title: Anti-unc-119 piRNAi, rep 2, ChIP input

extract_protocol:
101-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions


title: FA2-L-4

status: Public on Jan 21 2021

type: SRA

city: Guangzhou

first: Shixue

last: Gou

address: No. 190, Kaiyuan Avenue, Huangpu District, Guangzhou

country: China

institute: GUANGZHOU INSTITUTES OF BIOMEDICINE AND HEALTH,CHINESE ACADEMY OF SCIENCES

library_source: transcriptomic

data_processing:
High-throughput sequencing was performed on the llumina NovaSeq .
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
quality filtered reads were mapped to the rabbit reference genome using Salmon 0.14.1
Genome_build: oryCun2
Supplementary_files_format_and_content: comma-delimited csv files include Raw reads counts of each Sample ...

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: rabbits liver tissue

extract_protocol:
The livers of treated rabbits' were trypsinized and collected, and total mRNA was extracted using TRIzol reagent
The TruSeq RNA Sample Preparation kit (Illumina) was used to construct RNA-seq libraries

tag: tissue

value: liver

tag: disease state

value: rabbit model of hereditary tyrosinemia type I (HT1)


title: Sample_60: DLBCL tissue RNA

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

country: USA

institute: Weill Cornell Medicine

data_processing:
Bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark. CpG-context methylation call output files are in txt format and filtered for at least 10 covered cytosines per site. Tab-delimited csv file includes Kallisto TPM values for protein-coding genes for RNA-sequenced samples
Illumina Casava-1.8.2 software used for basecalling

organism: Homo sapiens

source_name: DLBCL tumor sample

extract_protocol: trizol extraction and TruSeq RNA sample prep kit.

value: Diffuse large B-cell lymphoma (DLBCL)


title: Sample_60: DLBCL tissue eRRBS

library_source: genomic

molecule: genomic DNA

extract_protocol: enhanced reduced representation bisulfite sequencing method (eRRBs) was followed as reported in Garrett-Bakelman et al 2015 doi: 10.3791/52246


title: 14: TCDD-Infected2_WGBS

city: Rochester

first: B. Paige

last: Lawrence

state: NY

address: 601 Elmwood Ave.

institute: University of Rochester

data_processing:
bcltofastq-2.19.0
trim_galore-0.4.3, "--paired --clip_r1 8 --clip_r2 8 --three_prime_clip_r1 8 --three_prime_clip_r2 8"
bismark-0.18.1, bismark "--bowtie2 --maxins 1000 --multicore 3"
bismark-0.18.1, filter_non_conversion
bismark-0.18.1, deduplicate_bismark
smtools-1.4.1, sort
MethylKit-1.4.0, processBismarkAln "save.context="CpG",read.context="CpG",nolap=TRUE,mincov=2,minqual=10,phred64=FALSE"
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited, MethylKit CpG extracted data

organism: Mus musculus

source_name: TCDD-Infected

extract_protocol:
Peripheral lymph nodes (cervical, axillary, brachial, inguinal, and sacral) were harvested from naïve adult developmentally exposed mice. Mediastinal lymph nodes were harvested from adult developmentally exposed mice on day 9 post IAV infection. Lymph nodes were processed to single cell suspensions, and CD4+ T cells were purified to >90% purity using the MojoSort Mouse CD4+ T cell negative selection isolation kit protocol (BioLegend, San Diego, CA). DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Valencia, CA), and then processed for whole genome bisulfite sequencing. Genomic DNA was quantified using the Qubit fluorometer (Life Technologies, Grand Island, NY). DNA integrity was determined using the TapeStation with genomics DNA tape reagents (Agilent, Santa Clara, CA).
Methylation libraries were generated with Illumina’s TruSeq DNA Methylation Kit.Briefly, bisulfite conversion was carried out on 100 ng of genomics DNA using Zymo EZ DNA Methylation Gold per manufacturer’s recommendations (Zymo Research, Irvine, CA) and conversion efficiency was determined with the Bioanalyzer 2100 (Agilent, Santa Clara, CA). Single-stranded cDNA was generated and tagged from Bisulfite converted DNA using random hexamers containing a 5` tag followed by terminal tagging to mark the 3` end of the DNA. Illumina specific adaptors were added during PCR amplification. DNA libraries were purified with AmpureXP beads and quantified with Bioanalyzer 2100 and Qubit fluorometer. The amplified libraries were hybridized to the Illumina pair end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Pair end reads of 126nt were generated on the Illumina HiSeq2500 for each sample.

treatment_protocol: Impregnated and lactating dams were gavaged with vehicle (peanut oil) or 1ug 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)/kg body weight on gestational day 0, 7, 14, and post natal day 2. Offspring were aged to maturity (6-10 weeks old), and CD4+ T cells were purified from naive mice or mice infected with 120 HAU Influenza A virus (HKx31).

value: CD4+  T cells


title: 15: Vehicle-Infected3_WGBS

source_name: Vehicle-Infected


title: Sample_63: DLBCL tissue RNA


title: FK-L1-1


title: Sample_59: DLBCL tissue eRRBS


title: FA3-L-4


title: FA2-L-3


title: Sample_58: DLBCL tissue eRRBS


title: 10: TCDD-Infected1_WGBS


title: Anti-unc-119 piRNAi, rep 1, ChIP input

city: Piscataway

first: Sam

middle: Guoping

last: Gu

state: New Jersey

address: 604 Allison Road

department: Molecular Biology and Biochemistry

institute: Rutgers University

description:
Genomic DNA extracted from fragmented chromatin
rawcounts_genebygene_SG0919_lib1_to_12.csv

data_processing:
Genomic alignment was performed by using Bowtie 1.2.3
Genome_build: WS190(ce6)
Supplementary_files_format_and_content: File format: csv text file. The content includes raw counts for each protein coding gene (row)  for each library (column) used in this study.

organism: Caenorhabditis elegans

source_name: Young adult animals

extract_protocol:
100-200 μl frozen synchronized young adult worm pellets were used for each chromatin immnuoprecipitation experiment. Crushed pellets (pulverized by grinding in liquid nitrogen with a mortar and pestle) were resuspended in 1ml of pre-chilled RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, and 1X HALT combined protease and phosphatase inhibitor cocktail [ThermoScientific]).  To crosslink, formaldehyde was added to the crude extract to a final concentration of 2%.  The lysate was rotated at 4°C for 10 minutes. 0.1 ml of 1M Tris-HCl (pH 7.5) was added to quench formaldehyde.  Lysate was spun at 6000 x g for 30 second and the supernatant was removed. The pellet was resuspended in 0.5ml of pre-chilled RIPA buffer. The lysate was transferred to a 1.5 ml TPX tube (Diagenode) and sonicated (Bioruptor [Diagenode], output level: high, interval: 0.5, three times of 8-minute sonication). 50 μl of the lysate was used to make IP input library. For each immumoprecipiation experiment, 2 μg of anti-H3K9me3 (ab8898, Abcam) or anti-Pol II-S2 (ab5095, Abcam) was added to 400 μl of the lysate (containing approximately 50 μg DNA). The IP mix was rotated overnight at 4°C.  50 μl of Protein A Dynabeads (Life Technology) was added and rotated for another 2 hours.  The beads were then washed three times with 800 μl ice-cold LiCl washing buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40 and 1% sodim deoxycholate).  To elute the immunoprecipitation product and reverse crosslink, beads were incubated with 400 μl of worm lysis buffer (0.1 M Tris-HCl, pH 7.5, 100 mM NaCl, 50 mM EDTA, 1% SDS, and 200 μg/ml of proteinase K) at 65 °C for 2 hours with agitation every 30 minutes (IP input lysate was treated similarly to reverse crosslink) and then subject to organic extraction and precipitation of DNA and RNA.
DNA libraries were prepared using KAPA Hyper Prep Kits (KAPA Biosystems) according to the manufacturer's instructions

tag: genotype

tag: pirnai target gene

tag: chip antibody

tag: rna-seq method

tag: 5’ barcodes for srna or rna-seq


title: FA3-L-2


title: 13: Vehicle-Infected2_WGBS


title: Sample_57: DLBCL tissue RNA


title: FA2-L-2


title: FA2-L-1


title: Sample_56: DLBCL tissue eRRBS


title: 9: Vehicle-Infected1_WGBS


title: FA1-L-4


title: FA1-L-3


title: 7: Vehicle-Naive3_WGBS

source_name: Vehicle-Naive


title: Sample_54: DLBCL tissue RNA


title: Sample_55: DLBCL tissue eRRBS


title: 6: TCDD-Naive2_WGBS

source_name: TCDD-Naive


title: Sample_54: DLBCL tissue eRRBS


title: 5: Vehicle-Naive2_WGBS


title: FA1-L-2


title: FA1-L-1


title: WT-L3-4


title: 2: TCDD-Naive1_WGBS


title: WT-L3-3


title: 1: Vehicle-Naive1_WGBS


title: WT-L3-2


title: Sample_52: DLBCL tissue RNA


title: 8: TCDD-Naive3_WGBS


title: miR-neg_48h_rep2

type: RNA

city: Milano

first: Davide

last: Marangon

state: MI

address: Via Giuseppe Balzaretti 9

country: Italy

institute: Università degli studi di Milano

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing Agilent fragmentation buffer and Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent  SurePrint G3 Rat Gene Expression v2 8x60K Microarray (G4858A-074036) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: oligodendrocytes, 48h, miR-neg, replicate 2

label_protocol: Labelled cRNA was synthesized from 100 ng of total RNA using the Low Input Quick-Amp Labelling Kit, one colour (Agilent Technologies) in the presence of cyanine 3-CTP.

growth_protocol: Oligodendrocyte precursor cells were isolated from post-natal 2 rat cortices and plated in presence of bFGF and PDGF for 3 days to promote cell proliferation.

extract_protocol: Cells were lysed and RNA was extracted by means of  RNeasy mini kit (Qiagen).

treatment_protocol: OPCs were transfected with 50 nM miR-125a-3p mimics (or the negative control) by means of Lipofectamine RNAiMax by following manufacturer's protocol.

tag: cell type

value: oligodendrocytes

tag: maturation

value: 2 Days in vitro

tag: treatment

value: 48 h after transfection of RNA negative control


title: miR-125a-3p_48h_rep1

source_name: oligodendrocytes, 48h, miR-125a-3p, replicate 1

value: 48 h after transfection of miR-125a-3p mimics


title: miR-125a-3p_48h_rep2

source_name: oligodendrocytes, 48h, miR-125a-3p, replicate 2


title: Sample_50: DLBCL tissue eRRBS


title: miR-neg_48h_rep1

source_name: oligodendrocytes, 48h, miR-neg, replicate 1


title: WT-L2-4


title: BMMs unstimulated, washed and left unstimulated (negative control) RNA 2

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
Reads were mapped to mm10 (Mus musculus) reference genome using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml) toaccount for spliced reads alignments, allowing two  mismatches (n = 2).
Resulting BAM aligment files were used in as input for a Differential Expression Analysis pipeline based on DESeq2 BioconductoR package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: mm10
Supplementary_files_format_and_content: Tables of raw counts, obtained from the BAM files of the samples in each comparative. These tables are in tab separated plain text format.

source_name: Bone marrow

growth_protocol: Mice were breed and housed at the Animal Facility of CIC bioGUNE under controled conditions according to the animal care international gidelines.

