (DG) before electroconvulsive treatment (ECT）
D_m6A_RIP_seq_ECT_processed.xlsx

value: wildtype


title: Ovarian CA-MSC 6


title: Ume6 ChIP-exo 1.1

description:
PSU09573
Ume6_ChIP-exo1.1_peaks.gff


title: Normal omental MSC 1


title: Ovarian CA-MSC 3


title: Ume6 ChIP-exo 4.0 Replicate 1

description:
PSU10379
Ume6_ChIP-exo4.0_peaks.gff


title: Ume6 ChIP-seq

description:
PSU09091
Ume6_ChIP-seq_peaks.gff


title: Ume6 ChIP-exo 4.1 Replicate 1

description:
PSU10375
Ume6_ChIP-exo4.1_peaks.gff


title: Ume6 ChIP-exo 3.0 Replicate 1

description:
PSU10237
Ume6_ChIP-exo3.0_peaks.gff


title: Reb1 ChIP-exo 5.0 Replicate 1

description:
PSU10857
Reb1_ChIP-exo5.0_peaks.gff

value: Reb1-TAP (Sigma i5006-100MG, Lot#SLBM2617V)


title: Reb1 ChIP-seq 1-step (alt ChIP-seq)

description:
PSU10746
Reb1_ChIP-seq1step_peaks.gff


title: Reb1 ChIP-exo 5.0 Low Chromatin


title: Reb1 ChIP-exo 5.0 Replicate 2

description:
PSU11257
Reb1_ChIP-exo5.0_peaks.gff


title: Reb1 ChIP-seq

description:
PSU09093
Reb1_ChIP-seq_peaks.gff


title: Reb1 ChIP-exo 4.1 Replicate 2

description:
PSU10731
Reb1_ChIP-exo4.1_peaks.gff


title: Reb1 ChIP-exo 4.1 Replicate 3

description:
PSU10883
Reb1_ChIP-exo4.1_peaks.gff


title: Reb1 ChIP-exo 4.1 Replicate 1

description:
PSU10670
Reb1_ChIP-exo4.1_peaks.gff


title: TE-9 co-culture with TAM-like PBMo-derived macrophages

city: Kobe

first: Himiko

last: Kodaira

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

hyb_protocol: Following fragmentation, 09μL Hybridization Master Mix and 3.5μg Fragmented and Labeled cDNA were hybridized for 16 hr (60rpm) at 45C using GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using theGeneChip Scanner 3000 7G.

data_processing: The data were analyzed by using MicroArray Data Analysis Tool Ver3.2 (Filgen).

source_name: TE-9 ESCC cells co-cultured with TAM-like PBMo-derived macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng of total RNA.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were obtained from healthy male volunteer donors who provided informed consent. CD14+ PBMo were purified from PBMCs by positive selection using the auto MACS® Pro Separator (Miltentyi Biotec, Bergisch Gladbach, Germany). PBMo were cultured with macrophage-colony stimulating factor (M-CSF) (25 ng/mL, R&D Systems, Minneapolis, MN) for 6 days to induce macrophages. We added 50% TECM (TE-8 and TE-9) to the cultures for 2 days to induce TAM-like polarization.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: ESCC cells

tag: cell line


title: Ume6 ChIP-exo 3.0 Replicate 2

description:
PSU10238
Ume6_ChIP-exo3.0_peaks.gff


title: Reb1 ChIP-exo 4.0 Replicate 1

description:
PSU10913
Reb1_ChIP-exo4.0_peaks.gff


title: Reb1 ChIP-exo 3.0 Replicate 2

description:
PSU09859
Reb1_ChIP-exo3.0_peaks.gff


title: TE-8 monoculture

source_name: TE-8 ESCC cells monocultured


title: TE-9 monoculture

source_name: TE-9 ESCC cells monocultured


title: TE-8 co-culture with TAM-like PBMo-derived macrophages

source_name: TE-8 ESCC cells co-cultured with TAM-like PBMo-derived macrophages


title: Reb1 ChIP-exo 1.1 Replicate 3

description:
PSU09300
Reb1_ChIP-exo1.1_peaks.gff


title: Control (DMSO)

city: kyoto

first: partha sarathi

last: chowdhury

address: Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan

institute: kyoto university

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC)

source_name: In vitro stimulated naive CD8+ T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Naïve CD8+ T cells were stimulated with anti-CD3 and CD28 mAb-coated beads (Thermo Fisher Scientific) with recombinant human IL-2 (100 U/mL) (PeproTech, Rocky Hill, NJ, USA). The expanded T cells on 13 were used for proliferation assays and apoptosis assays, respectively.

extract_protocol: cDNA was synthesized from 100ng Total RNA using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer.

treatment_protocol: Cells were treated with bezafibrate and DMSO as a control. Bezafibrate was freshly prepared immediately before use in DMSO. Bezafibrate was added at the concentration of 30 μM for the entire culture period.

value: In vitro stimulated naive CD8+ T cells

tag: treatment

value: DMSO


title: Reb1 ChIP-exo 3.0 Replicate 1

description:
PSU09858
Reb1_ChIP-exo3.0_peaks.gff


title: Treated (bezafibrate)

value: bezafibrate


title: Reb1 ChIPmentation (alt ChIP-seq)

description:
PSU09779
Reb1_ChIPmentation_peaks.gff


title: snR4_Mutant_Ice_3

city: Edinburgh

first: Hywel

last: Dunn-Davies

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
(For all samples)  Raw reads were reverse complemented using FASTX-Toolkit,  and trimmed using Trimmomatic
(For U3 samples only) Transcript level quantification was performed using kallisto, and differential expression was quantified using sleuth
(For snR4 and BY control samples only) Reads were aligned to the yeast genome using STAR
(For snR4 and BY control samples only) Gene level quantification was performed using htseq-count (with options -f bam -r pos -s yes -t exon -i gene_name -m union)
(For snR4 and BY control samples only) Differential expression analysis was carried out using DESeq2
Genome_build: Ensembl yeast R64-1-1 assembly, release 77
Supplementary_files_format_and_content: Results of differential expression analysis are provided as tab separated text files

source_name: BY4741 cells

extract_protocol:
From total RNA samples (10mkg total RNA), poly(A)-tailed RNAs were selected using Dynabeads™ mRNA Purification Kit (Thermo Fisher Scientific) according to manufacturer’s protocol.
RNA-seq cDNA libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina according to the instruction manual provided (https://international.neb.com/-/media/catalog/datacards-or-manuals/manuale7420.pdf) using 50-100ng Poly(A)-selected RNA samples as starting material. NEBNext Multiplex Oligos (NEB) adaptors and primers were used to multiplex cDNA Illumina libraries.

tag: mutation

value: Deleted the SNR4 gene

tag: growth protocol

value: SD (glucose) medium at 30°C , following stress induced by brief transfer to ice-cold PBS


title: snR4_Mutant_Glucose_3

tag: strain

value: SD (glucose) medium at 30°C


title: snR4_Mutant_Ice_2


title: snR4_Mutant_Ice_1


title: snR4_Mutant_Glucose_1


title: Reb1 ChIP-exo 4.0 Replicate 2

description:
PSU10907
Reb1_ChIP-exo4.0_peaks.gff


title: Reb1 ChIP-exo 1.1 Replicate 1

description:
PSU09277
Reb1_ChIP-exo1.1_peaks.gff


title: BY_Control_Glucose_1


title: BY_Control_Ice_1


title: snR4_Mutant_Glucose_2


title: Reb1 ChIP-exo 1.1 Low Chromatin


title: BY_Control_Ice_3


title: U3_WT_Control_1

value: Deleted the SNR17B genetic locus and placed the expression of SNR17A under the control of a repressible PGAL promoter, wild type snR17A expressed from pRS413 (centromeric, -His) plasmid


title: U3_WT_Control_2


title: Reb1 ChIP-exo 1.1 Replicate 2

description:
PSU09278
Reb1_ChIP-exo1.1_peaks.gff


title: BY_Control_Glucose_3


title: BY_Control_Glucose_2


title: BY_Control_Ice_2


title: U3_WT_Control_3


title: U3_Mutant_1

value: Deleted the SNR17B genetic locus and placed the expression of SNR17A under the control of a repressible PGALpromoter, truncated U3 mutant expressed from pRS413 (centromeric, -His) plasmid


title: U3_Mutant_3


title: U3_Mutant_2


title: BY4741 ChIP-exo 4.1

description:
PSU10687
BY4741_ChIP-exo4.1_peaks.gff

value: No TAP (Sigma i5006-100MG, Lot#SLBM2617V)


title: BY4741 ChIP-seq 1-step (alt ChIP-seq)

description:
PSU10869
BY4741_ChIP-seq1step_peaks.gff


title: BY4741 ChIP-exo 5.0

description:
PSU11014
BY4741_ChIP-exo5.0_peaks.gff


title: NOP58_Glucose_5

data_processing:
Library strategy: CLASH
Demultiplexing, adapter trimming and PCR collapsing of raw reads was performed using the hyb pipeline (https://github.com/gkudla/hyb), using the command hyb demultiplex preprocess check in=[RAW FASTQ FILE] code=[BARCODES FILE]
The preprocessed files were aligned to a Saccharomyces Cerevisiae unspliced genes database, using the command blastall -p blastn -d "[DATABASE]" -i "[PRE-PROCESSED READS]" -o "[ALIGNED READS]" -m 8 -W 11 -e 0.1 -a 1
The aligned files were analysed using the hyb pipeline, with a modification to prefer snoRNA hybrids rather than miRNA hybrids. Output files were in hyb format.
Reproducible hybrids were identified using the hybtools package (https://github.com/hyweldd/hybtools), using the command hybtools combine -d -12 -s -b 2 -f 1 -c [UA_DG_HYB FILES] > [REPRODUCIBLE HYBRIDS FILE]
Genome_build: Ensembl yeast R64-1-1 assembly, release 77, with snoRNAs extended by 20bps on each side and masked out of mRNAs, and duplicated rRNA sequences removed.
Supplementary_files_format_and_content: Unique hybrids are provided in hyb format, specified in Travis et al., Hyb: A bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data, Methods, 2013.

