title: GFP_Input_2

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce St

institute: Wistar Institute

description:
Analysis of STAU1-binding to APA
rip.cluster.all.reads.csv

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered out low-quality sequence using Cutadaptor
Sequenced reads were masked for 5'-Ts then mapped to hg19 whole genome using STAR. Reads with a mapping quality score (MAPQ) of ≥10 were kept for further analysis.
Reads with ≥2 non-genomic 5'-Ts after alignment were called polyA site supporting (PASS) reads.
pAs within 24 nt from one another were clustered as previously described (Hoque et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: csv files include all cluster sites with count values for each Sample.

source_name: Embryonic kidney

growth_protocol: Human HEK293T cells were propagated in Dulbecco’s Modified Eagle’s Medium (Gibco) supplemented with 10% fetal bovine serum.

extract_protocol:
RNA was extracted using phenol/chloroform and precipitated using ethanol.
The 3'READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 1 µg of total-cell RNA was captured using 10 µl of oligo(dT)25 magnetic beads (NEB) in 100 µl of 1x Binding Buffer (10 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl of RNase III Buffer (10 mM Tris-Cl pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) for 15 min at 37 °C. After washing away unbound RNA fragments using Binding Buffer, polyA+ fragments were eluted from the beads using TE Buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated using ethanol, followed by ligation to 3 pmol of heat-denatured 5'-adapter (5'-CCUUGGCACCCGAGAAUUCCANNNN-3') in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (ThermoFisher Scientific), and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 hr. Ligation products were captured using 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific). After washing with Washing Buffer (10 mM Tris-Cl pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) for 30 min at 37 °C in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H Buffer, RNA fragments were eluted from the beads in Elution Buffer (1 mM NaCl, 1 mM EDTA pH7.5, and 0.05% TWEEN 20) at 50 °C, precipitated using ethanol, and then ligated to 3 pmol of heat-denatured 5'-adenylated 3'-adapter (5'-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC-3') using 0.25 µl of T4 RNA ligase 2 (truncated KQ version) for 1 hr at 22 °C in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. Ligation products were precipitated and reverse-transcribed using M-MLV reverse transcriptase, and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers (Sigma-Aldrich) for 15 cycles.

treatment_protocol: STAU1-KO (STAU1 C8) human embryonic kidney (HEK)293T-cell lines were established using the CRISP-Cas9n double-nicking strategy with isogenic control (C9). Total-cell lysates from STAU1-KO HEK293T cells (C8) transiently expressing FLAG-GFP or STAU1-FLAG were prepared using Hypotonic Gentle Lysis Buffer (10 mM Tris [pH 7.4], 10 mM NaCl, 10 mM EDTA, 1% [w/w] Triton X-100, 1x Protease and Phosphatase Inhibitor (Pierce)) and two 30-sec rounds of sonication (Branson Sonifier 250, duty cycle 30%, output control = 3).     Separation of HEK293T-cell nuclear and cytoplasmic fractions was performed using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Fisher Scientific) following manufacturer instructions. Polysome profiling was performed as described (Esposito et al., 2010) with minor modifications.

tag: sample treatment

value: FLAG-GFP input replicate 2

tag: transfection

value: FLAG-GFP

tag: rip antibody

value: none (input)

tag: protocol

tag: rna fraction

value: Total Poly(A)+ RNA


title: GFP_Input_1

status: Public on Nov 05 2020

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

value: FLAG-GFP input replicate 1

tag: genotype


title: Genomic DNA from umbilical cord blood buffycoat 90

type: genomic

city: Oxford

first: Elie

last: Antoun

state: United Kingdom

address: Nuffield Department of Medicine

department: CAMS China Oxford Institute (CAMS-COI

country: United Kingdom

institute: University of Oxford

description:
U103
Umbilical cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

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

data_processing:
R v3.4.2
Beta_for_GEO.txt includes Beta-mixture Quantile (BMIQ) normalized Beta Values.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: umbilical cord blood buffy coat 90

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from cord blood samples using QIAamp Blood DNA mini kit according to standard instructions.

tag: gender

value: Male

tag: tissue

value: Umbilical cord blood buffy coat

tag: maternal gdm status

value: GDM


title: Genomic DNA from umbilical cord blood buffycoat 89

description:
U102
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 89

value: Female

value: No GDM


title: STAU1_Input_2

value: STAU-FLAG input replicate 2


title: ChIP-seq input DNA: V5-Spn1 background: wild type, 30C, 1

city: Boston

first: Fred

last: Winston

state: MA

address: 77 Avenue Louis Pasteur, Room 239

department: Genetics

institute: Harvard Medical School

description:
full genotype name:
MATα (V5)x3-SPN1 ura3-52 lys2-128δ leu2Δ1 his3Δ200
V5-Spn1 ChIP-seq input library from a wild-type strain shifted to 30°C for 80 minutes.