extract_protocol:
RNA was extracted from BMMs using NucleoSpin® RNA kit  (Macherey-Nagel, Düren, GE)
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)

tag: strain

tag: age

value: 8 weeks

value: Unstimulated control


title: WT-L2-3


title: BMMs unstimulated, washed and left unstimulated (negative control) RNA 1


title: Sample_48: DLBCL tissue RNA


title: 40-4_P9 Blood

city: Davis

first: Smita

last: Iyer

state: CA

address: county rd 98 & hutchison, ccm room 2075

department: Center for Immunology and Infectious Disease

institute: University of California-Davis

data_processing:
The raw read data was filtered using HTStream (version 1.3.1) which included screening for contaminants (such as PhiX and rRNA), quality-based trimming, and adapter trimming. (https://github.com/s4hts/HTStream)
STAR (version 2.7.3a) was used to align the processed data to the rhesus genome (Mmul_10). Dobin, Alexander, et al. "STAR: ultrafast universal RNA-seq aligner." Bioinformatics 29.1 (2013): 15-21.
MultiQC (custom version) was then used for read and alignment quality assessment. https://github.com/s4hts/MultiQC
Differential expression analyses were conducted using the limma-voom Bioconductor pipeline, using edgeR version 3.30.3 and limma version 3.44.3 in R 4.0.1  The model used in limma included effects for brain region, infection status, and their interaction, and standard errors of log fold changes were adjusted for within-animal correlations.
Supplementary_files_format_and_content: Tables of normalized counts per gene. Comparison between tissue types and characteristics.

organism: Macaca mulatta

source_name: Blood

extract_protocol:
2000 sorted cells were flash frozen in 300 ul of RLT buffer and extracted using the Qiagen mini lipid RNA isolation kit according to manufacturers instructions.
The libraries were constructed following the 3' TagSeq protocol using Lexogen kit (QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina). 500ng of total RNA was used as input.

tag: cell type code

value: B7- CD8


title: Sample_49: DLBCL tissue eRRBS


title: Sample_51: DLBCL tissue eRRBS


title: WT-L3-1


title: Sample_53: DLBCL tissue eRRBS


title: BMMs unstimulated, washed and left unstimulated (negative control) RNA 4


title: BMMs unstimulated, washed and restimulated with B. burgdorferi RNA 3

value: Acutely stimulated


title: WT-L2-2


title: WT-L2-1


title: BMMs unstimulated, washed and left unstimulated (negative control) RNA 3


title: WT-L1-4


title: 39-4_P8 Blood

value: B7+ CD8


title: Sample_47: DLBCL tissue RNA


title: BMMs unstimulated, washed and restimulated with B. burgdorferi RNA 2


title: Sample_47: DLBCL tissue eRRBS


title: BMMs unstimulated, washed and restimulated with B. burgdorferi RNA 1


title: Sample_48: DLBCL tissue eRRBS


title: Sample_46: DLBCL tissue RNA


title: 37-4_P6 Blood

value: B7+ CD4


title: WT-L1-3


title: BMMs stimulated with B. burgdorferi, washed and left unstimulated RNA 4

value: Stimulated and rested


title: Sample_46: DLBCL tissue eRRBS


title: 38-4_P7 Blood

value: B7- CD4


title: 36-4_P5 Blood

value: Naive CD4


title: BMMs stimulated with B. burgdorferi, washed and left unstimulated RNA 3


title: Sample_45: DLBCL tissue RNA


title: BMMs stimulated with B. burgdorferi, washed and left unstimulated RNA 2


title: Sample_45: DLBCL tissue eRRBS


title: WT-L1-1

value: liver


title: 35-4_P4 GUT

source_name: GUT


title: WT3#OT-2M

data_processing:
High-throughput sequencing was performed on the NOVA SEQ system (Illumina).
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
The types and proportions of SNVS are analyzed using customized shell scripts
Genome_build: oryCun2
Supplementary_files_format_and_content: comma-delimited csv files include SNV percentage of each Sample …

source_name: rabbits liver's DNA

extract_protocol:
Genomic DNAs were extracted from the liver tissues of the  FAH-/- rabbits injected virus by using TIANamp Genomic DNA Kit (TIANGEN)
Amplification primers containing Illumina forward and reverse adapters were used for a first round of PCR (PCR 1) amplifying the genomic region of interest. Unique Illumina barcoding primer pairs were  added to each sample in a secondary PCR reaction (PCR 2).

value: rabbit model of hereditary tyrosinemia type I (HT1)


title: BMMs stimulated with B. burgdorferi, washed and left unstimulated RNA 1


title: 34-4_P3 GUT


title: BMMs stimulated with B. burgdorferi, washed and restimulated RNA 3

value: Restimulated


title: WT2#OT-2M


title: Sample_44: DLBCL tissue eRRBS

value: Diffuse large B-cell lymphoma (DLBCL)


title: Sample_44: DLBCL tissue RNA


title: BMMs stimulated with B. burgdorferi, washed and restimulated RNA 2


title: WT-L1-2


title: 32-4_P1 GUT


title: Sample_43: DLBCL tissue RNA


title: WT1#OT-2M


title: 31-4_P0 Blood

value: Naive CD8


title: Sample_43: DLBCL tissue eRRBS


title: BMMs stimulated with B. burgdorferi, washed and restimulated RNA 1


title: 30-3_P9 Blood


title: FA2#OT-2M


title: KYSE510C-t-3

city: Shanghai

first: Yuxiang

last: Wang

address: No. 501 Haike Road

institute: Shanghai Institute of Materia Medica

data_processing:
Illumina BCLfastq (v2.20.0.422) software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatics (v0.36), then mapped to hg19 whole genome using STAR (v2.4.2a).
Transcript quantification was performed using Salmon (v0.8.0)
Differential expression analysis was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample

source_name: Cell lines

extract_protocol:
RNA was isolated and purified using AllPrep DNA/RNA mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: esophagus

value: CYH33-resistant ESCC cells


title: Sample_42: DLBCL tissue RNA


title: 33-4_P2 GUT


title: KYSE510C-t-2


title: FA1#OT-2M


title: FA3#-L6

data_processing:
High-throughput sequencing was performed on NOVA SEQ system (Illumina).
Trimmed reads were obtained by removing adapter sequences, and reads with low complexity or of low quality were removed.
The types and proportions of SNVS are analyzed using customized shell scripts
Genome_build: oryCun2
Supplementary_files_format_and_content: comma-delimited csv files include SNV percentage of each Sample …


title: KYSE510C-t-1


title: 29-3_P8 Blood


title: KYSE510-t-3

value: ESCC cellss


title: FA3#-L5


title: FA3#OT-2M


title: Sample_40: DLBCL tissue RNA


title: 27-3_P6 Blood


title: Sample_41: DLBCL tissue RNA


title: Sample_42: DLBCL tissue eRRBS


title: FA3#-L4


title: KYSE510-t-2


title: 28-3_P7 Blood


title: 26-3_P5 Blood


title: KYSE510-t-1


title: FA3#-L3


title: 25-3_P4 GUT


title: Sample_41: DLBCL tissue eRRBS


title: Sample_40: DLBCL tissue eRRBS


title: KYSE410C-t-3


title: FA3#-L2


title: 24-3_P3 GUT


title: 23-3_P2 GUT


title: KYSE410C-t-2


title: Sample_39: DLBCL tissue eRRBS


title: Sample_38: DLBCL tissue RNA


title: Sample_39: DLBCL tissue RNA


title: KYSE410C-t-1


title: Sample_38: DLBCL tissue eRRBS


title: KYSE410-t-2


title: 20-2_P9 Blood


title: FA2#-L3


title: FA2#-L6


title: 21-3_P0 Blood


title: 22-3_P1 GUT


title: FA2#-L4


title: 19-2_P8 Blood


title: Sample_37: DLBCL tissue eRRBS


title: FA3#-L1


title: FA2#-L5


title: Sample_36: DLBCL tissue RNA


title: Sample_37: DLBCL tissue RNA


title: KYSE180C-t-2


title: KYSE410-t-1


title: KYSE410-t-3


title: FA2#-L2


title: FA2#-L1


title: KYSE180C-t-3


title: 16-2_P5 Blood


title: KYSE180-t-3


title: FA1#-L5


title: KYSE180C-t-1


title: 17-2_P6 Blood


title: FA1#-L6


title: 15-2_P4 GUT


title: 14-2_P3 GUT


title: FA1#-L4


title: Sample_34: DLBCL tissue RNA


title: Sample_35: DLBCL tissue RNA


title: 13-2_P2 GUT


title: Sample_34: DLBCL tissue eRRBS


title: KYSE180-t-2


title: Sample_36: DLBCL tissue eRRBS


title: FA1#-L3


title: KYSE180-t-1


title: Sample_33: DLBCL tissue eRRBS


title: KYSE70C-t-3


title: FA1#-L2


title: 12-2_P1 GUT


title: Sample_32: DLBCL tissue RNA


title: KYSE70C-t-2


title: 11-2_P0 Blood


title: CDF_8_3

city: Madison

first: Sean

middle: M

last: Ronnekleiv-Kelly

state: Wisconsin

address: 1400 University Ave

department: Surgery

institute: University of Wisconsin

data_processing:
Illumina bcl2fastq v2.20
Fastq data from lanes 1 and 2 merged
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0
Genome_build: GRCm38.p5

source_name: Pancreas

extract_protocol:
All pancreatic RNA was prepared using a modified RNeasy mini protocol following cervical dislocation.
RNA libraries were prepared for sequencing using standard Truseq Illumina protocols

value: Pancreas

tag: Sex

value: Female

tag: condition

value: Circadian Disrupted

tag: day

tag: zeitgeber time (zt)

tag: sample name


title: KYSE70C-t-1

tag: tissue


title: 10-2_P9 Blood

value: B7- CD8


title: Sample_31: DLBCL tissue eRRBS


title: CDF_8_2


title: KYSE70-t-3


title: 9-1_P8 Blood

value: B7+ CD8


title: CDF_8_1


title: KYSE70-t-2


title: Sample_29: DLBCL tissue eRRBS


title: KYSE70-t-1


title: CDM_9_3

value: Male


title: 18-2_P7 Blood


title: Sample_30: DLBCL tissue eRRBS


title: FA1#-L1

tag: disease state


title: Sample_28: DLBCL tissue eRRBS


title: CDM_9_2


title: 8-1_P7 Blood


title: KYSE510C-3

value: Vehicle


title: 6-1_P5 Blood


title: 7-1_P6 Blood

value: B7+ CD4


title: CDM_9_1


title: Sample_32: DLBCL tissue eRRBS


title: KYSE510C-2


title: NCF_8_3

value: Normal Circadian


title: 5-1_P4 GUT


title: KYSE510C-1


title: Sample_27: DLBCL tissue eRRBS


title: 4-1_P3 GUT


title: 2-1_P1 GUT


title: MP_CPT_42

type: genomic

city: Cairo

first: Shahenda

last: El-Naggar

address: 1 Sekket El Emam, El Madbah El Kadeem Yard, Sayeda Zeinab

department: Research Department

country: Egypt

institute: Children’s Cancer Hospital Egypt 57357

description: FFPE

hyb_protocol: Sodium bisulfite-converted genomic DNA samples were hybridized to the Illumina Infinium Human Methylation 850K EPIC Bead Chips array.

scan_protocol: EPIC BeadChip array were scanned using the Illumina iScan microarray scanner according to the manufacturer’s recommendations

data_processing: IDAT files were processed using minfi R package. Samples quality control steps included; sample swap and detection of p-value. Samples with p-value > 0.01 (n=2) were excluded from further analysis. Normalization was performed using Functional normalization (FunNorm). Beta and M values were then extracted.

source_name: Pediatric Choroid plexus Tumors

label_protocol: Illumina protocol

extract_protocol: Genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor samples using QIAamp DNA FFPE tissue kit (Qiagen) and fresh frozen (FF) tumor samples using the Gene JET genomic DNA (Thermo Fisher) according to the manufacturer’s instructions.