growth_protocol: YMM, 30 degrees celsius, OD 0.5

extract_protocol:
Extraction was performed following the protocol described in Kudla et al., Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast, PNAS, 2011.
Library construction was performed following the protocol described in Kudla et al., Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast, PNAS, 2011.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking, following the protocol described in Kudla et al., Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast, PNAS, 2011.

tag: bait protein

tag: growth medium

value: Glucose


title: NOP58_Glucose_6


title: NOP56_Ethanol_1

value: Glucose, followed by 20 minutes in Ethanol / Glycerol


title: NOP1_Ethanol_1


title: NOP56_Ethanol_2


title: NOP1_Ethanol_2


title: MTR4_Glucose_1


title: BY4741 ChIP-exo 3.0

description:
PSU09864
BY4741_ChIP-exo3.0_peaks.gff


title: MTR4_Ethanol_1

value: Glucose, followed by 20 minutes in Ethanol/Glycerol


title: BY4741 ChIP-exo 1.1

description:
PSU09588
BY4741_ChIP-exo1.1_peaks.gff


title: Abf1 ChIP-seq

description:
PSU08663
Abf1_ChIP-seq_peaks.gff

value: Abf1-TAP (Sigma i5006-100MG, Lot#SLBM2617V)


title: NOP58_Glucose_3


title: NOP58_Glucose_2


title: Abf1 ChIPmentation (alt ChIP-seq)

description:
PSU10246
Abf1_ChIPmentation_peaks.gff

value: GRF88, MATa his4-38, S288C background


title: BY4741 ChIPmentation (alt ChIP-seq)

description:
PSU10245
BY4741_ChIPmentation_peaks.gff


title: NOP58_Glucose_4


title: NOP56_Glucose_6


title: NOP56_Glucose_7


title: NOP58_Glucose_1


title: NOP56_Glucose_8


title: Abf1 ChIP-exo 5.0 Replicate 3

description:
PSU11150
Abf1_ChIP-exo5.0_peaks.gff


title: NOP56_Glucose_5


title: NOP56_Glucose_3


title: NOP56_Glucose_4


title: Abf1 ChIP-exo 5.0 Replicate 2

description:
PSU11149
Abf1_ChIP-exo5.0_peaks.gff


title: NOP56_Glucose_2


title: BY4741 ChIP-exo 4.0

description:
PSU10686
BY4741_ChIP-exo4.0_peaks.gff


title: Abf1 ChIP-exo 5.0 Replicate 1

description:
PSU11019
Abf1_ChIP-exo5.0_peaks.gff


title: NOP1_Glucose_1


title: Abf1 ChIP-exo 4.1 Replicate 2

description:
PSU10635
Abf1_ChIP-exo4.1_peaks.gff


title: Abf1 ChIP-exo 3.0 Replicate 2

description:
PSU10395
Abf1_ChIP-exo3.0_peaks.gff


title: NOP1_Glucose_4


title: NOP1_Glucose_3


title: NOP1_Glucose_2


title: Abf1 ChIP-exo 4.0 Replicate 1

description:
PSU10377
Abf1_ChIP-exo4.0_peaks.gff


title: Abf1 ChIP-exo 4.0 Replicate 2

description:
PSU10495
Abf1_ChIP-exo4.0_peaks.gff


title: Abf1 ChIP-exo 3.0 Replicate 3

description:
PSU10396
Abf1_ChIP-exo3.0_peaks.gff


title: Abf1 ChIP-exo 3.0 Nextera Replicate 3

description:
PSU10400
Abf1_ChIP-exo3.0_Nextera_peaks.gff


title: Abf1 ChIP-exo 4.0 Replicate 3

description:
PSU10628
Abf1_ChIP-exo4.0_peaks.gff


title: NOP1_Glucose_8


title: Abf1 ChIP-exo 3.0 Replicate 1

description:
PSU10394
Abf1_ChIP-exo3.0_peaks.gff


title: Uterus

city: Beijing

first: Dan

last: Lu

address: 38# Xueyuan Rd

country: China

institute: Peking University Health Science Center

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the  housekeeping gene: Actb.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]

label: SYBR Green

source_name: C57BL/6 mice, under steady state

label_protocol: PCR assays were performed using the TransStart Top Green qPCRSuperMix (TransGen Biotech) following the Manufacturer’s instructions. Reverse transcription was performed from 2,000 ng total RNA using the Transcript Reverse Transcription System (Promega). Quantitative real-time PCR were performed (7500/7500 Fast Real-Time PCR Systems,  Applied Biosystems ) with 45 cycles at 94 oC for 15 seconds and 60 oC for 30 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: gender

value: female

tag: age

value: 8 week old

tag: tissue

value: uterus


title: Bone marrow

description: Test

value: male

value: bone marrow


title: Embryo

description: Test

value: embryo


title: Lymph node

description: Test

value: lymph node


title: Testis

description: Test

value: testis


title: Thymus

description: Test

value: thymus


title: Liver

description: Test

value: liver


title: Small intestine

description: Test

value: small intestine


title: Kidney

description: Test

value: kidney


title: NOP1_Glucose_7

value: Glucose


title: Abf1 ChIP-exo 3.0 Nextera Replicate 2

description:
PSU10399
Abf1_ChIP-exo3.0_Nextera_peaks.gff


title: Stomach

description: Test

value: stomach


title: Lung

description: Test

value: lung


title: Abf1 ChIP-exo 3.0 Nextera Replicate 1

description:
PSU10398
Abf1_ChIP-exo3.0_Nextera_peaks.gff

value: Abf1-TAP (Sigma i5006-100MG, Lot#SLBM2617V)


title: Skeletal muscle

description: Test

value: skeletal muscle


title: Abf1 ChIP-exo 1.1

description:
PSU08806
Abf1_ChIP-exo1.1_peaks.gff

value: GRF88, MATa his4-38, S288C background


title: Abf1 ChIP-exo 4.1 Replicate 1

description:
PSU10373
Abf1_ChIP-exo4.1_peaks.gff


title: kyp/suvh5/6_H3_ChIPseq

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
ChIP-seq reads were aligned to the tair10 genome assembly using Bowtie (v1.1.2): bowtie -q -v 0 -p 8 -S -m 1
Bam files were deduplicated with samtools: samtools rmdup
Differential peaks were called by bdgdiff function in MACS2.
ChIP-seq data metaplots were plotted by deeptools (v2.5.1)
Genome_build: tair10
Supplementary_files_format_and_content: wig

organism: Arabidopsis thaliana

source_name: seedling tissue

growth_protocol: Plants were grown under constant light at 22 °C.

extract_protocol:
Samples were crosslinked in vitro, sheared using a Bioruptor Plus (Diagenode), chromatin was then split for each sample.
Libraries generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions, proceeding from step F (DNA purification) and were sequenced on an Illumina HiSeq 4000 instrument.

tag: cell type

value: developmental stage

tag: antibody

tag: catalog#/vendor

value: abcam1791 (Abcam)

tag: genotype/variation


title: kyp/suvh5/6_H3K9me2_ChIPseq

value: abcam1220 (Abcam)


title: suvh5_H3_ChIPseq


title: suvh6_H3_ChIPseq


title: suvh6_H3K9me2_ChIPseq


title: Brain

description: Test

value: male

value: 8 week old

value: brain


title: suvh5_H3K9me2_ChIPseq


title: kyp_H3_ChIPseq

value: kyp


title: Heart

description: Test

value: heart


title: kyp_H3K9me2_ChIPseq


title: WT_H3_ChIPseq

value: wild type


title: 2_Ret_3

city: San Francisco

first: Charlie

last: Kim

state: CA

address: 1001 Potrero Ave

department: Medicine

institute: University of California, San Francisco

hyb_protocol: 600 ng of each Cy3-labeled aaRNA hybridized to a SurePrint G3 Custom Gene Expression 8x60K microarray (Agilent) as per manufacturers protocol.

scan_protocol: Arrays were scanned on an Agilent scanner, 3 um resolution, 20-bit tiff

data_processing: Custom in-house scripts and the Bioconductor Limma package were used for filtering and normalization.  Expression values were log2 transformed and quantile normalized.

organism: Drosophila melanogaster

source_name: Sorted class IV da neurons, ret mutant

label_protocol: 1.5 ug of aRNA coupled to Cy3 in 0.1 M sodium bicarbonate pH 9 buffer and purified over spin columns

growth_protocol: Total  RNA extraction from FACS-isolated class IV da neurons marked with ppk-CD4-tdTomato

extract_protocol: RNA was isolated from samples (RNAqueous Micro, Life Technologies).  Purified RNA was amplified (MessageAmp II , Life Technologies) with minor modifications to manufacturer’s instructions to generate amino-allyl incorporated amplified RNA.