library_source: genomic

data_processing:
Reads were demultiplexed using fastq-multx (Aronesty, 2013), allowing one mismatch to the index sequence and A-tail. Cutadapt (Martin, 2011) was then used to remove index sequences and low-quality base calls from the 3′ end of the read. Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 2 (Langmead and Salzberg, 2012), and alignments with a mapping quality of at least 5 were selected using SAMtools (Li et al., 2009). The median fragment size estimated by MACS2 (Zhang et al., 2008b) cross-correlation over all samples of a factor was used to generate coverage of fragments and fragment midpoints by extending alignments to the median fragment size or by shifting the 5′ end of alignments by half the median fragment size, respectively. The quality of raw, cleaned, non-aligning, and uniquely aligning reads was assessed using FastQC (Andrews, 2014).
Genome_build: S. cerevisiae R64-2-1, S. pombe ASM294v2
Supplementary_files_format_and_content: BigWigs of spike-in normalized estimated factor protection and estimated fragment midpoints.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures were grown in YPD at 30ºC or were shifted to growth at 37ºC for 80 minutes before further processing or collection of the cells, as described previously (Cheung et al., 2008)

extract_protocol:
The cultures were processed for cross-linking and collecting as previously described (Doris et al., 2018). Chromatin was prepared using standard methods (Gopalakrishnan et al., 2019). Each chromatin sample was mixed with S. pombe chromatin (strain FWP570) at 10% level by protein mass for spike-in normalization and split into aliquots of 500 µg of chromatin for immunoprecipitation. Chromatin precipitations were performed overnight at 4°C using either 50 µl of anti-FLAG M2 affinity gel (Sigma) for Spt6, 30 µl of anti-Myc antibodies (9E10, Santa Cruz Biotechnology), 8 µl of 8WG16 antibodies (Millipore Sigma) for Rpb1, or 5 µl of anti-V5 antibodies (Invitrogen) per 500 µg of chromatin.
DNA isolated from each sample before precipitation (inputs) and after precipitation (IP) was used for library generation as previously described (Gopalakrishnan et al., 2019).

tag: strain

value: V5-Spn1 background wild type

tag: rna population


title: Genomic DNA from umbilical cord blood buffycoat 93

description:
U106
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 93


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.

value: Spt16-myc background spt6-YW pob3-E154K


title: H37Rv_Glycerol_5

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description:
RBB458
gene_read_counts_mux5708.txt.gz

data_processing:
Raw reads (FASTQ files) were mapped to the M. tuberculosis H37Rv (GenBank accession AL123456) using bowtie2 using default parameters.
The read counts of genes were then counted using featureCounts v1.6.3 using the genome annotations provided in the GenBank file.
Computations were done using the R statistical language version 3.3.1.
Genome_build: M. tuberculosis H37Rv (GenBank accession AL123456)
Supplementary_files_format_and_content: Tab delimited text file with read counts for genes

organism: Mycobacterium tuberculosis

growth_protocol: The logphase culture of Mtb strains was washed with PBST twice and grown in “minimal media” (pH6.5; 0.5 g/L asparagine, 1 g/L KH2PO4, 2.5 g/L Na2HPO4, 50mg/L ferric ammonium citrate, 0.5g/L MgSO4*7H2O, 0.5mg/L CaCl2, 0.1 mg/L ZnSO4) containing either 0.1% glycerol (v/v) or 0.01% cholesterol (w/v). To assess the effect of rifampicin (RIF) on the generation of persisters, in some conditions RIF was added. RNA was isolated from the cultures at day4 using Qiagen RNaeasy Minikit according to manufacturer’s protocols (Qiagen 74104). The RNA was DNase treated using Turbo DNA free kit using manufacturer’s protocol (Thermo Fischer scientific) to remove any genomic DNA contamination. All Mycobacterial total RNAs were analyzed using an Agilent Bioanalyser (Agilent, Santa Clara, CA, USA) for quality assessment with RNA Integrity Number (RIN) range of 5.6 to 9.7 and a median of 7.5. Ribosomal RNA (rRNA) were depleted from 500ng of bacterial RNA using RiboMinus™ Bacteria transcriptome isolation kit (Invitrogen Thermo Fisher Scientific Waltham, MA, USA), according to manufacturer's protocol.

extract_protocol:
cDNA libraries were prepared from the resultant rRNA depleted RNA and 1 ul of a 1:500 dilution of ERCC RNA Spike in Controls (Ambion® Thermo Fisher Scientific, Waltham, MA, USA) using Lexogen SENSE Total RNA-Seq Library Prep Kit (Lexogen GmnH, Vienna, Austria) according to manufacturer's protocol except with 21 PCR cycles. The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA).
All samples were subjected to an indexed paired-end sequencing run of 2x51 cycles on an Illumina HiSeq 2000 system (Illumina, San Diego, CA, USA) (16 samples/lane).