tag: disease

value: pediatric choroid plexus

tag: gender


title: 3-1_P2 GUT

value: B7- CD4


title: KYSE510-1


title: MP_CPT_42 F

description: Frozen


title: NCM_9_3


title: KYSE510-3


title: MP_CPT_51

description: FFPE


title: NCF_8_1


title: Sample_24: DLBCL tissue RNA

source_name: DLBCL tumor sample


title: NCF_8_2


title: KYSE410C-3


title: Sample_24: DLBCL tissue eRRBS


title: Sample_26: DLBCL tissue RNA


title: NCM_9_2


title: Sample_25: DLBCL tissue eRRBS


title: Sample_26: DLBCL tissue eRRBS


title: KYSE410C-2


title: NCM_9_1


title: MP_CPT_52

description: FFPE


title: MP_CPT_41 F

description: Frozen


title: Sample_23: DLBCL tissue RNA


title: CDF_1_3


title: CDF_1_2


title: KYSE410C-1


title: Sample_22: DLBCL tissue eRRBS


title: KYSE410-3


title: KYSE410-2


title: MP_CPT_43_F

description: Frozen


title: Sample_23: DLBCL tissue eRRBS


title: KYSE410-1


title: Sample_21: DLBCL tissue RNA


title: Sample_20: DLBCL tissue RNA


title: MP_CPT_45

description: FFPE


title: KYSE180C-3


title: Sample_21: DLBCL tissue eRRBS


title: CDM_1_2


title: KYSE180C-2


title: CDM_1_3


title: CDM_1_1


title: 1-1_P0 Blood


title: CDF_1_1


title: Sample_20: DLBCL tissue eRRBS


title: KYSE180C-1


title: NCF_1_2


title: Sample_19: DLBCL tissue RNA


title: KYSE180-3


title: KYSE180-2


title: Sample_19: DLBCL tissue eRRBS


title: NCM_1_3


title: Sample_18: DLBCL tissue eRRBS


title: KYSE180-1


title: Sample_18: DLBCL tissue RNA


title: NCF_1_3


title: NCM_1_2


title: KYSE70C-3


title: Sample_17: DLBCL tissue RNA


title: NCM_1_1


title: KYSE70C-2


title: NCF_1_1


title: MP_CPT_44

description: FFPE


title: ZT44-4

description: Pooled 3 biologic replicates

data_processing:
Illumina bcl2fastq v2.20
Fastq data from lanes 1 and 2 merged
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Genome_build: GRCm38.p5

tag: species

tag: zt


title: Sample_17: DLBCL tissue eRRBS


title: KYSE70C-1

tag: cell type


title: Sample_16: DLBCL tissue RNA


title: KYSE70-3


title: ZT44-3

description: Pooled 3 biologic replicates


title: Sample_16: DLBCL tissue eRRBS


title: Sample_15: DLBCL tissue eRRBS


title: KYSE70-2


title: ZT44-2

description: Pooled 3 biologic replicates


title: Sample_14: DLBCL tissue eRRBS


title: HYM-15

city: Nottingham

first: Nigel

middle: P

last: Mongan

address: University Park

department: Biodiscovery Institute

country: United Kingdom

institute: University of Nottingham

data_processing:
CASAVA-1.8.2 / HiSeq Control Software 2.2.58 / RTA 1.18.64.0
Low quality reads (phred <30) and adapter sequences were removed using the Trimgalore wrapper for Cutadapt and FastQC.
The resulant fastq reads were trimmed to a unifrom length (110bp) and aligned using the STAR aligner to the Amel4.5 genome and splicing analyzed using rMATs.
For differential gene expression, reads were aligned using Tophat and differenital expression determined using Cuffdiff.
bedtools was used to generate bedgraph files from Tophat generated BAM alignments.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: bedgraph

organism: Apis mellifera

source_name: Neurons

growth_protocol: 10 day ad libidum feeding

extract_protocol:
Trizol-based RNA extraction
Illumina Sequencing - Standard Library preparation protocol for stranded mRNA
HiSeq High-Output, Paired-reads, 2x125 bp, Full lane - V4 chemistry

treatment_protocol: sugar solution with, or without Thiamethoxam

value: sugar-fed + 50 ug/l Thiamethoxam pooled RNA 15 brains of worker bees


title: ZT40-4

description: Pooled 3 biologic replicates


title: Sample_13: DLBCL tissue eRRBS

value: Diffuse large B-cell lymphoma (DLBCL)


title: ZT40-3

description: Pooled 3 biologic replicates


title: ZT44-1

description: Pooled 3 biologic replicates


title: Sample_27: DLBCL tissue RNA


title: HYM-14


title: ZT40-2

description: Pooled 3 biologic replicates


title: Sample_11: DLBCL tissue RNA


title: HYM-13


title: Sample_12: DLBCL tissue eRRBS


title: HYM-12

value: sugar-fed + 2 ug/l Thiamethoxam pooled RNA 15 brains of worker bees


title: KYSE70-1

value: esophagus


title: KYSE510-2


title: Sample_11: DLBCL tissue eRRBS


title: ZT36-4

description: Pooled 3 biologic replicates


title: HYM-11


title: ZT40-1

description: Pooled 3 biologic replicates


title: ZT36-3

description: Pooled 3 biologic replicates


title: Sample_10: DLBCL tissue RNA


title: Sample_10: DLBCL tissue eRRBS


title: MP_CPT_40

description: FFPE


title: HYM-10


title: MP_CPT_39

description: FFPE


title: MP_CPT_36

description: FFPE


title: ZT36-1

description: Pooled 3 biologic replicates


title: MP_CPT_41_S

description: FFPE


title: ZT36-2

description: Pooled 3 biologic replicates


title: HYM-8

value: sugar-fed / pooled RNA 15 brains of worker bees


title: Sample_9: DLBCL tissue RNA


title: MP_CPT_40 F

description: Frozen


title: MP_CPT_39 F

description: Frozen


title: MP_CPT_38

description: FFPE


title: Sample_9: DLBCL tissue eRRBS


title: ZT32-4

description: Pooled 3 biologic replicates


title: MP_CPT_35

description: FFPE


title: HYM-7


title: ZT32-3

description: Pooled 3 biologic replicates


title: MP_CPT_30

description: FFPE


title: Sample_8: DLBCL tissue RNA


title: MP_CPT_31

description: FFPE


title: ZT32-2

description: Pooled 3 biologic replicates


title: Sample_8: DLBCL tissue eRRBS


title: MP_CPT_37

description: FFPE


title: GF4

city: Jerusalem

first: Khaled

last: Zubeidat

address: Faculty of Medicine, Ein-Kerem

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Raw fastq files were created with bcl2fastq, v2.18.0.12.
Reads were trimmed for adapter sequences and low-quality bases with cutadapt, v1.18, using parameters -q32,32; -O 1; -m 15; --match-read-wildcards.
Processed reads were aligned against the mouse genome GRCm38 with Ensembl release 99 annotations. Alignment was done with TopHat, v2.1.1, using parameters -G genes.gtf; -N 5; --read-gap-length 5; --read-edit-dist 10; --segment-length 18; --read-realign-edit-dist 3; --no-coverage-search; --library-type fr-firststrand;
Raw counts were obtained with htseq-count, v0.6.0, then genes with less than 10 reads were filtered out and DESeq2, v1.22.2, was used with default parameters for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel with all relevant data. First row has column headers, then each row has data for a gene. Columns A-L have general gene details; M-T are raw counts; U-AB are normalized counts; AC has the baseMean value; AD-AH are the results of comparing SPF to germ-free samples.

source_name: buccal epithelium Germ Free 4

extract_protocol:
The oral mucosa was extracted, epithelium was separated using dispase II, epithelial cells were FACS sorted, frozen on dry ice, and RNA was harvested using Qiagen's Rneasy micro kit.
RNA libraries were prepared for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit, with rRNA-depletion.

treatment_protocol: No tretament before isolation of the tissue

value: buccal epithelium

value: Adult

tag: group

value: germ free


title: MP_CPT_31 F

description: Frozen


title: MP_CPT_32 F

description: Frozen

value: Female


title: HYM-9

tag: treatment


title: MP_CPT_30 F

description: Frozen


title: ZT32-1

description: Pooled 3 biologic replicates

value: Pancreas

value: Circadian Disrupted


title: Sample_7: DLBCL tissue eRRBS


title: ZT28-4

description: Pooled 3 biologic replicates


title: GF3

source_name: buccal epithelium Germ Free 3

tag: strain


title: Sample_6: DLBCL tissue RNA


title: ZT28-3

description: Pooled 3 biologic replicates

value: Male


title: MP_CPT_27 F

description: Frozen


title: MP_CPT_28 F

description: Frozen


title: Sample_6: DLBCL tissue eRRBS


title: GF1

source_name: buccal epithelium Germ Free 1

tag: age


title: GF2

source_name: buccal epithelium Germ Free 2


title: ZT28-2

description: Pooled 3 biologic replicates


title: MP_CPT_34

description: FFPE


title: ZT28-1

description: Pooled 3 biologic replicates


title: SPF 5

source_name: buccal epithelium WT 4

value: SPF


title: SPF 4

source_name: buccal epithelium WT 3


title: Sample_5: DLBCL tissue eRRBS


title: MP_CPT_32

description: FFPE


title: MP_CPT_27

description: FFPE


title: SPF 3

source_name: buccal epithelium WT 2


title: Sample_4: DLBCL tissue RNA


title: MP_CPT_28

description: FFPE


title: Sample_7: DLBCL tissue RNA


title: ZT24-4

description: Pooled 3 biologic replicates


title: MP_CPT_34 F

description: Frozen


title: SPF 1

source_name: buccal epithelium WT 1


title: Sample_4: DLBCL tissue eRRBS


title: MP_CPT_29_F

description: Frozen


title: 8 week 3

data_processing:
Raw fastq files were created with bcl2fastq, v2.20.0.422.
Reads were trimmed for adapter sequences and low-quality bases with cutadapt, v2.10, using parameters -q32,32; -O 1; -m 15; --match-read-wildcards.
Processed reads were aligned against the mouse genome GRCm38 with Ensembl release 99 annotations. Alignment was done with TopHat, v2.1.1, using parameters -G genes.gtf; -N 6; --read-gap-length 5; --read-edit-dist 11; --segment-length 20; --read-realign-edit-dist 3; --no-coverage-search; --library-type fr-firststrand;
Raw counts were obtained with htseq-count, v0.6.0, then genes with less than 10 reads were filtered out and DESeq2, v1.26.0, was used with default parameters for differential expression analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel with all relevant data. First row has column headers, then each row has data for a gene. Columns A-L have general gene details; M-T are raw counts; U-AB are normalized counts; AC has the baseMean value; AD-AH are the results of comparing old (8 weeks) to young (1 week) samples.

source_name: 8 week old mice buccal epithelium


title: Sample_3: DLBCL tissue RNA


title: ZT24-2

description: Pooled 3 biologic replicates


title: ZT24-3

description: Pooled 3 biologic replicates


title: 8 week 4


title: ZT24-1

description: Pooled 3 biologic replicates


title: 8 week 2


title: Sample_1: DLBCL tissue RNA


title: 8 week 1


title: Sample_2: DLBCL tissue eRRBS


title: Sample_1: DLBCL tissue eRRBS


title: ZT20-3

description: Pooled 3 biologic replicates


title: 1 week 4

source_name: 1 week old mice buccal epithelium

value: postnatal


title: ZT20-2

description: Pooled 3 biologic replicates


title: ZT20-4

description: Pooled 3 biologic replicates

value: Normal Circadian


title: LNCaP_R1881 RNA-seq2

city: Houston

first: Basil

last: Paul

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
Raw read sequences from fastq files for each sample were quality trimmed using Trim Galore with a Phred score of 20.
RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 using default parameters.
Total aligned reads for each sample at each features were then quantified using featureCounts and a transcript annotation reference for the hg19 genome build (V24).
Genome_build: hg19
Supplementary_files_format_and_content: Aligned reads were normalised to counts per million bases for each feature quantified using featureCounts are provided as text files.

source_name: LNCaP_R1881 RNA-seq

growth_protocol: LNCaP AR-V7 and VCaP AR-V7 cells grown in their corresponding medium were supplemented with 10% FBS and maintained under constant G418 antibiotic selection. Cells were ligand starved in 10% CSS medium for 24 hours before treatment.