treatment_protocol: Wild type or ret mutant Drosophila 3rd instar larvae

tag: genotype

value: ret mutant

value: purified class IV da neurons


title: 1_ppk_8

source_name: Sorted class IV da neurons, wild type


title: 1_ppk_15


title: NOP1_Glucose_5

value: Glucose


title: 1_ppk_10


title: 1_ppk_14


title: 1_ppk_7


title: 1_ppk_12


title: 2_Ret_4


title: 2_Ret_2


title: 1_ppk_13


title: 1_ppk_5


title: 2_Ret_6


title: 1_ppk_11


title: 1_ppk_6


title: 1_ppk_9


title: WT_H3K9me2_ChIPseq


title: 1_ppk_4


title: 2_Ret_5


title: 2_Ret_1


title: A10_18DAS_rep4

city: St. Louis

first: Andrea

middle: L

last: Eveland

state: MO

address: 975 N. Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Data were quality cheked with FASTQC.
Reads were mapped and the transcripts were quantified by Salmon (v0.8.1) (Patro et al., 2017) in a quasi mapping mode with the option –numBootstraps 30.
Salmon outputs were imported into R and TPMs, counts and transcript lengths were summarized into matrices by using the Bioconductor package tximport (v1.0.3).
Genome_build: Sviridis_311_v1
Supplementary_files_format_and_content: The biocondutor package tximport was used to import and summarize gene-level abundances.

organism: Setaria viridis

source_name: inflorescence primordia

growth_protocol: The reference S. viridis genotype A10.1 was used for this study. A10.1 seeds from two-year old stocks were used to ensure full loss of dormancy and promote synchronized germination. Seeds were planted in MetroMix 360 soil (Sun Gro Horticulture company) and grown in a controlled growth chamber with the following conditions: temperature of 31°C/23°C (day/night), light intensity of 200 µmol/sq.meter/sec for 12 hours (6am-6pm) and 50% relative humidity, at the Donald Danforth Plant Science Center’s Integrated Plant Growth Facility. Plants were fertilized with Jack’s 15-16-17 (Hummert International) twice a week.

extract_protocol:
Inflorescences were hand-dissected into fresh 100% acetone on dry ice from S. viridis seedlings at 10, 12, 14, 15, 16 and 18 DAS. Depending on the representative size at a given stage, 10-30 individual inflorescence primordia were pooled per biological replicate; three to four biological replicates were collected for each stage. All sampling was performed within a two-hour window in the morning to control for circadian effects. Acetone was removed and samples were flash-frozen in liquid nitrogen and ground into a fine powder using 3mm tungsten-carbide beads (Qiagen) in a Tissue Lyser-II. Total RNA was isolated using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific) with in-column DNase I treatment following manufacturer's protocols.
RNA-seq libraries were generated from 1µg total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) and size-selected for 200 bp inserts. Libraries were quantified on a bioanalyzer (Agilent 2100) using a DNA 1000 chip to confirm the insert size and quantified again on a Qubit 3.0 Fluorometer (Life Technologies) to ensure different libraries were equally loaded
Libraries were sequenced using standard Illumina protocols (Illumina, Inc.) for either paired-end (PE) or single-end (SE) sequencing at 100bp on the Illumina HiSeq 2500 platform at the University of Illinois at Urbana-Champaign W.M. Keck Center.

value: accession A10.1

tag: developmental stage

value: 18 Days after sowing

value: pool of inflorescence primordia


title: U-10-4-0373-29mm

city: Dublin 4

first: PATRICK

last: LONERGAN

address: Belfield

country: Ireland

institute: University College Dublin

description:
Sample34
readcounts.txt

data_processing:
The raw sequences (fastq) were subjected to adapter removal and quality trimming using fqtrim (https://ccb.jhu.edu/software/fqtrim/).
The quality reads were then mapped to the bovine reference genome UMD3.1 using Hisat2 mapper (https://ccb.jhu.edu/software/hisat2/) .
To produce a global gene annotation file (GTF) for comprehensive quantification of gene expressions across the samples, the sorted binary alignment maps of sequence reads from each sample were assembled to generate transcriptomes those were then merged, along with the gene annotations from reference genome assembly.
The transcript assembly step was accomplished using the software ‘Stringtie’ (https://ccb.jhu.edu/software/stringtie/) .
The merged global transcriptome was then used in Stringtie to quantify transcript abundance of each sample. Differential expression analysis between sample groups were performed by robustly fitting the expression data to a weighted generalized linear model using edgeR robust.
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-limited text file of read count data.

organism: Bos taurus

source_name: Endometrium

growth_protocol: Following dissection with an 8-mm biopsy punch, intercaruncular endometrial explants (50-80 mg) were washed in Hank’s Balanced Salt Solution (HBSS; Gibco, ThermoFisher Scientific) containing 1% ABAM before placement in culture wells (4-well plate) containing 1 mL of Roswell Park Memorial Institute (RPMI) medium (Gibco, ThermoFisher Scientific) with 1% ABAM. Explants were cultured endometrial side up in 5% CO2 and air at 38.8°C for 1 to 5 h before treatment.

extract_protocol:
Total RNA was extracted from ~50 mg of endometrial explant tissue using Trizol reagent (Invitrogen) per the manufacturer´s instructions. On-column RNA clean-up was performed using the Qiagen mini kit (Qiagen).
RNA library preparation and sequencing was conducted by the University of Missouri DNA Core facility. Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq mRNA stranded sample preparation kit.

treatment_protocol: Explants (endometrial side up) were cultured for 6 h with: (i) RPMI medium alone (Control; n=6 explants); (ii) RPMI medium containing 100 ng/mL of recombinant ovine IFNT (n=6 explants); (iii) a Day 15 conceptus derived from the transfer of in vivo-derived blastocysts (AI, n=4 explants) in RPMI media; or (iv) a Day 15 conceptus derived from the transfer of in vitro produced blastocysts (IVF, n=7 explants) in RPMI media. Explants were incubated in 5% CO2 and air at 38.8°C during treatment. Following treatment, explants were immediately snap frozen in liquid nitrogen until total RNA extraction.

value: IVF

tag: conceptus sex

value: Male

value: Endometrium


title: 1_ppk_2


title: A10_18DAS_rep3


title: U-7-9-0092-54mm

description:
Sample32
readcounts.txt


title: A10_18DAS_rep2


title: A10_18DAS_rep1


title: U-5-4-0541-33mm

description:
Sample30
readcounts.txt


title: A10_16DAS_rep4

value: 16 Days after sowing


title: U-4-7-0216-19mm

description:
Sample27
readcounts.txt

value: Female


title: U-3-7-0216-21mm

description:
Sample25
readcounts.txt


title: KO cDC1 non-drain 4

first: Kenneth

middle: M

last: Murphy

address: 660 S. Euclid

department: Pathology and Immunology

institute: Wustl/HHMI

description: Gene expression of unactivated cDC1

hyb_protocol: RNA was hybridized ot the Mouse gene 1.0 ST array

scan_protocol: Affymetrix

data_processing: Data was analyzed using DNASTAR Arraystar software with RMA and quantile normalization

source_name: Skin draining LN cDC1

label_protocol: Affymetrix

growth_protocol: Cells were harvested ex vivo

extract_protocol: Inguinal lymph nodes were harvested from draining or non-draining flank and digested with Collagenase B and DNaseI before sorting cDC1

treatment_protocol: Mice were injected with regressor tumors in the back flank six days before harvest

tag: location

value: Non-Draining

value: Inguinal Lymph Node

value: WDFY4 KO


title: KO cDC1 non-drain 2

description: Gene expression of unactivated cDC1


title: A10_16DAS_rep3


title: KO cDC1 non-drain 3

description: Gene expression of unactivated cDC1


title: 1_ppk_3


title: Het cDC1 non-drain 1

description: Gene expression of unactivated cDC1

value: WDFY4 Het


title: KO cDC1 non-drain 1

description: Gene expression of unactivated cDC1


title: Het cDC1 non-drain 3

description: Gene expression of unactivated cDC1


title: U-2-5-0282-8mm

description:
Sample22
readcounts.txt

tag: treatment


title: KO cDC1 draining 4

description: Gene expression of activated cDC1

value: Draining


title: Het cDC1 non-drain 2

description: Gene expression of unactivated cDC1


title: 1_ppk_1

value: wild type


title: A10_16DAS_rep2


title: U-1-5-0282-14mm

description:
Sample21
readcounts.txt


title: Het cDC1 non-drain 4

description: Gene expression of unactivated cDC1


title: A10_16DAS_rep1


title: U-4-0-146-21mm

description:
Sample20
readcounts.txt

value: AI


title: KO cDC1 draining 3

description: Gene expression of activated cDC1


title: Het cDC1 draining 4

description: Gene expression of activated cDC1


title: Het cDC1 draining 3

description: Gene expression of activated cDC1


title: KO cDC1 draining 1

description: Gene expression of activated cDC1


title: U-2-0-146-29mm

description:
Sample18
readcounts.txt


title: U-3-0-146-23.5mm

description:
Sample19
readcounts.txt


title: A10_15DAS_rep3

value: 15 Days after sowing


title: A10_15DAS_rep2


title: KO cDC1 draining 2

description: Gene expression of activated cDC1


title: Het cDC1 draining 1

description: Gene expression of activated cDC1


title: A10_15DAS_rep1


title: NOP1_Glucose_6

value: Glucose


title: A10_14DAS_rep4

value: accession A10.1

value: 14 Days after sowing


title: A10_15DAS_rep4

value: pool of inflorescence primordia


title: U-10-Control

description:
Sample11
readcounts.txt

value: Control


title: U-5-IFNT

description:
Sample10
readcounts.txt

value: IFNT


title: RCAP_10Klux_1h_2

city: Tekirdag

first: Muazzez

middle: Gürgan

last: Gürgan Eser

address: Degirmenaltı Kampusu Fen Edebiyat Fakultesi Biyoloji Bolumu Ofis 238

department: Department of Biology

country: Turkey

institute: Namık Kemal University

hyb_protocol: Labeled samples were hybridized with Rhodobacter capsulatus TR_RCH2a520699F array (Affymetrix) at 50°C for 17 hours, washed and stained at GeneChip Fluidics Station 450 at the METU Central Laboratory, Ankara, Turkey.

scan_protocol: Arrays were scanned using GeneChip® Scanner 3000 which was operated by GCOS according to instructions of the manufacturer (Affymetrix).

data_processing: CHP files from the scanned arrays were generated by Expression Console and analyzed by using GeneSpring GX 14.8 software (Agilent Technologies, Santa Clara, CA). CHP files include RMA values.

organism: Rhodobacter capsulatus

source_name: Bacterial cell

label_protocol: The fragmented cDNA was biotinylated with the GeneChip DNA Labeling Reagent (Affymetrix).

growth_protocol: 1.5x10e9 bacterial cells from cultures of optimum condition and stress applications were collected via centrifugation.

extract_protocol: Total RNA isolation was performed by using Trizol Reagent (Invitrogen).

treatment_protocol: The cell pellets were frozen in liquid nitrogen and stored at -80°C until RNA isolation.

value: high light 1h


title: U-1-0-146-31mm

description:
Sample17
readcounts.txt

value: Endometrium


title: A10_14DAS_rep3


title: U-10-IFNT

description:
Sample12
readcounts.txt


title: A10_14DAS_rep2


title: Spleen

description: Test

value: male

value: 8 week old

value: spleen


title: Liver, LiSel1lKO mouse, 9 wks of age, replicate 2

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

source_name: Liver of a hepatocyte-specific Sel1L-deficient mouse, aged 9 weeks

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: The Sel1ltm1e(KOMP)Wtsi (Sel1Lflox/+) ES cells on the C57BL/6J background were purchased from the KOMP Repository Project (ID CSD44577, UC Davis, http://www.knockoutmouse.org/martsearch/project/44577). Exon 6 of Sel1L gene is flanked by two loxP sites (floxed). The lacZ-neo cassette was deleted by crossing the animals onto the βActin-FLPe deleted mice on the C57BL/6J background (JAX 003800). The resulting Sel1Lflox/+ animals were intercrossed to generate Sel1Lflox/flox mice.  The Sel1Lflox/flox mice were then crossed with albumin promoter-driven Cre mice (JAX 003574, B6.Cg-Tg(Alb-Cre)21Mgn/J) to generate hepatocyte-specific Sel1L-deficient mice.

extract_protocol: Total RNA was extracted using Trizol and RNA miniprep kit (Sigma RTN350) with DNaseI digestion (Roche). Total RNA yield (Nanodrop ND-1000, Nanodrop Products, Maarssen, The Netherlands) and RNA integrity (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) were assessed. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Livers were isolated from 3-week-old and 9-week-old WT and hepatocyte-specific Sel1L-deficient mice and snap frozen in liquid nitrogen. Mice were routinely fasted in the morning for 5-6 hours before sacrifice.

tag: strain/background

tag: age of mice (wks)

value: liver


title: A10_14DAS_rep1


title: RCAP_10Klux_15min_2

tag: strain

value: high light 15min


title: Het cDC1 draining 2

description: Gene expression of activated cDC1

value: Draining

value: Inguinal Lymph Node

value: WDFY4 Het


title: Liver, wildtype mouse, 9 wks of age, replicate 1

source_name: Liver of a wildtype mouse, aged 9 weeks

value: wildtype


title: Liver, LiSel1lKO mouse, 9 wks of age, replicate 1


title: Liver, LiSel1lKO mouse, 9 wks of age, replicate 3


title: U-4-IFNT

description:
Sample8
readcounts.txt


title: Liver, wildtype mouse, 9 wks of age, replicate 3


title: A10_12DAS_rep4

value: 12 Days after sowing


title: Liver, LiSel1lKO mouse, 3 wks of age, replicate 4

source_name: Liver of a hepatocyte-specific Sel1L-deficient mouse, aged 3 weeks


title: Liver, wildtype mouse, 3 wks of age, replicate 3

source_name: Liver of a wildtype mouse, aged 3 weeks


title: Liver, LiSel1lKO mouse, 3 wks of age, replicate 1


title: Liver, LiSel1lKO mouse, 3 wks of age, replicate 2


title: Liver, LiSel1lKO mouse, 3 wks of age, replicate 3


title: Liver, wildtype mouse, 3 wks of age, replicate 2


title: Liver, wildtype mouse, 9 wks of age, replicate 2


title: RCAP_10Klux_15min_1


title: A10_12DAS_rep2

value: accession A10.1


title: RCAP_2Klux_1h_2

value: low light 1h


title: U-4-Control

description:
Sample7
readcounts.txt


title: RCAP_10Klux_1h_1


title: ZAPKO46_uIFN_2_viral RNA

first: Molly

last: Ohainle

address: 1100 Fairview Ave N, C2-023

institute: Fred Hutchinson Cancer Research Center

description: viral RNA

data_processing:
Library strategy: CRISPR screen
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by generation of  fastq files using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads) /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to demultiplexing  using FASTX-Toolkit v0.0.13
Reads were trimmed and aligned to the PIKA HIV guide library using Bowtie v1.0.0, allowing 0 mismatches in the guide sequence, followed by tabulation of read counts using R
Genome_build: PIKA HIV sgRNA Library.  FASTA is available on series record. More information on the library is also available on bioRxiv:
https://www.biorxiv.org/content/early/2018/07/20/363432
Supplementary_files_format_and_content: tab delimited files with read counts for each guide sequence

organism: Human immunodeficiency virus

source_name: Human Immunodeficiency Virus (HIV)

growth_protocol: THP-1 monocytic cells are grown in RPMI with 10% FBS and Pen/Strep (supplemented to 10mM HEPES, 4.5 g/L D-Glucose, 0.11 g/L Sodium Pyruvate + Glutamax), passaging between 2e5 cells/mL and 1e6 cells/mL.

extract_protocol:
Viral RNA was extracted using a QIAamp Viral RNA Mini Kit (Qiagen)
Genomic DNA or reverse-transcribed viral RNA were amplified by a two-step PCR (PCR1: 12 cycles, PCR2: 20 cycles) to amplify 20bp sgRNA sequences in the HIV-CRISPR vector. All Viral RNA was amplified for each sample where appropriate. For Genomic DNA samples a total of 500-fold coverage of the 15,414 sgRNAs were amplified (10^6 cells were estimated to contain 6.6μg gDNA) with a maximum of 2μg gDNA per PCR reaction. For each sample, PCR1 reactions were pooled, cleaned up over a QIAquick PCR purification Kit (2 columns per sample), pooled again and used as template for PCR2. For viral RNA, all PCR1 was amplified in the second round. For gDNA, 5uL of pooled PCR1 was used as input for PCR2 (PCR2 primers include Illumina barcodes and adaptor sequences). Amplicons from PCR2 were pooled, purified by double-sided SPRI (AMPureXP, Beckman Coulter), quantified with a Qubit HS dsDNA assay and pooled for sequencing.

value: ZAP-KO

tag: ifn treatment

value: yes

tag: hiv strain

value: HIV-1 LAI


title: A10_12DAS_rep1

value: pool of inflorescence primordia


title: RCAP_2Klux_1h_1


title: U-3-IFNT

description:
Sample6
readcounts.txt

value: IFNT

value: Endometrium


title: ZAPKO46_uIFN_1_viral RNA

description: viral RNA


title: U-5-Control

description:
Sample9
readcounts.txt

value: Control


title: U-3-Control

description:
Sample5
readcounts.txt


title: RCAP_2Klux_15min_2

value: low light 15min


title: A10_10DAS_rep4

value: 10 Days after sowing


title: A10_10DAS_rep3


title: U-2-IFNT

description:
Sample4
readcounts.txt


title: Liver, wildtype mouse, 3 wks of age, replicate 1

value: liver


title: ZAPKO11_uIFN_2_viral RNA

description: viral RNA


title: U-2-Control

description:
Sample3
readcounts.txt


title: RCAP_Dark_2

value: Dark


title: ZAPKO11_uIFN_1_viral RNA

description: viral RNA


title: RCAP_2Klux_15min_1


title: wt_uIFN_2_viral RNA

description: viral RNA


title: U-1-IFNT

description:
Sample2
readcounts.txt


title: A10_10DAS_rep2


title: RCAP_Dark_1


title: U-1-Control

description:
Sample1
readcounts.txt


title: wt_uIFN_1_viral RNA

description: viral RNA


title: A10_10DAS_rep1


title: Luminal A breast cancer LATP165

status: Public on Aug 16 2018

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: miRNA expression data from triple negative tumors.