extract_protocol:
LNCaP AR-V7 and VCaP AR-V7 cells treated with ethanol, 10uM R1881 or 20ng/mL DOX for 24 hours were harvested into PureXtract RNAzol solution. Total RNA was extracted, and column purified using RNAeasy kit (Qiagen, USA).
RNA-seq libraries were constructed using Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions. cDNA libraries were sequenced on the Illumina HiSeq 2500 platform at Genomic and RNA Profiling Core facility, Baylor College of Medicine.

treatment_protocol: Cells were treated with 10nM R1881 for hormone response and 20ng/mL Doxycycline for AR-V7 response.

tag: cell line background

value: LNCaP

value: Immortalised prostate cancer cell line

tag: genotype/variation

value: expressing AR-V7 in response to doxycycline (LNCaP AR-V7)

tag: passages

value: 10uM R1881 for 24 hrs


title: LNCaP_R1881 RNA-seq1


title: ZT20-1

description: Pooled 3 biologic replicates

tag: condition

tag: Sex


title: 1 week 2


title: LNCaP_Dox RNA-seq2

source_name: LNCaP_Dox RNA-seq

value: 20ng/mL Doxycycline for 24hrs


title: ZT16-4

description: Pooled 3 biologic replicates


title: 1 week 1


title: MP_CPT_26

description: FFPE

value: pediatric choroid plexus


title: MP_CPT_25

description: FFPE


title: LNCaP_Dox RNA-seq1


title: 1 week 3


title: ZT16-3

description: Pooled 3 biologic replicates


title: C20

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
mRNA
processed data file: Normalized_Data.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation.
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file using custom Python code.
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file.
Reads were normalized using scran, and normalized values are stored in Normalized_Data.tsv.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file, Normalized Data.tsv contains normalized (scran) counts of cells with genes labeled by their gene names.

source_name: Suprachiasmatic nucleus

extract_protocol:
Single cell cytosol extraction via patch pipette.
Nextera XT

tag: mouse line

value: SCNn+

tag: circadian

value: night

tag: cfos

tag: activation

value: a

value: 6-8 weeks


title: LNCaP_Veh RNA-seq2

source_name: LNCaP_Veh RNA-seq

value: ethanol (vehicle) for 24 hrs


title: LNCaP_Veh RNA-seq1


title: C18

tag: gender


title: ZT16-1

description: Pooled 3 biologic replicates

source_name: Pancreas

tag: tissue

value: Pancreas

tag: species


title: ZT16-2

description: Pooled 3 biologic replicates

tag: zt

value: Circadian Disrupted

value: Female


title: C19

tag: cell type

value: Male


title: PARC_primed_hESC_rep2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Library strategy: PCHi-C
Standard Illumina base-calling pipeline.
Hi-C reads were mapped and filtered with HiCUP (v0.5.8) and Bowtie2 (v.2.2.7).
PCHi-C reads were mapped and filtered with HiCUP (v0.5.8) and Bowtie2 (v2.2.7). Significant interactions were called with CHiCAGO (v0.2.4).
ChIP-seq reads were trimmed using Trim Galore (v0.4.5) and aligned using Bowtie2 (v2.3.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph file: A tab-separated file of log2RPM read counts per 500bp. Fields are "chomosome", "start", "end", "log2 RPM"
Supplementary_files_format_and_content: CHiCAGO output: CHiC: The tab-delimited text file was generated by the specialist CHiC software CHiCAGO, and lists significant interactions between restriction fragments. The file reports the co-ordinates of the restriction fragments and a CHiCAGO score reflecting the strength of each given interaction.
Supplementary_files_format_and_content: Hi-C interaction matrix Hi-C:  SeqMonk (v1.45.2) was used to create a raw read interaction matrix at a 100kb resolution, covering the entire genome.  The tab-delimited text file gives the coordinates of each 100kb tile and the number of observed interactions

source_name: Primed ESCs (NK2 H9 line)

extract_protocol:
PCHi-C libraries were generated essentially as described (Schoenfelder et al. 2015). Ligation products containing promoter sequences were captured using a custom-made RNA capture bait system (SureSelect Target Enrichment, Agilent Technologies) designed as previously described in Mifsud et al. 2015. Libraries were paired-end sequenced on an Illumina HiSeq machine at the Babraham Institute Sequencing Facility.
WA09/H9 NK2 naive and primed PSCs were kindly provided by Austin Smith (Takashima et al., 2014) with permission from WiCell. All PSCs were cultured in 5% O2, 5% CO2 at 37°C. Naive PSCs were maintained as previously described (Takashima et al., 2014) in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2 supplement, 0.5x B27 supplement, 1x nonessential amino acids, 2mM L-Glutamine, 1x Penicillin/Streptomycin (all from ThermoFisher Scientific), 0.1mM β-mercaptoethanol (Sigma-Aldrich), 1 μM PD0325901, 1 μM CHIR99021, 20ng/ml human LIF (all from WT-MRC Cambridge Stem Cell Institute) and 2 μM Go6983 (PKCi; Tocris) on Matrigel–coated plates (Corning). Primed PSCs were maintained on Vitronectin-coated plates (0.5 μg/cm2; ThermoFisher Scientific) in TeSR-E8 medium (StemCell Technologies).

value: Human embryonic stem cells (ESCs)

tag: cell line

value: Primed ESCs (NK2 H9 line)

tag: chip antibody


title: C17

tag: age


title: ZT12-4

description: Pooled 3 biologic replicates

value: Normal Circadian


title: MP_CPT_24

description: FFPE

source_name: Pediatric Choroid plexus Tumors

tag: disease


title: PARC_primed_hESC_rep1


title: MP_CPT_22

description: FFPE


title: MP_CPT_21

description: FFPE


title: ZT12-3

description: Pooled 3 biologic replicates


title: C16


title: MP_CPT_24 F

description: Frozen


title: PARC_naive_hESC_rep2

source_name: Naïve ESCs (NK2 H9 line)

value: Naive ESCs (NK2 H9 line)


title: ZT12-2

description: Pooled 3 biologic replicates


title: MP_CPT_17

description: FFPE


title: MP_CPT_20

description: FFPE


title: MP_CPT_17 F

description: Frozen


title: C15


title: PARC_naive_hESC_rep1


title: ZT12-1

description: Pooled 3 biologic replicates


title: HiC_hESC_primed

data_processing:
Library strategy: HiC-Seq
Standard Illumina base-calling pipeline.
Hi-C reads were mapped and filtered with HiCUP (v0.5.8) and Bowtie2 (v.2.2.7).
PCHi-C reads were mapped and filtered with HiCUP (v0.5.8) and Bowtie2 (v2.2.7). Significant interactions were called with CHiCAGO (v0.2.4).
ChIP-seq reads were trimmed using Trim Galore (v0.4.5) and aligned using Bowtie2 (v2.3.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph file: A tab-separated file of log2RPM read counts per 500bp. Fields are "chomosome", "start", "end", "log2 RPM"
Supplementary_files_format_and_content: CHiCAGO output: CHiC: The tab-delimited text file was generated by the specialist CHiC software CHiCAGO, and lists significant interactions between restriction fragments. The file reports the co-ordinates of the restriction fragments and a CHiCAGO score reflecting the strength of each given interaction.
Supplementary_files_format_and_content: Hi-C interaction matrix Hi-C:  SeqMonk (v1.45.2) was used to create a raw read interaction matrix at a 100kb resolution, covering the entire genome.  The tab-delimited text file gives the coordinates of each 100kb tile and the number of observed interactions

extract_protocol:
Hi-C libraries were generated essentially as described (Schoenfelder et al. 2015). Libraries were paired-end sequenced on an Illumina HiSeq machine at the Babraham Institute Sequencing Facility.
WA09/H9 NK2 naive and primed PSCs were kindly provided by Austin Smith (Takashima et al., 2014) with permission from WiCell. All PSCs were cultured in 5% O2, 5% CO2 at 37°C. Naive PSCs were maintained as previously described (Takashima et al., 2014) in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2 supplement, 0.5x B27 supplement, 1x nonessential amino acids, 2mM L-Glutamine, 1x Penicillin/Streptomycin (all from ThermoFisher Scientific), 0.1mM β-mercaptoethanol (Sigma-Aldrich), 1 μM PD0325901, 1 μM CHIR99021, 20ng/ml human LIF (all from WT-MRC Cambridge Stem Cell Institute) and 2 μM Go6983 (PKCi; Tocris) on Matrigel–coated plates (Corning). Primed PSCs were maintained on Vitronectin-coated plates (0.5 μg/cm2; ThermoFisher Scientific) in TeSR-E8 medium (StemCell Technologies).


title: ZT8-4

description: Pooled 3 biologic replicates


title: C14


title: MP_CPT_19

description: FFPE


title: C13

value: s


title: MP_CPT_23

description: FFPE


title: HiC_hESC_naive


title: C12


title: ZT8-3

description: Pooled 3 biologic replicates


title: SOX2_naive_rep2

data_processing:
Standard Illumina base-calling pipeline.
Hi-C reads were mapped and filtered with HiCUP (v0.5.8) and Bowtie2 (v.2.2.7).
PCHi-C reads were mapped and filtered with HiCUP (v0.5.8) and Bowtie2 (v2.2.7). Significant interactions were called with CHiCAGO (v0.2.4).
ChIP-seq reads were trimmed using Trim Galore (v0.4.5) and aligned using Bowtie2 (v2.3.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: bedGraph file: A tab-separated file of log2RPM read counts per 500bp. Fields are "chomosome", "start", "end", "log2 RPM"
Supplementary_files_format_and_content: CHiCAGO output: CHiC: The tab-delimited text file was generated by the specialist CHiC software CHiCAGO, and lists significant interactions between restriction fragments. The file reports the co-ordinates of the restriction fragments and a CHiCAGO score reflecting the strength of each given interaction.
Supplementary_files_format_and_content: Hi-C interaction matrix Hi-C:  SeqMonk (v1.45.2) was used to create a raw read interaction matrix at a 100kb resolution, covering the entire genome.  The tab-delimited text file gives the coordinates of each 100kb tile and the number of observed interactions

extract_protocol:
ChIP-Seq samples were generated essentially as described (Schoenfelder et al. 2015). Libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina. Libraries were single-end sequenced on an Illumina NextSeq machine at the Babraham Institute Sequencing Facility.
WA09/H9 NK2 naive and primed PSCs were kindly provided by Austin Smith (Takashima et al., 2014) with permission from WiCell. All PSCs were cultured in 5% O2, 5% CO2 at 37°C. Naive PSCs were maintained as previously described (Takashima et al., 2014) in a 1:1 mixture of DMEM/F12 and Neurobasal, 0.5x N2 supplement, 0.5x B27 supplement, 1x nonessential amino acids, 2mM L-Glutamine, 1x Penicillin/Streptomycin (all from ThermoFisher Scientific), 0.1mM β-mercaptoethanol (Sigma-Aldrich), 1 μM PD0325901, 1 μM CHIR99021, 20ng/ml human LIF (all from WT-MRC Cambridge Stem Cell Institute) and 2 μM Go6983 (PKCi; Tocris) on Matrigel–coated plates (Corning). Primed PSCs were maintained on Vitronectin-coated plates (0.5 μg/cm2; ThermoFisher Scientific) in TeSR-E8 medium (StemCell Technologies).


title: MP_CPT_16

description: FFPE


title: ZT8-2

description: Pooled 3 biologic replicates


title: ABE8sQ

city: Seoul

first: You Kyeong

last: Jeong

address: 222, Wangsimni-ro, Seongdong-gu

country: South Korea

institute: Hanyang University

data_processing:
. The paired-end RNA-seq results were aligned to reference genome (GRCh38) by using bwa mem with default options.
The align result was sorted by samtools sort
the information of substitutions was analyzed by reditools (https://github.com/BioinfoUNIBA/REDItools2)
Genome_build: GRCh38
Supplementary_files_format_and_content: base counts

molecule: polyA RNA

growth_protocol: HEK293T (ATCC®CRL-3216™) cells were cultivated in DMEM medium supplemented with 10% FBS, 1% ampicillin in a humidified incubator at 37℃ with 5% CO2.