hyb_protocol: total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

scan_protocol: Washed and stain processes were performed in the GeneChip Fluidics Station 450. The probe arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Computational analysis of the microarray data Cel files was processed with the Oligo library in R Bioconductor. Microarray background correction and normalization was done using Robust Multichip Analysis (RMA) and quantile algorithm, respectively. To define subgroups a non-hierarchical analysis was performed by a non-negtaive matrix factorization (NMF). Differentially expression patterns between triple negative tumors, subtypes and other immunophenotypes were determined using the limma package to perform an adjusted Student’s t-test using a Bayesian estimation of the variance.

source_name: Macrodissection of FFPE breast cancer tumor

extract_protocol: Total RNA including the small fraction was isolated using RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE

treatment_protocol: Paraffin embedded tissue from breast cancer tumors in adjuvance

value: breast cancer tissue

tag: ihc subtype

value: Luminal A

tag: miRNA subtype

tag: population

value: Mexico Hispanic


title: Her2 breast cancer HTP76

label_protocol: total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

tag: tissue

value: Her2 tumor


title: Luminal A breast cancer LATP65


title: Luminal A breast cancer LAT169


title: Triple negative breast cancer TN25

value: Triple negative


title: Luminal A breast cancer LATP194


title: Triple negative breast cancer TN27


title: Triple negative breast cancer TN11


title: Triple negative breast cancer TN15


title: Triple negative breast cancer TN20


title: Triple negative breast cancer TNB122


title: Her2 breast cancer HTP191


title: Triple negative breast cancer TN13


title: Her2 breast cancer HTP75


title: Triple negative breast cancer TN21


title: Triple negative breast cancer TN22


title: Triple negative breast cancer TN17


title: Triple negative breast cancer TN26


title: Triple negative breast cancer TN14


title: Triple negative breast cancer TN12


title: Triple negative breast cancer TN18


title: Luminal B breast cancer LBtp150

value: Luminal B


title: Her2 breast cancer HTP193


title: Triple negative breast cancer TN23


title: Triple negative breast cancer TN28


title: Triple negative breast cancer TN24


title: Triple negative breast cancer TN19


title: Triple negative breast cancer TN29


title: Triple negative breast cancer TN30


title: NOP56_Glucose_1

tag: bait protein

tag: growth medium

value: Glucose


title: Triple negative breast cancer TN31


title: Triple negative breast cancer TN33


title: Triple negative breast cancer TN34


title: Triple negative breast cancer TN1


title: Triple negative breast cancer TN6


title: Triple negative breast cancer TN38


title: Triple negative breast cancer TNB162


title: Triple negative breast cancer TNB195


title: Triple negative breast cancer TNB45


title: Triple negative breast cancer TN32


title: Triple negative breast cancer TN9


title: Triple negative breast cancer TN3


title: Triple negative breast cancer TN8


title: Triple negative breast cancer TN5


title: Triple negative breast cancer TN37


title: Triple negative breast cancer TN44


title: Triple negative breast cancer TNB174


title: Triple negative breast cancer TN42


title: Triple negative breast cancer TNB201


title: Triple negative breast cancer TN10


title: Triple negative breast cancer TN40


title: Triple negative breast cancer TN39


title: Triple negative breast cancer TN2


title: Triple negative breast cancer TN35


title: Triple negative breast cancer TN41


title: Triple negative breast cancer TN4


title: Triple negative breast cancer TN36


title: Triple negative breast cancer TN47


title: Triple negative breast cancer TN7


title: Triple negative breast cancer TN48


title: Triple negative breast cancer TN45


title: Triple negative breast cancer TN51


title: Triple negative breast cancer TN50


title: Triple negative breast cancer TNB64


title: Triple negative breast cancer TN54


title: Triple negative breast cancer TN53


title: Triple negative breast cancer TNB264.62


title: Triple negative breast cancer TN55


title: Triple negative breast cancer TN60


title: shA2.3 ins 1 GW_Experiment 3

city: Lille

first: Lefebvre

last: Philippe

address: Bld Pr Jules Leclerc

country: France

institute: Inserm

description: Experiment 3

hyb_protocol: Following fragmentation, 5,5µg of ssDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

data_processing: The data were analyzed with Genespring 14,3 software using global scaling as normalization method.

label: Biotin

source_name: shA2.3 ins 1 GW_Experiment 3

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

growth_protocol: DMEM 1g/l de glucose w/o glutamin + 0,1% BSA + 1% glutamin + 100 nM dexametason

extract_protocol: Extract-All extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: AdshlacZ or  shFOXA2.3 (MOI5) +/-insulin 1nM +/-GLG 100nM +/-GW4064 2µM during 4h (cotreatment)

tag: Sex

value: male

tag: cell type

value: Mouse primary hepatocytes (MPH)

tag: RNAi

tag: insulin vs glucagon

value: insulin

tag: drug treatment


title: Triple negative breast cancer TN52


title: shlacZ GLG DMSO_Experiment 3

description: Experiment 3

source_name: shlacZ GLG DMSO_Experiment 3

value: shlacZ

value: glucagon

value: DMSO


title: shA2.3 GLG GW_Experiment 3

description: Experiment 3

source_name: shA2.3 GLG GW_Experiment 3


title: shA2.3 ins 1 DMSO_Experiment 3

description: Experiment 3

source_name: shA2.3 ins 1 DMSO_Experiment 3


title: shA2.3 GLG DMSO_Experiment 3

description: Experiment 3

source_name: shA2.3 GLG DMSO_Experiment 3


title: Triple negative breast cancer TN56


title: shA2.3 GLG GW_Experiment 2

description: Experiment 2

source_name: shA2.3 GLG GW_Experiment 2


title: Triple negative breast cancer TN58


title: shlacZ GLG GW_Experiment 3

description: Experiment 3

source_name: shlacZ GLG GW_Experiment 3


title: Colon

description: Test

source_name: C57BL/6 mice, under steady state

tag: gender

tag: age

value: 8 week old

value: colon


title: shlacZ ins 1 GW_Experiment 3

description: Experiment 3

source_name: shlacZ ins 1 GW_Experiment 3


title: Triple negative breast cancer TN49


title: shlacZ ins 1 DMSO_Experiment 3

description: Experiment 3

source_name: shlacZ ins 1 DMSO_Experiment 3


title: shA2.3 GLG GW_Experiment 1

description: Experiment 1

source_name: shA2.3 GLG GW_Experiment 1


title: shlacZ ins 1 DMSO_Experiment 2

description: Experiment 2

source_name: shlacZ ins 1 DMSO_Experiment 2


title: shlacZ ins 1 GW_Experiment 2

description: Experiment 2

source_name: shlacZ ins 1 GW_Experiment 2


title: shA2.3 ins 1 DMSO_Experiment 2

description: Experiment 2

source_name: shA2.3 ins 1 DMSO_Experiment 2


title: shlacZ GLG DMSO_Experiment 2

description: Experiment 2

source_name: shlacZ GLG DMSO_Experiment 2


title: shlacZ GLG GW_Experiment 2

description: Experiment 2

source_name: shlacZ GLG GW_Experiment 2


title: shA2.3 ins 1 GW_Experiment 2

description: Experiment 2

source_name: shA2.3 ins 1 GW_Experiment 2


title: shA2.3 GLG DMSO_Experiment 2

description: Experiment 2

source_name: shA2.3 GLG DMSO_Experiment 2


title: shA2.3 GLG DMSO_Experiment 1

description: Experiment 1

source_name: shA2.3 GLG DMSO_Experiment 1


title: shA2.3 ins 1 GW_Experiment 1

description: Experiment 1

source_name: shA2.3 ins 1 GW_Experiment 1


title: shlacZ GLG GW_Experiment 1

description: Experiment 1

source_name: shlacZ GLG GW_Experiment 1


title: GW4064 2µM_6h_Experiment 2

treatment_protocol: Glucagon 100nM +/-GW4064 2µM during 6h

tag: treated with

value: GW4064 2µM for 6hrs


title: shlacZ GLG DMSO_Experiment 1

description: Experiment 1

source_name: shlacZ GLG DMSO_Experiment 1

tag: strain


title: shlacZ ins 1 DMSO_Experiment 1

description: Experiment 1

source_name: shlacZ ins 1 DMSO_Experiment 1


title: Glucagon 100nM + GW4064 2µM_6h_Experiment 2

source_name: Glucagon 100nM + GW4064 2µM_6h

value: Glucagon 100nM + GW4064 2µM for 6hrs


title: GW4064 2µM_6h_Experiment 1


title: DMSO_6h_Experiment 2

value: DMSO for 6hrs


title: DMSO_6h_Experiment 1


title: Glucagon 100nM_6h_Experiment 1

source_name: Glucagon 100nM_6h

value: Glucagon 100nM for 6hrs


title: Triple negative breast cancer BQ39

hyb_protocol: Total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

source_name: Macrodissection of FFPE breast cancer tumor

extract_protocol: From FFPE breast cancer tissues, total RNA was extracted with miRNeasy mini kit (Qiagen)

value: breast cancer tissue

tag: subtype

value: Italy caucasian


title: Glucagon 100nM_6h_Experiment 2


title: shA2.3 ins 1 DMSO_Experiment 1

description: Experiment 1

source_name: shA2.3 ins 1 DMSO_Experiment 1


title: Triple negative breast cancer BQ24

label_protocol: Total RNA was labeled with Flashtag HSR kit and hybridized to the Affymetrix GeneChip

value: Triple negative


title: Glucagon 100nM + GW4064 2µM_6h_Experiment 1


title: Triple negative breast cancer BQ21


title: Triple negative breast cancer BQ58


title: Triple negative breast cancer BQ15


title: Triple negative breast cancer BQ56


title: Triple negative breast cancer BQ26


title: Triple negative breast cancer BQ12


title: Triple negative breast cancer BQ44


title: Triple negative breast cancer BQ62


title: Triple negative breast cancer BQ30


title: Triple negative breast cancer BQ17


title: Triple negative breast cancer BQ29


title: Triple negative breast cancer BQ14


title: shlacZ ins 1 GW_Experiment 1

description: Experiment 1

source_name: shlacZ ins 1 GW_Experiment 1


title: Triple negative breast cancer BQ08


title: Triple negative breast cancer BQ02


title: Triple negative breast cancer BP98


title: Triple negative breast cancer BQ09


title: Triple negative breast cancer BP96


title: Triple negative breast cancer BP83


title: Triple negative breast cancer BQ07


title: Triple negative breast cancer BP90


title: Triple negative breast cancer BP81


title: Triple negative breast cancer BQ00


title: Triple negative breast cancer BP82


title: Triple negative breast cancer BP94


title: Triple negative breast cancer BP77


title: Lung Cells FVB strain

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: mouse lung cells, FVB mouse strain

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.

source_name: Lung Cells FVB strain

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Not applicable

extract_protocol: Trizol followed by RNAeasy spin columns

treatment_protocol: Not applicable

value: FVBs


title: Triple negative breast cancer BP92


title: Triple negative breast cancer BP85


title: Triple negative breast cancer BP73


title: Triple negative breast cancer BP78


title: Triple negative breast cancer BP68


title: Triple negative breast cancer BP79


title: Triple negative breast cancer BP69


title: Triple negative breast cancer BP71


title: Triple negative breast cancer BP61


title: Triple negative breast cancer BP60


title: Triple negative breast cancer BQ10


title: Triple negative breast cancer BQ06


title: Triple negative breast cancer BP56


title: Triple negative breast cancer BP55


title: Triple negative breast cancer BP50


title: Triple negative breast cancer BP51


title: Triple negative breast cancer BP46


title: Triple negative breast cancer BP49


title: Triple negative breast cancer BP72


title: Triple negative breast cancer BP48


title: Triple negative breast cancer BP45


title: D2_WT-RSPO2

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

description: WT H1 samples after R-spondin2 treatment for 1 day collected from day 2 after hematopoietic differentiation

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H1 were induced into hematopoietic differentiation in mAGM-S3 co-culture. Single cells of H1 were cultured in mTeSR1 for 48 h into small colonies and then plated onto confluent mAGM-S3 stromal cells. Medium was changed with IMDM hematopoietic differentiation medium with 10% fetal bovine serum supplemented with nonessential amino acids, L-glutamine, L- ascorbic acid, transferrin, plasmocin, and β-mercaptoethanol after 2 days.

extract_protocol:
H1 drived cells was enriched by FACS sorting by TRA-1-85+ cells at day 2 of differentiation and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: R-spondin2 was treated in 20ng/mL in IMDM hematopoietic differentiation medium for the first day of differentiation

tag: cell line

tag: treatment/growth

tag: genotype

value: wild type


title: Exercise_12

city: Lethbridge

first: Yaroslav

last: Ilnytskyy

state: AB

address: 4401, University Drive W

department: Biology

institute: University of Lethbridge

description:
counts_out
expressions_raw.txt
expressions_normalized.txt
expressions_vsd.txt
day5_results.txt

data_processing:
Basecalling and demultiplexing: CASAVA1.9
Initial quality control: FastQC  v.0.11.4
Mappping reads to the genome with tophat v.2.0.10 with bowtie 1.1.2 as an internal aligner. Command: tophat -o <outdir> -p 4 --bowtie1 --no-coverage-search --transcriptome-index <transcriptome_index> --library-type fr-firststrand <genome_index> <fastq>
Counting reads mapping to features using FeatureCounts v. 1.5.0-p1: featureCounts -a <genes.gtf> -o <counts_out>  -s 1 <tophat_bam>
Data processing in R and pair-wise comparisons using DESeq2 v.1.12.4
Genome_build: Mouse Ensembl, GRCm38
Supplementary_files_format_and_content: [expressions_normalized.txt] tab delimited: DESeq2 normalized expression values
Supplementary_files_format_and_content: [expressions_raw.txt] tab delimited: Raw counts
Supplementary_files_format_and_content: [expressions_vsd.txt] tab delimited: DESeq2 variance stabilized expression values
Supplementary_files_format_and_content: [counts_out.txt] tab delimited: raw counts generated with FeatureCounts: col1: gene id; col2: Chr; col3: Start; col4: End; col5: Strand; col6: Length; col7 – colN: raw counts for each of the samples
Supplementary_files_format_and_content: [day10_results.txt] tab delimited: DESeq2 differential expression results: col1: Gene ID; col2: mean of normalized values of all samples; col3: log2 Fold Change; col4: standart error of log2 Fold Change estimate; col5: Wald statistic; col6: Wald test pvalue; col7: FDR adjusted pvalue; rest of the columns contain normalized expression values and gene annotations.
Supplementary_files_format_and_content: [day5_results.txt] tab delimited: raw counts generated with FeatureCounts: col1: gene id; col2: Chr; col3: Start; col4: End; col5: Strand; col6: Length; col7 – colN: raw counts for each of the samples

source_name: Exercise Day_5, spinal cord lesion

extract_protocol:
Tissue samples for RNA extractions were prepared from frozen spinal cords using laser micro dissections. Total RNA was isolated using Rneasy Mini Kit (Qiagen).
Due to small amount of RNA available from laser micro dissected sections, RNA samples were amplified using REPLI-g protocol and sequenced on Illumina NextSeq 500 platform for 75 cycles. The libraries were poly-A selected, strand specific, single-end with 75 bp read length.

treatment_protocol: All experimental animals where subjected to lysolecithin induced demyelination, then part of lysolecithin injected animals exercised in the running wheel, while control animals were subjected to same conditions minus the exercise.

value: 8-12 weeks

tag: treatment

value: Exercise

tag: time

value: Day 5

value: spinal cord


title: Exercise_17

description:
counts_out
expressions_raw.txt
expressions_normalized.txt
expressions_vsd.txt
day10_results.txt

source_name: Exercise Day_10, spinal cord lesion

value: Day 10

tag: tissue


title: D5_control_2

source_name: Control Day_5, spinal cord lesion

value: Control


title: D2_LGR4KO1

description: H1 LGR4-/--1 samples collected from day 2 after hematopoietic differentiation


title: Exercise_19


title: Exercise_2


title: Exercise_1


title: Exercise_18


title: D2_WT-CONTROL

description: WT H1 control samples collected from day 2 after hematopoietic differentiation


title: D5_control_5


title: Exercise_13


title: D2_LGR4KO2

description: H1 LGR4-/--2 samples collected from day 2 after hematopoietic differentiation


title: D10_control_3

source_name: Control Day_10, spinal cord lesion


title: Exercise_7


title: D5_control_1


title: D10_control_5


title: D10_control_4


title: D5_control_6


title: Triple negative breast cancer BP44

tag: miRNA subtype

tag: population


title: SCAR_seq_mESC_K5ac_MCM2_2A#2_r1

city: Copenhagen

first: Nataliya

last: Petryk

address: Ole Maaloees Vej 5

department: BRIC - Biotech Research and Innovation Centre

country: Denmark

institute: University of Copenhagen

data_processing:
Library strategy: SCAR-seq
SCAR-seq data were demultiplexed in Illumina Basespace (trimmed>30bp), fastq files were trimmed and mapped to ENCODE mm10 by BWA aln version 0.7.13 (quality threshold - , seed length :32, maximum differences in seed = 2, MAPQ = 30). OK-seq data were demultiplexed with Illumina bcl2fastq (version v2.18), trimmed with Trim Galore! (Galaxy version 0.4.2), filtered FASTQ (Galaxy version 1.0.0) 10-70bp and mapped with Bowtie for Illumina (Galaxy Version 1.1.5) to mm10.
Duplicated reads were marked and removed by picard-tools (version 2.8.2), ENCODE mm10 blacklist regions were masked.
Processed read files were split into forward and reverse strand according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively.
Histone partition was computed from mapped, trimmed and de-duplicated SCAR-seq reads within book-ended 1kb bins as follows: Partition = (F - R)/(F + R). F and R correspond to the number of mapped reads to forward and reverse strand, respectively. Partition value relate to the rates of histones with a specific modification being segregated to the nascent forward (above 0) and nascent reverse (below 0) within each window, respectively. The histone partition was normalized by the total read counts.
OK-seq RFD was computed from mapped, trimmed and de-duplicated OK-seq data in book-ended bins of 1kb as follows: RFD = (R - F)/(F + R).F and R correspond to reads mapped on forward and reverse strand respectively. RFD value reveals the proportions of forks moving rightward (>0, replicating forward strand by leading strand mechanism) and leftward (<0, replicating reverse strand by leading strand mechanism) within each window, respectively.
Partition signal from SCAR-seq and RFD signal from OK-seq were smoothed similarly. Smoothing was computed across consecutive book-ended 1kb bins, performing a uniform blur considering the neighboring 30 bins on each side. Smoothing radius was increased to 80 bins for genome views of SCAR-seq H4K5ac, H4K20me2- and H3K36me3 wild-type samples. Bins from chromosome 1 - 19 with normalized read-counts CPM > 0.3 were included in downstream analysis.
Initiation zone detection. Nonparametric derivative estimation of RFD signal were computed on non-filtered bins to detect sharp transitions between neighboring bins, defining the replication fork initiation zones (ascending slopes). These initiation zones were defined as bins with RFD derivative above the 0.9 quantile and zero-crossing. For initiation zones less than 3 bins apart, the bin with the highest RFD derivative was selected.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files contain smoothed partition and RFD scores. txt file contain coordinates of detected replication initiation zones. The headers are as follows: break-ID: Coordinates for IZ ID.max: Coordines for IZ downstream edge (max smoothed RFD) dist.max: Distance (bp) from IZ to downstream edge ID.min: Coordinates for IZ upstream (min smoothed RFD) dist.min: : Distance (bp) from IZ to upstream edge size: Distance (bp) from upstream to downstream edge nearest: Distance (bp) to the nearest IZ.