extract_protocol:
Cells were washed with DPBS 24 hours after electroporation. RNA was isolated by using a NucleoSpin® RNA Plus kit (MACHEREY-NAGEL, 740984. 250).
The isolated RNAs were analyzed by the customer NGS service of the Macrogen. RNA library preparation was performed using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) with an initial input of ~1ug extracted RNA per sample. RNA-seq libraries were sequenced on an Illumina NovaSeq 6000 machine.

treatment_protocol: . In a 6-well plate, HEK293T cells were transfected with 1500ng of ABE expression plasmid or Cas9(D10A) expression plasmid through electroporation.

tag: treatment


title: SOX2_naive_rep1


title: ZT8-1

description: Pooled 3 biologic replicates


title: ABE8s


title: ABE8eWQ


title: C10


title: ZT4-4

description: Pooled 3 biologic replicates


title: C9


title: NANOG_naive_rep2

value: NANOG (R&D AF1997)


title: ABE8eW

value: pCMV-ABE8e(TadA-8e V106W)


title: MP_CPT_13 F

description: Frozen

value: pediatric choroid plexus


title: NANOG_naive_rep1


title: C11

value: SCNn+


title: C8

value: night


title: ZT4-3

description: Pooled 3 biologic replicates


title: ABE8e


title: Input_naive_rep2


title: ZT4-2

description: Pooled 3 biologic replicates


title: MP_CPT_12

description: FFPE


title: C7

value: a


title: MP_CPT_10

description: FFPE


title: nCas9 only


title: ZT4-1

description: Pooled 3 biologic replicates


title: C6

value: 6-8 weeks


title: ZT0-4

description: Pooled 3 biologic replicates


title: MP_CPT_10 F

description: Frozen


title: Input_naive_rep1


title: S15_4M1

city: Chicago

first: Ines

last: Maldonado-Lasuncion

state: Illinois

address: 355 E Erie Street

department: Biologics Lab

institute: Shirley Ryan Ability Lab

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads where quality controlled anf filtered for adaptor contamination and low quality reads. Clean reads were mapped to rnor6 using bowtie2 (v2.2.3) and Tophat (v2.0.12, with amismatch of 2).
Quantification of FPKM was performed using HTSeq (v0.6.1, -m union) and Differential Expression Analysis between conditions was calculated using DESeq R package (1.18.0, with p(adj) < 0.05).
GO Enrichment was performed using Goseq, topGO, hmmscan softwares (release 2.12), and KEGG enrichment with KOBAS software (v3.0), both with a corrected p-value < 0.05.
All processed data is presented in a summary table "processedDataSummary_RNAseq_IML.xls"
Genome_build: Rnor6.0_release 79
Supplementary_files_format_and_content: Excel spreadsheet containing a summary per gene of: gene information, raw reads per sample, fpkm per sample, normalized group (condition) reads, differential expression results, and GO and KEGG analysis annotations.

growth_protocol: MSC and macrophages were extracted from the bone marrow of four different rats' femurs and tibias. Monocytes were sorted through FACS to be cultured separately from MSC on plastic dishes. MSC were cultured on PDL coated dishes and D10 medium (DMEM+10%FBS+0.1%Gentamycin) until passage 2, then FACS sorted for purification using the criteria CD29+/CD45-. Sorted cells were cultured on PDL coated dishes until ready for conditioning. Their medium was changed to the treatment media and cultured for 24h, before RNA extraction.

extract_protocol:
MSC were washed, trypsinized, and then lysed with the reagent from the Qiagen Rneasy Mini-kit, which was used for RNA extraction and elution into Rnase-free water.
RNA libraries were prepared for sequencing using using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations for a Eukaryotic Transcriptome Library.

treatment_protocol: Four different treatments were applied to different sets of cells, as described in the SAMPLES section.

tag: strain

value: Sprague-Dawley

tag: animal id

value: rat # 4

value: female

tag: genotype/variation

value: wild type

tag: msc source

value: Adult bone marrow - CD29+/CD45- Sorted

value: Mesenchymal stromal cells (MSCs)

tag: culture condition

value: M1CM = supernatant from inflammatory primary macrophages


title: IMR 90 Mock Infection Native ChIP- Total H3 IP

city: Seattle

first: Daphne

last: Avgousti

state: WA

address: 1100 Fairview Avenue North C1-201

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description: Cells contain protein VII induction plasmid (DA0203)

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v3.4.4 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v2.20.
ChIP-seq reads were aligned to human genome hg38 and yeast genome sacCer3 separately using Bowtie2.3.4.3 with following options: -p --no-discordant --no-mixed.
Peaks in H3 and VII with respect to ChIP input in the yeast genome were called using MACS2 callpeak function in narrow peak mode with the following options: -f BAMPE -g 12100000 --bdg --keep-dup 1 -q 0.05
Genome_build: hg38; sacCer3
Supplementary_files_format_and_content: bedGraph files produced by MACS2 callpeak --bdg
Supplementary_files_format_and_content: narrowPeak files produced by MACS2

source_name: Native chromatin: human with S. cerevisiae spike-in

growth_protocol: Human cells were grown in EMEM with 10% FBS + 1% penicillin and streptomycin. Yeast were pre-grown in selection media lacking uracil with 2% raffinose.

extract_protocol:
Human chromatin was purified by cell lysis, MNase digest, and ultrasonic liquid sonication in a custom ChIP buffer for protein VII purification. Yeast native chromatin was purified from cells and ChIP performed as in PMID: 23468649.
Libraries were prepared from the ChIP samples as well as a 10% input, following manufacturer recommendations, with KAPA Biosystems Unique Dual-Indexed Adapter Kit (#KK8727), Hyper Prep Kit (#KK8504), and Beckman Coulter AMPure XP Beads (#A63880) for library cleanup and size selection. Library concentrations were measured with Invitrogen Qubit dsDNA HS Assay Kit (#Q32851), then analyzed with Agilent High Sensitivity D5000 ScreenTape System, and pooled. Libraries were sequenced with 50-bp paired-end reads using the Illumina NovaSeq 6000 SP Flow Cell at the Fred Hutch Genomics Core Facility.

treatment_protocol: Human cells were grown to 90% confluence, then mock infected and harvested 20 hours later. Yeast were induced to express adenovirus protein VII by adding 2% galactose for 4 hours before purifying nuclei.

tag: human cell type

value: IMR 90

tag: yeast strain

value: Total H3 (abcam, #1791)

value: Human cells:mock infection at 20 hours; Yeast:4 hours galactose induction


title: ZT0-3

description: Pooled 3 biologic replicates

value: Pancreas

tag: condition

value: Normal Circadian

tag: Sex

value: Male


title: S16_8M1

value: rat # 8


title: C5

tag: mouse line

value: SCNn+

tag: circadian

value: night

tag: cfos

tag: activation

value: s

tag: gender


title: MP_CPT_13

description: FFPE

value: pediatric choroid plexus

value: Female


title: MP_CPT_07

description: FFPE


title: S14_3M1

value: Sprague-Dawley

value: rat # 3

value: female

tag: cell type


title: C4

value: a

tag: age

value: 6-8 weeks


title: IMR 90 Mock Infection Native ChIP- input sample

value: IMR 90

tag: chip antibody

tag: treatment


title: ZT0-1

description: Pooled 3 biologic replicates

tag: tissue

tag: species

tag: zt

value: Circadian Disrupted


title: S12_8M0

tag: strain

tag: animal id

tag: genotype/variation

value: wild type

tag: msc source

value: Adult bone marrow - CD29+/CD45- Sorted

value: Mesenchymal stromal cells (MSCs)

tag: culture condition

value: M0CM = supernatant from unpolarized primary macrophages


title: 4947-JS-7

city: Nashville

first: John

middle: Caleb

last: Snider

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped and gene counts were quantified using Illumina DRAGEN RNA pipeline v. 3.6.3
Gene count data was compiled using tximport
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.05 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.

source_name: Cardiac PDGFRa+ cells (fibroblast-like)

extract_protocol:
Hearts were removed and scar tissue was isolated. Tissue was minced in collagenase type II, filtered, and PDGFRa+ cells were obtained via FACS. Cells were homogenized in TRIzol reagent and RNA isolated via Zymo Direct-zol RNA Microprep kit
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits according to standard protocols.

treatment_protocol: All mice administered tamoxifen chow 1 week prior and throughout the course of the experiment.

value: Cardiac

value: Cardiac fibroblast-like cell

value: Mixed 129S2/C57Bl6

tag: genotype


title: C1

tag: mouse line

value: SCNn+

tag: circadian

value: night

value: Male


title: C3

tag: cfos

tag: activation


title: MP_CPT_06 F

description: Frozen

tag: disease

value: pediatric choroid plexus

tag: gender


title: S11_4M0

value: Sprague-Dawley

value: rat # 4

tag: Sex

tag: cell type


title: 4947-JS-6

tag: tissue


title: MP_CPT_06 _S

description: FFPE


title: S10_3M0

value: rat # 3

value: female


title: 4947-JS-5


title: S9_2M0

value: rat # 2


title: S8_8Pol1

value: rat # 8

value: Pol1 = D10 + LPS(100ng/ml) + IFNg(20ng/ml)


title: 4947-JS-2


title: MP_CPT_15

description: FFPE


title: S7_4Pol1

value: wild type

value: Adult bone marrow - CD29+/CD45- Sorted


title: MP_CPT_05 F

description: Frozen


title: IMR 90 Mock Infection Native ChIP- Protein VII IP

tag: human cell type

value: IMR 90

tag: yeast strain

tag: chip antibody

value: Adenovirus protein VII (custom anti-VII raised in mouse; publushed in PMID:26332038)

tag: treatment

value: Human cells:mock infection at 20 hours; Yeast:4 hours galactose induction


title: MP_CPT_05

description: FFPE


title: MP_CPT_11

description: FFPE


title: Max-KO rep3

city: Nanjing

first: Su

last: Ting

address: No. 12, Xuefu Road, Pukou District

department: Model Animal Research Center

institute: Nanjing University

data_processing:
FastQc were used for data quality control.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SeqPrep and Sickle.
Paired-end clean reads were aligned to the reference genome using the HISAT2 2.1.0; RSEM was used to calculate FPKM.
Differential expression analysis was performed using the DESeq v1.26.0.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values for each Sample.