source_name: embryomic stem cell line

growth_protocol: Mouse embryonic stem cells E14TG2a were grown on gelatin-coated dishes in 2i/LIF media (30) at 37 °C with 5% CO2. Custom-made 2i media ("2i SILAC", Gibco), which contains a 1:1 mix of DMEM/F-12 and Neurobasal media, 2 mM Glutamax and 1 mM sodium pyruvate but depleted for L-arginine and L-lysine, was supplemented with 50 µM beta-mercaptoethanol, 1x Penicillin-Streptomycin (Gibco), N-2 and B-27 supplements (Gibco), 3 µM GSK3 inhibitor (CHIR99021), 1 µM MEK inhibitor (PD0325901), Leukemia Inhibitory Factor (LIF; homemade by K. Helin lab), 548 µM L-arginine hydrochloride (Sigma) and 648 µM L-lysine hydrochloride (Sigma). Cells were passaged using Trypsin-EDTA (Gibco) and Soybean Trypsin inhibitor (Gibco) in PBS (final concentration 0.25 mg/mL). Cells were routinely tested for mycoplasma contamination.

extract_protocol:
Native chromatin was extracted and digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, biotinylated in click reaction, nascent DNA fragments EdU-biotin pulled-down, newly-synthesized EdU strand were purified and sequenced.
Illumina TruSeq LT

treatment_protocol: EdU labeling 10µM 15 min

tag: genotype/variation

tag: antibody

value: Abcam ab51997


title: SCAR_seq_mESC_K5ac_MCM2_2A#2_r2


title: SCAR_seq_mESC_input_K5ac_MCM2_2A#1_r1


title: Triple negative breast cancer BP58


title: SCAR_seq_mESC_input_K5ac_MCM2_2A#2_r1


title: D10_control_2


title: SCAR_seq_mESC_K5ac_MCM2_2A#1_r2


title: SCAR_seq_mESC_K5ac_MCM2_2A#1_r1


title: OK_seq_mESC

treatment_protocol: EdU labeling 10µM 2 min


title: SCAR_seq_mESC_input_MCM2_2A#1

treatment_protocol: EdU labeling 10µM 30 min


title: SCAR_seq_mESC_K5ac_r2


title: SCAR_seq_mESC_input_EdU15min_r2


title: SCAR_seq_mESC_K36me3_r3

value: Abcam ab9050


title: SCAR_seq_mESC_K36me3_MCM2_2A#2_r2


title: SCAR_seq_mESC_K5ac_r1


title: SCAR_seq_mESC_input_EdU15min_r3


title: SCAR_seq_mESC_K36me3_MCM2_2A#2_r1


title: SCAR_seq_mESC_K36me3_MCM2_2A#1_r2


title: SCAR_seq_mESC_input_EdU30min_r1


title: SCAR_seq_mESC_K36me3_MCM2_2A#1_r1


title: SCAR_seq_mESC_K36me3_r1


title: SCAR_seq_mESC_K20me2_MCM2_2A#2_r1

value: Diagenode C15200205


title: SCAR_seq_mESC_K36me3_r2


title: SCAR_seq_mESC_K20me2_parental


title: SCAR_seq_mESC_K20me2_MCM2_2A#1_r1


title: SCAR_seq_mESC_K20me2_MCM2_2A#1_r2


title: SCAR_seq_mESC_input_MCM2_2A#2


title: SCAR_seq_mESC_K20me2_r2


title: SCAR_seq_mESC_K20me2_MCM2_2A#2_r2


title: SCAR_seq_mESC_K20me2_r3


title: SCAR_seq_mESC_K5ac_parental


title: SCAR_seq_mESC_K20me2_r1


title: ChIP-seq_nontarget_Sp_GFP_Abcam

city: Stanford

first: Daniel

last: Fuentes

address: 265 Campus Drive, G3065

department: Chemical and Systems Biology

institute: Stanford University

description:
processed data file:
ChIP-seq_nontarget_Sp_overlap.bed

data_processing:
Base calling was performed using CASAVA 1.8
Reads were aligned to hg38 genome using bowtie2 2.2.9: “bowtie2 -p $threads --end-to-end --no-mixed --no-discordant --minins 100 --maxins 1000 -x hg38 -1 $read1 -2 read2 > aligned.sam”
Duplicate reads were removed using MarkDuplicates function of Picard tools 1.95: "picard-tools MarkDuplicates REMOVE_DUPLICATES=true I=$bam O=$unique.bam M=$metrics.txt"
Bigwig plots were generated using Deeptools 2.5.4: "bamCoverage --bam $.bam -o $.bw --binSize 10 --normalizeTo1x 2451960000 --extendReads --numberOfProcessors $threads"
Peaks were called using macs2 callpeak 2.1.1.20160309. For each ChIP, peaks were called using ChIP as "treatment" and the other two condition ChIPs as "control." e.g. LTR5HS Sp Cas9 antibody as "treatment" with LTR5HS Sa and nontarget Sp as "control": "macs2 callpeak -t $treatment.bam -c $control1.bam $control2.bam -f BAMPE -B --SPMR -n $name"
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files (scores represent enrichment normalized to 1x genome coverage) and peak call bed files (scores are macs2 enrichment)

growth_protocol: NCCIT cells were obtained from ATCC. NCCIT cells were grown in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA, USA), supplemented with 10% FBS (Omega Scientific, Tarzana, CA, USA), 1x Glutamax (Thermo Fisher Scientific), 1x non-essential amino acids (Thermo Fisher Scientific), and 1x antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
ChIP assays were performed as described previously (Rada-Iglesias et al., 2011). Briefly, approximately 107 NCCIT cells were fixed in 1% formaldehyde for 10 minutes at room temperature in PBS, then quenched with glycine to a final concentration of 0.125 M for 10 minutes. Chromatin was sonicated to 0.5-2.0 kb using Bioruptor (Diagenode, Liège, Belgium), cleared by centrifugation, divided into separate aliquots for each antibody, and incubated with 5 mg of antibody overnight at 4° C. Subsequently, 100 mL of Dynabeads protein G (Thermo Fisher Scientific) were added to the ChIP reactions and incubated for 4-6 hours at 4° C. Magnetic beads were washed and chromatin was eluted, followed by reversal of crosslinks overnight at 65° C, proteinase K and RNase A treatment, and DNA purification by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. ChIP DNA was resuspended in water.
ChIP DNA (10 ng) was end-repaired, A-tailed, and ligated to NEBNext adapter for Illumina (New England Biolabs, Ipswich, MA, USA), followed by cleavage with USER enzyme (New England Biolabs). Adapter-ligated DNA was size-selected using a left/right AMPure XP size selection (Beckman Coulter, Brea, CA, USA). Size-selected DNA was amplified by qPCR using one universal primer and one indexed primer (NEB), then cleaned up with two AMPure XP cleanups. Library DNA was analyzed on Bioanalyzer DNA HS (Agilent, Santa Clara, CA, USA), then pooled and sequenced on a HiSeq 4000 (Illumina, San Diego, CA, USA) at the Stanford Genome Sequencing Service Center, using 2x150 sequencing with index read.

treatment_protocol: NCCIT cells were treated with doxycycline for four days before extraction to induce dCas9 expression

value: NCCIT (ATCC CRL-2073)

tag: cell type

value: Human embryonal carcinoma

tag: chip antibody

value: GFP (Abcam ab290)

tag: grna target

value: nontarget

tag: grna scaffold species

value: S. pyogenes


title: ChIP-seq_nontarget_Sp_Cas9

value: Cas9 (Active Motif 61757)


title: ChIP-seq_nontarget_Sp_GFP_Invitrogen

value: GFP (Invitrogen/Thermo A-11122)


title: ChIP-seq_LTR5HS_Sp_GFP_Abcam

description:
processed data file:
ChIP-seq_LTR5HS_Sp_overlap.bed


title: ChIP-seq_LTR5HS_Sa_GFP_Invitrogen

description:
processed data file:
ChIP-seq_LTR5HS_Sa_overlap.bed

value: S. aureus


title: ChIP-seq_LTR5HS_Sa_Cas9


title: ChIP-seq_LTR5HS_Sa_GFP_Abcam


title: HCMV_72h rep3

city: Cambridge

first: Michael

middle: Paul

last: Weekes

address: Hills Road

department: Cambridge Institute for Medical Research

institute: University of Cambridge

description:
Human_HCMV_RNAseq_processed_data.txt
72-3

data_processing:
Reads were aligned to the Human genome (hg19) and HCMV Merlin strain genome (NC_006273.2) using the aligner STAR version 2.5.2b (Dobin et al., Bioinformatics, 2013; Fonseca et al., bioRxiv, 2014).
Read counts for each gene/transcript were determined using HTSeq version 0.61 (Anders et al., Bioinformatics, 2015) with the following optional parameters: --m union,-r pos,-i transcript_id,-a 10,--stranded=no.
For human genes, normalization assumed equal human reads per run; HCMV reads were not included in this normalization since by 72 h HCMV accounted for a significant proportion of all reads (0h: <0.01%, 24 h: 4.7-5.8%; 72 h: 41.8-42.3% HCMV reads).
For HCMV, reads for each barcode were normalized assuming equal total reads (human plus HCMV) per sequencing run. Reads per Kilobase per Million (RPKM) values were calculated in Excel.
Genome_build: hg19, NC_006273.2
Supplementary_files_format_and_content: Text file containing identifiers and normalized RPKM values for each of 9 conditions (3 replicates, 3 time points).

source_name: Human foreskin fibroblasts (HFFs)

extract_protocol:
For each sample, RNA was extracted from a 75 cm2 flask of HFFs infected at moi 10 or mock-infected using an RNeasy Plus kit (Qiagen).
Poly(A) RNA was enriched using a Poly(A)Purist MAG kit (Thermo). 250 ng of poly(A) RNA from each sample was used to prepare a cDNA library using a PrepX RNA-Seq Library Kit (Wafergen biosystems) on an Apollo 324 (WaferGen biosystems), according to the manufacturer's protocol. The following barcode sequences were used: Mock1 (ATCACGAT); Mock2 (CGATGTAT); Mock3 (TTAGGCAT); 24h_1 (TGACCAAT); 24h_2 (ACAGTGAT); 24h_3 (GCCAATAT); 72h_1 (CAGATCAT); 72h_2 (ACTTGAAT); 72h_3 (GATCAGAT). The resulting libraries were quantified using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), then were pooled for sequencing on a single lane of Illumina HiSeq2500 (1 × 50 bp reads).

value: HFF

tag: passages

tag: infection

value: HCMV


title: ChIP-seq_LTR5HS_Sp_Cas9


title: Placebopre_203-1

type: genomic

city: Ariel

first: Elad

last: Lax

address: 65 Ramat HaGolan st.

department: Molecular Biology

country: Israel

institute: Ariel University

hyb_protocol: Samples were randomized with respect to slide and position on arrays and all samples were hybridized and scanned concurrently to mitigate batch effects as recommended by McGill genome center using Illumina Infinum HD technology user guide.

scan_protocol: All samples scanned concurrently to mitigate batch effects as recommended by McGill genome center using Illumina Infinum HD technology user guide.

data_processing: Illumina arrays were analyzed using the ChAMP Bioconductor package in R (Morris, Butcher et al. 2014). IDAT files were used as input in the champ.load function using minfi quality control and normalization options. Raw data were filtered for probes with a detection value of P>0.01 in at least one sample. We filtered out probes on the X or Y chromosome to mitigate sex effects and probes with SNPs as identified in (Marzouka, Nordlund et al. 2016), as well as probes that align to multiple locations as identified in (Marzouka, Nordlund et al. 2016).  Batch effects were analyzed on the non-normalized data using the function champ.svd. Intra-array normalization to adjust the data for bias introduced by the Infinium type 2 probe design was performed using beta-mixture quantile normalization (BMIQ) with function champ.norm (norm="BMIQ") (Morris, Butcher et al. 2014). We corrected for batch effects after BMIQ normalization using champ.runcombat function. Differentially methylated CGs (MVP) were called using the Bioconductor package Limma (Smyth, Michaud et al. 2005) as implemented in ChAMP using “fdr” for multiple testing correction (adjusted P value (Q) of <0.05). ANOVA analysis was performed for CGs that were short listed for association with addiction using “loop_anova lmFit” function with Bonferroni adjustment for multiple testing.

label: Cy3, Cy5

label_protocol: Samples were subjected to Illumina HumanMethyaltion450k BeadChip analysis. effects as recommended by McGill genome center using Illumina Infinum HD technology user guide.

extract_protocol: DNA was extracted from T cells isolated using anti-CD3 immuno-magnetic beads (Dynabed Life Technologies) and bisulfite-converted

treatment_protocol: Addicts received oral DHEA or placebo for one month. Healthy volunteers were not treated.

tag: gender

value: male

value: T cells


title: healthy_119c


title: healthy_111c


title: HCMV_72h rep1

description:
Human_HCMV_RNAseq_processed_data.txt
72-1


title: healthy_104c


title: healthy_105c


title: HCMV_24h rep2

description:
Human_HCMV_RNAseq_processed_data.txt
24-2


title: healthy_114-c


title: HCMV_72h rep2

description:
Human_HCMV_RNAseq_processed_data.txt
72-2


title: healthy_106-c


title: healthy_117-c


title: ChIP-seq_LTR5HS_Sp_GFP_Invitrogen

tag: cell line


title: HCMV_24h rep1

description:
Human_HCMV_RNAseq_processed_data.txt
24-1


title: HCMV_0h rep2

description:
Human_HCMV_RNAseq_processed_data.txt
Mock-2

value: control


title: Placebopre_231-1


title: HCMV_0h rep3

description:
Human_HCMV_RNAseq_processed_data.txt
Mock-3


title: healthy_107c


title: healthy_101-c


title: HCMV_0h rep1

description:
Human_HCMV_RNAseq_processed_data.txt
Mock-1


title: DHEApost_222-2


title: Placebopre_254-1

value: female


title: Placebopre_210-1


title: HCMV_24h rep3

description:
Human_HCMV_RNAseq_processed_data.txt
24-3


title: Placebopre_213-1


title: Placebopre_214-1


title: Placebopre_212-1


title: DHEApost_206-2


title: Placebopost_220-2


title: DHEApost_233-2


title: DHEApost_226-2


title: Placebopost_254-2


title: DHEApost_202-2


title: DHEApost_207-2


title: Placebopost_234-2


title: Placebopost_210-2


title: Placebopre_220-1


title: Placebopost_213-2


title: Placebopost_214-2


title: DHEApost_229-2


title: DHEApost_201-2


title: DHEApre_233-1


title: Placebopre_234-1


title: DHEApre_253-1


title: DHEApre_229-1


title: DHEApre_222-1


title: DHEApre_226-1


title: DHEApre_243-1


title: DHEApre_206-1


title: DHEApre_202-1


title: DHEApost_253-2


title: DSS-treated regulatory T cells

city: Chiba

first: Shigeru

last: Tanaka

address: 1-8-1 Inohana

department: Allergy and Clinical Immunology

institute: Chiba University

data_processing:
Sequencing was performed on an Illumina Hiseq1500. Sequencing reads were mapped to mm9 reference genome and mRNA profiles were calculated with Cufflinks software.
For further analysis, protein-coding genes whose expression were more than 1 RPKM in either one or both conditions were selected.
Genome_build: mm9

source_name: regulatory T cells (spleen)

extract_protocol:
total RNA was purified using PureLink RNA Mini kit.
RNA libraries were prepared using a SureSelect Strand Specific RNA Library Preparation kit.

treatment_protocol: Foxp3-hCD2 reporer mice were given 3% DSS water for 7days and hCD2 positive cells were purified.

tag: strain

value: Balb/c

value: Foxp3-hCD2 reporter mouse

value: regulatory T cells (spleen)


title: non-treat regulatory T cells

tag: genotype


title: CD4 T cells: mock vector

data_processing:
Sequencing was performed on an Illumina Hiseq1500. Sequencing reads were mapped to mm9 reference genome and mRNA profiles were calculated with Cufflinks software.
RPKM value +1 was transformed to log2
Genome_build: mm9

source_name: CD4 T cells

treatment_protocol: Naïve CD4 positive Tcells were purified and transduced with either mock vector or Sox12 vector.

value: Wild type

value: CD4 T cells


title: Placebopost_212-2


title: CD4 T cells: Sox12 vector


title: Post LPS (time 4h; no intervention) 1

city: Pittsburgh

first: Josiah

last: Radder

address: 200 Lothrop St

department: Pulmonary, Allergy, and Critical Care Medicine

institute: University of Pittsburgh

data_processing:
Trimmomatic (Version 0.36)
TopHat (Version 2.1.1)
Cufflinks (Version 2.2.1)
Genome_build: GRCH37
Supplementary_files_format_and_content: Cufflinks (Version 2.2.1)

source_name: Lung parenchymal homogenate

extract_protocol:
Tissue was placed in RNA later, then RNA extracted using Qiazol
TuruSeq stranded mRNA (PolyA+)

treatment_protocol: For LPS injury, E. coli 055:B5 endotoxin was diluted in 20ml sterile PBS at 5 mg/kg ideal body weight for the donor and infused into the pulmonary arterial limb of the circuit over 5 min via automated syringe pump at T=1 hour. BC1215 was dissolved in 50ml sterile PBS and BC1215 or PBS alone was administered via a bronchoscope with 2-3 ml of solution directed into each segmental bronchus immediately following T-2 hour BAL and biopsy collection.

tag: group

value: Post LPS Control