source_name: Embryonic stem cells

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA sample prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Max-/-

value: Embryonic stem cells


title: S5_2Pol1

tag: animal id

tag: genotype/variation

tag: msc source

value: Mesenchymal stromal cells (MSCs)


title: Max-KO rep1

tag: genotype


title: Max-KO rep2


title: S4_8D10

tag: culture condition

value: D10 (DMEM+10%FBS+0.1%Genta)


title: S2_3D10


title: S3_4D10


title: S6_3Pol1


title: WT rep2


title: MP_CPT_03

description: FFPE

value: pediatric choroid plexus

value: Male


title: WT rep1


title: S1_2D10

value: Sprague-Dawley


title: MP_CPT_14_S

description: FFPE

value: Female


title: WT rep3


title: MP_CPT_01

description: FFPE


title: MP_CPT_02

description: FFPE


title: ZT0-2

description: Pooled 3 biologic replicates

value: Pancreas

tag: species

tag: zt

tag: condition

value: Circadian Disrupted


title: MP_CPT_03 F

description: Frozen

tag: disease

tag: gender


title: ShFTO-Light-1

status: Public on Jan 20 2021

city: MONTPELLIER

first: Julie

last: Ripoll

state: OCCITANIE

address: 860 rue de St Priest

department: Informatics

country: France

institute: LIRMM

description:
POL-seq
Traductome_counts.txt

data_processing:
Transcriptome and translatome libraries read quality were assessed using FastQC v0.11.5 (Babraham Institute, Cambridge, UK).
Ribosomal RNA were discarded using SortMeRNA v2.1b.
High quality reads were then aligned on the Homo sapiens reference transcriptome, version GRCh38.cdna, and quantified using pseudocounts with Kallisto v0.45.0. Kallisto quantification parameters were fixed at 25 for k-mer size, 20 for standard deviation and 100 for bootstraps.
Statistical differential analyses were performed on each dataset using Wald test from DESeq2 R package. Each count dataset was filtered at 1 count per millions per biological sample after size factors estimation, then dispersion was estimated. Primary risk of probabilities to false discovery fold change was corrected by Benjamini and Hochberg multiple test adjustment. Corrected p-values < at 0.05 % were kept.
MeRIP-seq libraries read quality were assessed using FastQC v0.11.5 (Babraham Institute, Cambridge, UK) and adaptors were filtered using cutadapt v2.10 [1]. Ribosomal RNAs were discarded using SortMeRNA v2.1b [2]. High quality reads were then aligned on the Homo sapiens reference genome version GRCh38 using CRAC v2.5 (ATGC, LIRMM, FR). Alignment files were indexed using Samtools v1.9 [3]. Detection of m6A peak enrichment and statistical analysis were performed using m6aViewer (University of Leeds, Leeds, UK) [4]. Duplicate reads and read not in a proper pairs were discarded from the analysis using options of m6aViewer. Primary risk of probabilities to false discovery fold change was corrected by Benjamini and Hochberg multiple test adjustment. Corrected p-values < at 0.05 % were kept.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample.

source_name: CRC cancerous colorectal cell – Light shFTO

growth_protocol: Cell culture and generation of stable cell lines.  Cells were maintained at 37 °C under humidified 5% CO2 in DMEM medium supplemented with 10% FCS (Invitrogen) and 2 mM glutamine. Stable knockdown of FTO was achieved by lentiviral delivery (5 D.O.I) of anti-FTO sh-RNA (Origene, #TL308064, sh-FTO#B). Isolation of infected cells was performed by GFP positive cells sorting on FACSAria.

extract_protocol:
Transcriptome Analysis. Total RNA was extracted using TRIzol method.
Polysome fractionation. 6 plates (150 cm2) were seeded with 2 x 106 cells. After 72 h, cells were treated with 20 µg / ml emetine for 5 min at 37°C, washed twice with ice-cold PBS, and scraped in ice cold PBS. Cells were centrifuged, resuspended into 1mL of polysome lysis buffer, homogenized by hard shaking with 1,4mm ceramix spheres (Lysing matrix D MPBio) in FastPrep machine (MPBio), centrifuges 10 min at full speed at 4°C. Lysates were loaded on 15-50% sucrose gradient and centrifuged at 35,000 rpm for 2.5 h at 4°C in a SW41 rotor (Beckman Coulter). Polysomes were separated through a live optical density (OD) 254 nm UV spectrometer and collected with an ISCO (Lincoln, NE) density gradient fractionation system. The absorbance at 254 nm was measured continuously as a function of gradient depth.
Translatome Analysis. mRNA associated with 1 to 3 ribosomes “Light polysomes”  and mRNA associated with more than 3 ribosomes “Heavy polysomes” were extracted using TRIzol LS (Invitrogen) according to manufacturer’s instructions.
Merip Analysis. 5 µg of mRNA were fragmented (Invitrogen AM8740) by adding 1 µL of 10X fragmentation reagent to 9 µL mRNA and incubated at 95˚C for 1 min. The same samples were then pooled prior to overnight EtOH precipitation (0.1 volume of 3M sodium acetate pH5.2, 2.5 volume of pure EtOH, 1 µL glycogen). The fragmented mRNA were recovered by centrifugation at 14,000rpm 25 min at 4˚C and the pellets were washed once with 70% EtOH and centrifuged again 14,000rpm 10 min at 4 ˚C. The pellets were resuspended in 429 µL DEPC water and 390 µL was used for m6A-methylated RNA immunoprecipitation and 39 µL for inputs (10%).
Transcriptome Analysis. RNA samples were send to Eurofins Genomics /GATC to perform next generation sequencing on Illumina platform (2 x 150bp). Library preparation was performed using TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol.
Translatome Analysis.  Library preparation was performed using TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. cDNA libraries were sequenced using the sequencer HiSeq 2500 (Illumina).
Merip Analysis. Multiplex cDNA Library was produced using NEBNext Small RNA Library Prep Set for Illumina (NE BiolabsInc E7330S), according to manufacturer procedure. Sequencing was performed using NextSeq 500.

treatment_protocol:
Plasmid constructions. FTO coding sequence was amplified from pDONOR plasmid (Montpellier Genomic Collection MGC Facility) and inserted into pCDNA3-Flag Cter plasmid into HindIII and XbaI restriction sites.
Transfections. Transfection of 100 nM of si-RNA duplex was performed using Lipofectamine RNAimax (Invitrogen) according to the manufacturer’s instructions. The sequences of siRNA are provided in Table S3.  300,000 cells in 6-well plate were transfected for 48 h with 2 µg of plasmid DNA using Lipofectamine 2 000 (Invitrogen) according to the manufacturer’s instructions.


title: 4947-JS-1

value: Cardiac

tag: cell type

value: Cardiac fibroblast-like cell

value: Mixed 129S2/C57Bl6


title: ShFTO-Light-2

description:
POL-seq
Traductome_counts.txt


title: ShFTO-Light-3

description:
POL-seq
Traductome_counts.txt


title: ShFTO-Heavy-3

description:
POL-seq
Traductome_counts.txt

source_name: CRC cancerous colorectal cell – Heavy shFTO


title: ShCTL-Light-3

description:
POL-seq
Traductome_counts.txt

source_name: CRC cancerous colorectal cell – Light control


title: ShFTO-Heavy-1

description:
POL-seq
Traductome_counts.txt


title: MRC5→ IFN gamma-rep3

city: Shreveport

first: Seong

middle: K

last: Kim

state: Louisiana

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: LSU Health Sciences Center

hyb_protocol: Biotin labeled cRNA are hybridized with Mouse 430 array using Affymetrix Standard Protocol.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression Console (Affymetrix) for RMA summarizationand Quantile normalization.

label: Biotin

source_name: Cells

label_protocol: Amplified and biotinylated cRNA was generated from total RNA using 3' IVT PLUS kit from (Affymetrix)

growth_protocol: ARPE19, MRC-5, and MeWo cells were maintained at 37°C in complete Eagle’s Minimum Essential Medium (EMEM) supplemented with 100 U/ml of penicillin, 100 mg/ml of streptomycin, nonessential amino acids, and 5% fetal bovine serum.

extract_protocol: Poly(A)+ RNA was isolated from total RNA using the FastTrack 2.0 kit (Invitrogen, San Diego, CA) according to the manufacturer's instructions.

treatment_protocol: ARPE19, MRC-5, and MeWo cells were treated with 0 or 20 ng/ml of human IFN-γ (Cell Sciences, Canton, MA). The untreated and treated cells were harvested at 8 h post-treatment. Affymetrix microarray analyses were performed with IFN-g-treated and untreated RNA. Untreated RNAs were used as a control.

tag: cell line

value: MRC

value: IFN gamma-treated


title: Mewo→ IFN gamma-rep1

value: Mewo


title: Mewo→ IFN gamma-rep3


title: ARPE-19→ IFN gamma-rep1


title: ARPE-19-rep3

value: untreated


title: MRC5→ IFN gamma-rep1


title: ARPE-19-rep1


title: MRC5→ IFN gamma-rep2


title: ARPE-19-rep2


title: ARPE-19→ IFN gamma-rep3


title: MRC-5-rep3


title: MRC-5-rep2


title: ShFTO-Heavy-2

description:
POL-seq
Traductome_counts.txt


title: MRC-5-rep1


title: Mewo-rep1


title: ShCTL-Light-2

description:
POL-seq
Traductome_counts.txt


title: ShCTL-Light-1

description:
POL-seq
Traductome_counts.txt


title: Mewo-rep3


title: Sh_FTO_C1

description:
RNA-seq
Transcriptome_counts.txt

source_name: CRC cancerous colorectal cell – shFTO sample


title: ShCTL-Heavy-1

description:
POL-seq
Traductome_counts.txt

source_name: CRC cancerous colorectal cell – Heavy control


title: ShCTL-Heavy-3

description:
POL-seq
Traductome_counts.txt


title: ARPE-19→ IFN gamma-rep2


title: Mewo-rep2


title: Sh_FTO_B1_bis

description:
RNA-seq
Transcriptome_counts.txt


title: Sh_FTO_B1

description:
RNA-seq
Transcriptome_counts.txt


title: Sh_FTO_A1

description:
RNA-seq
Transcriptome_counts.txt


title: Mewo→ IFN gamma-rep2


title: Sh_CTL_C1

description:
RNA-seq
Transcriptome_counts.txt

source_name: CRC cancerous colorectal cell – control sample


title: ShCTL-Heavy-2

description:
POL-seq
Traductome_counts.txt


title: Sh_CTL_A1

description:
RNA-seq
Transcriptome_counts.txt


title: C2

tag: mouse line

value: SCNn+

tag: circadian

value: night

tag: cfos

tag: activation

value: a

tag: age

value: 6-8 weeks


title: R273H_ChIPSeq

city: Beijing

first: Yiran

last: Li

address: 北京市东城区东单三条五号

institute: 北京协和医院基础所

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using Bowtie version 1.2.2
Peak detection and signal intensity analyses for ChIP-seq data were performed using MACS14 and HOMER.
Genome_build: hg38

source_name: established cell lines(HCT116)

growth_protocol: HCT116 cells were grown in spheroid medium consisting of DMEM/F12 (Invitrogen) supplemented with B27 serum-free supplement (1:50; Invitrogen), 20 ng/ml epidermal growth factor (R&D systems), 20ng/ml basic fibroblast growth factor (R&D Systems). Spheroid cells (107) were collected to perform ChIP assay as described.

extract_protocol:
Spheroid cells were crosslinked with 1% formaldehyde for 5 minutes. Glycine was then added to a final concentration of 0.125 M for 5 minutes. Chromatin was disrupted by a Covaris S220 (power of 200 W and duty factor of 2.0) for 10 minutes.
Novogene was trusted to prepare the library and perform the sequencing.

tag: tissue

value: colon

tag: passages

tag: chip antibody


title: input-R273H

address: 北京市东城区东单三条五号

tag: genotype/variation


title: ctrl-19-7 rep3

address: 北京市东城区东单三条五号

data_processing:
The HISAT2 mapper (v2.1.0) mapped reads to human genome.
StringTie was applied to assemble the alignment and measure the expression of transcripts.
Ballgown was employed to analyze the expression levels of transcripts and to estimate which transcripts were differentially expressed between distinct experimental conditions.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

growth_protocol: Cells were grown in spheroid medium consisting of DMEM/F12 (Invitrogen) supplemented with B27 serum-free supplement (1:50; Invitrogen), 20ng/ml epidermal growth factor (R&D Systems), 20ng/ml basic fibroblast growth factor (R&D Systems), and penicillin-streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA derived from spheroids or cells was extracted using RNeasy Plus Mini kit.
Novogene was trusted to prepare the library and perform the sequencing.

tag: passage

value: wildtype control cell lines


title: ctrl-19-7 rep1

address: 北京市东城区东单三条五号


title: ctrl-19-7 rep2

address: 北京市东城区东单三条五号


title: ctrl-19-7_ChIPSeq

address: 北京市东城区东单三条五号

value: wildtype control


title: 4947-JS-4

tag: strain

tag: genotype


title: R273H rep3

address: 北京市东城区东单三条五号

value: p53-R273H colorectal cancer cell lines


title: S13_2M1

value: Sprague-Dawley

tag: animal id

value: rat # 2

tag: Sex

value: female

value: wild type

tag: msc source

value: Adult bone marrow - CD29+/CD45- Sorted

value: Mesenchymal stromal cells (MSCs)

tag: culture condition

value: M1CM = supernatant from inflammatory primary macrophages


title: R273H rep1

address: 北京市东城区东单三条五号


title: HBBP1_shRNA1_d8

first: Xu

middle: jia

last: yue

address: NO.3 Dongdan street, Beijing

institute: Peking Union Medical College

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 Tophat
fragments per kilobaseof exon per million fragments mapped (FPKM) were calculated with Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: Erythroid differentiation day8 of Cord blood derived CD34+ HPCs, treated with lentivirus carrying shRNA1 targeting HBBP1

extract_protocol:
RNA was harvested using Trizol reagent from fresh cultured cells. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cord blood

tag: days of differentiation

tag: differentiated cell type

value: CD34+ HPCs

tag: treated with lentivirus


title: HBBP1_shRNA1_d14

source_name: Erythroid differentiation day14 of Cord blood derived CD34+ HPCs, treated with lentivirus carrying shRNA1 targeting HBBP1


title: HBBP1_shRNA2_d8

source_name: Erythroid differentiation day8 of Cord blood derived CD34+ HPCs, treated with lentivirus carrying shRNA2 targeting HBBP1


title: HBBP1_shRNA2_d14

source_name: Erythroid differentiation day14 of Cord blood derived CD34+ HPCs, treated with lentivirus carrying shRNA2 targeting HBBP1


title: Ctrl-d14

source_name: Erythroid differentiation day14 of Cord blood derived CD34+ HPCs, treated with control lentivirus

value: Ctrl


title: Ctrl-d8

source_name: Erythroid differentiation day8 of Cord blood derived CD34+ HPCs, treated with control lentivirus


title: R273H rep2

address: 北京市东城区东单三条五号


title: input-ctrl-19-7

address: 北京市东城区东单三条五号

tag: cell line


title: SSTCre_Met_2

first: Fiona

last: Gribble

state: Cambridgeshire

address: Box 289 Addenbrooke's Hospital, Hills Road

department: Medical Research Laboratories

institute: University of Cambridge

description: Mouse duodenal organoids, SST-Cre tdRFP with 1mM metformin, sample 2

data_processing:
Sequenced reads were mapped to the primary mouse genome (GRCm38) using STAR v2.5.0.
Differential gene expression modelling and normalised counts per million were generated using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated text file includes raw count values for all samples.

source_name: Duodenal organoids

growth_protocol: Organoids were suspended in domes containing Basement Material Extract (BME) with growth media containing Epithelial Growth Factor (EGF), Noggin, R-Spondin and Rho-associated protein kinase (ROCK) inhibitor Y-27632.

extract_protocol:
Organoid samples were lysed in RLT Plus buffer. RNA extraction and isolation were performed using RNAeasy Micro Plus kit (Qiagen). RNA concentration and quality (RIN 8.1-9.4) were assessed using Bioanalyser RNA Nano Kit (Agilent) and Bioanalyser 2100 (Agilent).
The library was constructed with 1 µg total RNA using the TruSeq Stranded mRNA Library Prep kit (Illumina).

treatment_protocol: Organoids were plated as 2D monolayer cultures in 3 separate 24-well plates on day 1 followed by treatment with or without 1 mM metformin for 24 hours.

value: Duodenal organoids

tag: treatment

value: Metformin

tag: transgenic line

value: SST-Cre tdRFP


title: GIPCre_Met_3

description: Mouse duodenal organoids, GIP-Cre tdRFP with 1 mM metformin, sample 3

tag: tissue

value: GIP-Cre tdRFP


title: SSTCre_Ctrl_1

description: Mouse duodenal organoids, SST-Cre tdRFP with vehicle control, sample 1

value: Control


title: GIPCre_Met_2

description: Mouse duodenal organoids, GIP-Cre tdRFP with 1 mM metformin, sample 2


title: GIPCre_Ctrl_3

description: Mouse duodenal organoids, GIP-Cre tdRFP with vehicle control, sample 3


title: GIPCre_Met_1

description: Mouse duodenal organoids, GIP-Cre tdRFP with 1 mM metformin, sample 1


title: SSTCre_Met_3

description: Mouse duodenal organoids, SST-Cre tdRFP with 1mM metformin, sample 3


title: SSTCre_Ctrl_2

description: Mouse duodenal organoids, SST-Cre tdRFP with vehicle control, sample 2


title: GIPCre_Ctrl_1

description: Mouse duodenal organoids, GIP-Cre tdRFP with vehicle control, sample 1


title: GIPCre_Ctrl_2

description: Mouse duodenal organoids, GIP-Cre tdRFP with vehicle control, sample 2


title: SSTCre_Met_1

description: Mouse duodenal organoids, SST-Cre tdRFP with 1mM metformin, sample 1


title: SSTCre_Ctrl_3

description: Mouse duodenal organoids, SST-Cre tdRFP with vehicle control, sample 3


title: 19_TM2_7

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description: RIN: 10

data_processing:
Reads were mapped to the mouse genome mm10 using STAR (Dobin et al., 2013).
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq Version 3.0.2 (Kalari et al., 2014)
In order to correct for GC bias and gene length differences and obtain similar quantile-by-quantile distributions of gene expression levels across samples, we performed conditional quantile normalization (CQN) on the raw gene counts (Hansen et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated text file including raw gene counts for all samples

source_name: brain

extract_protocol:
Cerebellar tissue was harvested from 15-month-old Tmem106b mice [3 Tmem106b+/+ (WT), and 3 Tmem106b-/- (KO), 2 males and 1 females per genotype]. RNA extraction was performed using the RNeasy Plus Mini Kit (#74136; Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: brain

tag: age (months)

value: WT

value: F


title: 25_TM2_5

description: RIN: 10


title: 20_TM3_3

description: RIN: 10

value: M


title: 26_TM2_1

description: RIN: 10


title: Cortex_Normal-IgG3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina software BaseCaller was used to generate BCL files, which were demultiplexed using bcl2fastq v2.17.1.14
STAR version 2.5.2a was used to align the reads to the mm10 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in mm10 version 84
Genome_build: mm10 gene version 84
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: embryonic cortex

extract_protocol: Exosc10 RIP-seq was performed using Magna RIP™ Kit (merckmillipore) according to the manufacturer’s instructions. Dissociated cells from E12.5 cortex on 10 cm dish were lysed in 400 µl of complete RIP lysis buffer-containing protease inhibitors and RNase inhibitor. Exosc10 protein was pulled down by Dynabeads-associated Exosc10 antibody. A mock pull-down was done with normal rabbit IgG (Cell Signaling Technologies). The immunoprecipitated complex was washed intensively and the pulled down RNA was extracted using Trizol reagent.

value: cortex

tag: age

value: embryonic day 12.5

tag: antibody

value: normal rabbit IgG


title: Cortex_Normal-IgG1


title: Cortex_Normal-IgG2


title: Cortex_Normal-IgG4


title: 27_TM1_1

description: RIN: 10


title: 21_TM4_3

description: RIN: 10


title: Cortex_Exosc10-4

value: rabbit Exosc10 antibody


title: Cortex_Exosc10-3


title: Cortex_Exosc10-2


title: Cortex_Exosc10-1


title: Pggt1bKOeTreg2_ATACseq

city: Memphis

first: Hongbo

last: Chi

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

data_processing:
Adapter sequences were removed using trimmomatic v.0.36
and aligned them to the mouse genome mm9 (NCBIM37_um from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/NCBIM37_um.fa) using the Burrows–Wheeler algorithm32 (version 0.7.16, default parameter)
duplicated reads were then marked with Picard (version 2.9.4) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.1, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm9
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples

source_name: Treg cells directly sorted from mixed bone marrow chimera

extract_protocol:
Cells were lysed in 50 μl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630 detergent) on ice for 10 min. Resulting nuclei were pelleted at 500g for 10 min at 4 °C. Supernatant was carefully removed with a pipette and discarded. The pellet was resuspended in 50 μl transposase reaction mix (25 μl 2 × TD buffer, 22.5 μl nuclease-free water, 2.5 μl transposase) and incubated for 30 min at 37 °C. After the reaction, the DNA was cleaned up using the Qiagen MinElute kit
The barcoding reaction was run using the NEBNext HiFi kit on the basis of the manufacturer’s instructions and amplified for five cycles

value: Spleen and lymph nodes

tag: cell type

value: Treg


title: Pggt1bKOeTreg1_ATACseq


title: Pggt1bKOcTreg2_ATACseq


title: Pggt1bKOcTreg1_ATACseq


title: WSC037: Treg GGTI 48h

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Clariom S mouse GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

label: biotin

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice, pretreated with GGTI for 2 h and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for 48 h in the presence of GGTI

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Cells were sort-purified using specificed markers from spleen and pLN of Foxp3YFP-Cre mice and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 as indicated by time in the presence of prenylation inhibitors

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain

value: GGTI 48h


title: WTeTreg2_ATACseq


title: WSC035: Treg FTI 48h

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice, pretreated with FTI for 2 h and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for 48 h in the presence of FTI

value: FTI 48h


title: WSC033: Treg FTI 48h


title: WTcTreg2_ATACseq


title: WSC036: Treg GGTI 48h


title: WSC034: Treg FTI 48h


title: WTcTreg1_ATACseq


title: WSC030: Treg DMSO 48h

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for 48 h

value: DMSO 48h


title: FntbKO_eTreg2_ATACseq

data_processing:
Adapter sequences were removed using trimmomatic v.0.36
and aligned them to the mouse genome mm10 (GRCm38_68 from Sanger; ftp://ftp-mouse.sanger.ac.uk/ref/GRCm38_68.fa) using the Burrows–Wheeler algorithm32 (version 0.7.16, default parameter)
duplicated reads were then marked with Picard (version 2.9.4) and only non-duplicated reads were kept, using samtools (parameter ‘-q 1 -F 1024’ version 0.1.18 (r982:295))
After adjustment using the Tn5 shift (by which reads were offset by +4 bp for the sense strand and −5 bp for the antisense strand), we separated reads into nucleosome-free, mononucleosome, dinucleosome and trinucleosome by fragment size
performed peak-calling for nucleosome-free reads using MACS2 (version 2.1.1, default parameters with ‘–extsize 200 –nomodel’, merged by bedtools if within 100 bp) for individual samples
Genome_build: mm10
Supplementary_files_format_and_content: Consensus peaks and fragment counts for all samples


title: WSC038: Treg GGTI 48h


title: FntbKO_cTreg2_ATACseq


title: WSC032: Treg DMSO 48h


title: WSC025: Treg FTI 18h

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice, pretreated with FTI for 2 h and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for 18 h in the presence of FTI

value: FTI 18h


title: WSC021: Treg DMSO 18h

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for 18 h

value: DMSO 18h


title: WSC023: Treg DMSO 18h


title: WSC022: Treg DMSO 18h


title: Sh_CTL_B1

description:
RNA-seq
Transcriptome_counts.txt

source_name: CRC cancerous colorectal cell – control sample


title: WSC019: Treg DMSO 0h

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice

value: DMSO 0h


title: FntbKO_cTreg1_ATACseq


title: WTeTreg1_ATACseq


title: WSC024: Treg FTI 18h


title: WSC031: Treg DMSO 48h


title: WT_eTreg3_ATACseq


title: WSC020: Treg DMSO 0h


title: WT_cTreg3_ATACseq


title: WSC026: Treg FTI 18h


title: WT_eTreg2_ATACseq


title: WSC028: Treg GGTI 18h

source_name: CD4+YFP+CD44loCD62Lhi cTreg cells sorted from spleen and pLN of Foxp3YFP-Cre mice, pretreated with GGTI for 2 h and activated by 10 ug/ml anti-CD3/28 antibodies plus 200 U/ml IL-2 for 18 h in the presence of GGTI

value: GGTI 18h


title: WSC027: Treg GGTI 18h


title: WSC018: Treg DMSO 0h


title: WT_eTreg1_ATACseq


title: WT_cTreg1_ATACseq


title: WSC008: Pggt1b Het Treg

source_name: CD4+ YFP+ Cells from spleen and pLN of Foxp3CrePggt1bfl/wt chimeras

growth_protocol: Cells were sort-purified using specificed markers from spleen and pLN of Foxp3CrePggt1bfl/wt and Foxp3CrePggt1bfl/fl chimeras

tag: genotype

value: Pggt1b Het


title: WT_cTreg2_ATACseq


title: WSC004: Pggt1b Het Treg


title: WSC003: Pggt1b KO Treg

source_name: CD4+ YFP+ Cells from spleen and pLN of Foxp3CrePggt1bfl/fl chimeras

value: Pggt1b KO


title: Sh_FTO2_1_Input

description:
MeRIP-seq
Merip_counts.csv

source_name: CRC cancerous colorectal cell – shFTO sample – Input


title: Sh_CTL2_1_IP

description:
MeRIP-seq
Merip_counts.csv

source_name: CRC cancerous colorectal cell – control sample – IP


title: WSC005: Pggt1b KO Treg


title: WSC001: Pggt1b KO Treg


title: WSC009: Pggt1b Het Treg


title: Sh_CTL2_1_Input

description:
MeRIP-seq
Merip_counts.csv

source_name: CRC cancerous colorectal cell – control sample – Input


title: Sh_FTO2_1_IP

description:
MeRIP-seq
Merip_counts.csv

source_name: CRC cancerous colorectal cell – shFTO sample – IP


title: Sh_FTO1_1_IP

description:
MeRIP-seq
Merip_counts.csv


title: Sh_FTO1_1_Input

description:
MeRIP-seq
Merip_counts.csv


title: Sh_CTL1_1_IP

description:
MeRIP-seq
Merip_counts.csv

source_name: CRC cancerous colorectal cell – control sample - IP


title: Ribosome IP 1 (TRAP-seq)

city: Geneva

first: Robert

last: Maeda

address: 30 Quai E. Ansermet

department: Genetics and Evolution

institute: University of Geneva

data_processing:
Library strategy: TRAP-seq
Reads were mapped to the reference Drosophila genome (UCSC dm6) using the STAR aligner.
Gene count was performed using HTSeq-count (L50).
Genes with fewer than 10 total reads were excluded.
The Trimmed Mean of M-values (TMM) method was used to normalize gene counts
Genome_build: Differential expression analysis (wild type versus ∆MSAmiP) was performed using a General Linear Model, quasi-likelihood F-test with False Discovery Rate (Benjamini & Hochberg) correction.
Supplementary_files_format_and_content: raw counts

organism: Drosophila melanogaster

source_name: Male accessory gland secondary cells

growth_protocol: Flies were grown under standard Drosophila growth conditions.  Males were aged 5-11 days prior to dissection.

extract_protocol:
Secondary cells were isolated from dissected male accessory glands.  Briefly, glands were dissected and treated with 1X TrypLE in Schnieider's media in the presence of 1'%fetal bovine serum and 1% Pen-Strep.  The glands were then titurated to separate the cells and sorted by FACs.  RNA was then isolated from purified cells using the Epicentre Masterpure RNA purification kit.
2ng RNAs from either sorted SCs or TRAP experiments were used to generate cDNAs using polydT primers for reverse transcription and SMARTer technology for amplification (Takara). Libraries for sequencing were prepared using Nextera XT kit (Illumina), and were sequenced using multiplexed, single reads of 100 nucleotides (20-30Million reads per sample).

treatment_protocol: RNA-seq samples were treated with protease prior to FACS sorting.

value: male

value: Secondary cells

value: UAS GFP-RPL10Ab, D1:GAL4

tag: protocol

value: Ribosome immunoprecipitated with anti-GFP antibody

tag: rip antibody

value: anti-GFP antibody


title: Sh_CTL1_1_Input

description:
MeRIP-seq
Merip_counts.csv


title: miP 1 (RNA-seq)

data_processing:
Reads were mapped to the reference Drosophila genome (UCSC dm6) using the STAR aligner.
Gene count was performed using HTSeq-count (L50).
Genes with fewer than 10 total reads were excluded.
The Trimmed Mean of M-values (TMM) method was used to normalize gene counts
Genome_build: Differential expression analysis (wild type versus ∆MSAmiP) was performed using a General Linear Model, quasi-likelihood F-test with False Discovery Rate (Benjamini & Hochberg) correction.
Supplementary_files_format_and_content: raw counts

tag: Sex

value: D1:GAL4, UAS-GFP; delta MSAmiP

value: FACS sorted


title: control (TRAP-seq)

description:
Control for Ribosome immunoprecipitation.
Ctrl4

value: UAS GFP, D1:GAL4


title: miP 2 (RNA-seq)


title: miP 3 (RNA-seq)


title: Ribosome IP 3 (TRAP-seq)


title: Ribosome IP 2 (TRAP-seq)


title: D1 3 (RNA-seq)

value: D1:GAL4, UAS-GFP; iab-6cocuD1


title: D1 2 (RNA-seq)


title: D1 1 (RNA-seq)


title: Wild-type 3 (RNA-seq)

value: D1:GAL4, UAS-GFP


title: Methanol-fixed A549 cells

first: Hoang Van

last: Phan

address: 5640 S Ellis Ave

department: Priztker School of Molecular Engineering

institute: The University of Chicago

description: Drop-seq of methanol-fixed A549 cells

data_processing:
Base calling was done automatically in Illumina's BaseSpace platform
Single-cell data was processed using Drop-seq tools v2.3.0 and STAR aligner according to the online manual
Single-cell count data was analyzed with Seurat 3
Read mapping metrics were calculated using Picard v2.21.8. Read subsampling was performed with samtools v1.9
Genome_build: GRCh38
Supplementary_files_format_and_content: Single-cell data: tab-delimited text file of UMI counts per single cell

source_name: A549-H2B-Ruby cell line

growth_protocol: A549-H2B-Ruby cells were grown in DMEM with 10% FBS.

extract_protocol:
Single cells were captured and lysed in droplets in a microfluidic chip as per Drop-seq.
The single-cell cDNA was tagmented using Nextera XT kit as per Drop-seq protocol.

value: Human lung epithelial cells

tag: virus type

value: Methanol fixation


title: PFA-fixed A549 cells

description: FD-seq of PFA-fixed A549 cells

value: PFA fixation


title: VO-pop5-4

city: Melbourne

first: Ana Rita

last: Leitoguinho

state: VIC

address: 50 Flemington road

department: Cell Biology

country: Australia

institute: Murdoch Children's Research Institute

description: Population (Pop.) 5

data_processing:
FASTQ samples sequenced 2 times were pooled into a single file. Compressed (gzipped) FASTQ files  were aligned to the Human genome using STAR software (v2.5.2a) in a 2 pass mode (Dobin et al., 2013).
Uniquely mapped reads were indexed, sorted and summarised using Samtools (v1.8) and FeatureCounts (v1.4.6) using Gencode Release 19 comprehensive annotation (Liao, Smyth and Shi, 2014).
Genes lowly expressed were excluded (less than 10 counts per million in fewer than 3 samples). The data was TMM normalised, voom transformed and differential gene expression was assessed using moderate t-tests from the R (v3.3.2) Bioconductor limma (v3.30.13) package and edgeR (v3.16.5) (Robinson, McCarthy and Smyth, 2009; Robinson and Oshlack, 2010; Ritchie et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: ESC derived PGC-like cells were generated using Spin Embryoid body (EB). For each experiment, 3-4 × 10^6 cells in a T75 flask were seeded in 10x 96-well plates. Cells were left in PGC differentiation media until day 4 when Ebs were dissociated and cell sorrted into different fractions (populations)

extract_protocol:
Cells samples were lysed in RLY buffer (Bioline) supplemented with 2-Mercaptoethanol (Life Technologies) and subsequently frozen at -80C. All RNA extraction was performed simultaneously using the Isolate II RNA Micro kit (Bioline) to avoid artificial batch effects.
RNA libraries were prepared for sequencing using  Illumina TruSeq Stranded mRNA kit according to manufacturers' protocol or using an adjusted protocol for less than 100ng total RNA input. Sequencing was performed using the Illumina NextSeq 550 (Illumina) platform with using the 2x75 bp run setting (single indexing reads) and an average of 20 million reads per sample.

treatment_protocol: Day 0: 1.25 ng/ml ACTIVIN A; 40ng/ml BMP4; 100ng/ml SCF. Day 1: 280ng/ml BMP4. Day 2: 1microMolar of CHIR.

value: ES-derived primordial germ cells

tag: sorting profie

value: GFP+ mCHERRY+ EPCAM+ CD49f-

value: VENTX Wild type (VO)

tag: day

value: Day 4


title: Sh_CTL_C1_bis

description:
RNA-seq
Transcriptome_counts.txt


title: VO-pop5-1

description: Population (Pop.) 5


title: VO-pop4-4

description: Population (Pop.) 4

value: GFP- mCHERRY+ EPCAM+ CD49f+


title: VO-pop4-2

description: Population (Pop.) 4


title: Wild-type 1 (RNA-seq)

value: male

value: Secondary cells


title: X28_RFP14

city: Bethesda

first: Josh

last: Stone

state: MD

address: 9000 Rockville Pike

department: CCR

institute: National Cancer Institue

data_processing:
Reads were trimmed for adaptors and low-quality bases using Trimmomatic and were aligned with the reference genome (Human-hg38) and the annotated transcripts (Gencode_v24) using STAR (https://github.com/alexdobin/STAR).
The gene expression quantification analysis was performed using STAR/RSEM tools (http://deweylab.github.io/RSEM/) to obtain raw read counts and normalized read counts (RPKM) for each gene.
Differentially expressed genes were identified using DESeq2 in R with a false discovery rate (FDR) cutoff of 0.01, and analyzed by gene enrichment analysis for KEGG (https://www.genome.jp/kegg/) and Reactome Pathways (https://reactome.org/) using DAVID v6.8 (https://david.ncifcrf.gov/).

source_name: Cell line

extract_protocol:
RNA samples were treated with DNase I (no. 18068015, Thermo Fisher Scientific), followed by purification with RNeasy MinElute Cleanup kit (Qiagen).
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep kit (Illumina, San Diego, CA, USA).

value: Cell line

tag: genotype/variation


title: VO-pop4-1

description: Population (Pop.) 4


title: WSC002: Pggt1b Het Treg

value: Treg

value: Pggt1b Het


title: X27_ALK14


title: VO-pop3-5

description: Population (Pop.) 3

value: GFP+ mCHERRY+ EPCAM- CD49f-


title: X24_RFP.9


title: X22_ALK.8


title: VO-pop3-4

description: Population (Pop.) 3


title: X21_ALK_plus_8


title: VO-pop3-2

description: Population (Pop.) 3


title: X25_ALK5


title: VO-pop3-3

description: Population (Pop.) 3


title: VO-pop3-1

description: Population (Pop.) 3


title: X23_ALK_plus_9


title: VO-pop1-5

description: Population (Pop.) 1

value: GFP+ mCHERRY+ EPCAM+ CD49f+


title: Wild-type 2 (RNA-seq)

value: FACS sorted


title: VO-pop2-1

description: Population (Pop.) 2

value: GFP- mCHERRY+ EPCAM+ CD49f-


title: VO-pop2-2

description: Population (Pop.) 2


title: VO-pop1-4

description: Population (Pop.) 1