value: Wild type

tag: time point

tag: media

value: Glycerol

tag: agent

value: No drug


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 37C, 1

source_name: Spt16-myc ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 88

description:
U100
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 88


title: Genomic DNA from umbilical cord blood buffycoat 87

description:
U99
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 87


title: H37Rv_Cholesterol_Rifampicin_8

description:
RBB472
gene_read_counts_mux5708.txt.gz

value: Cholesterol

value: Rifampicin


title: GFP_IP_2

molecule: polyA RNA

value: FLAG-GFP IP replicate 2

value: FLAG-GFP

value: anti-FLAG

value: Poly(A)+ RNA pulled down by anti-FLAG


title: H37Rv_Cholesterol_Rifampicin_7

description:
RBB471
gene_read_counts_mux5708.txt.gz


title: Genomic DNA from umbilical cord blood buffycoat 85

description:
U97
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 85


title: Genomic DNA from umbilical cord blood buffycoat 86

description:
U98
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 86


title: STAU1_IP_2

value: STAU1-FLAG IP replicate 2


title: H37Rv_Cholesterol_Rifampicin_6

description:
RBB470
gene_read_counts_mux5708.txt.gz


title: GFP_IP_1

value: FLAG-GFP IP replicate 1


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 1

description:
full genotype name:
MATα SPT16-Myc spt6-YW pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: H37Rv_Cholesterol_Rifampicin_5

description:
RBB462
gene_read_counts_mux5708.txt.gz


title: STAU1_Input_1

value: STAU1-FLAG input replicate 1

value: none (input)

value: Total Poly(A)+ RNA


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW pob3-E154K, 30C, 2

source_name: Spt16-myc ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 81

description:
U93
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 81

value: Male

value: Umbilical cord blood buffy coat


title: ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 30C, 1

description:
full genotype name:
MATα SPT16-Myc pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from a pob3-E154K strain shifted to 30°C for 80 minutes.

value: Spt16-myc background pob3-E154K


title: H37Rv_Cholesterol_5

description:
RBB453
gene_read_counts_mux5708.txt.gz

value: Wild type


title: ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT16-Myc pob3-E154K leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: E88_1_1

city: Irvine

first: ABEL

last: PLAZA FLORIDO

state: California

address: 101 Academy, Suite 150 Irvine

department: Department of Pediatrics, UC Irvine School of Medicine

institute: Pediatric Exercise and Genomics Research Center (PERC)

data_processing:
The STRTprep pipeline (which is an open-source pre-processing and analysis package for STRT RNA-seq), available at https://github.com/shka/STRTprep/tree/v3dev, was used for processing raw sequencing reads, aligning to the hg19 genome, quantitating the expression levels
Genome_build: hg19 genome
Supplementary_files_format_and_content: MHO_MUO_I.txt contains raw count data, MHOMUO_sex_PHV_voom_quantiles.txt contains normalized data.

source_name: Whole blood

extract_protocol:
Total RNA was isolated from the blood samples that contained RNA later using RiboPureTM-Blood Kit (Thermo Fisher Scientific; Waltham, Massachusetts, USA). Subsequently, GlobinLock molecular mechanism was applied to block the high globin mRNA content of erythrocytes, which is abundant in the blood and could hamper the whole blood RNA analyses
Full transcriptome analysis was performed following the modified version of single-cell tagged reverse transcription (STRT) protocol, where 10 ng of high-quality input RNA was converted into cDNA and amplified to form an Illumina-compatible library. The STRTprep pipeline, available at https://github.com/shka/STRTprep/tree/v3dev, was used for processing raw sequencing reads, aligning to the hg19 genome, quantitating the expression levels.

treatment_protocol: 500 μL blood was collected into the tube that contained 1.3 mL RNAlater solution (Ambion Inc; Austin, Texas, USA) for transcriptome analysis and was stored at -80ºC until further processing

value: Whole blood

tag: age range

value: 9-11 years

tag: maturation (peak height velocity)

tag: Sex

value: male

tag: metabolic healthy group

value: metabHealth


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW, 37C, 2

description:
full genotype name:
MATα SPT16-Myc spt6-YW leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from an spt6-YW strain shifted to 37°C for 80 minutes.

value: Spt16-myc background spt6-YW


title: Genomic DNA from umbilical cord blood buffycoat 84

description:
U96
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 84

value: No GDM


title: STAU1_IP_1

tag: sample treatment

value: STAU1-FLAG IP replicate 1

tag: transfection

tag: rip antibody

value: anti-FLAG


title: E84_1


title: H37Rv_Cholesterol_7

description:
RBB468
gene_read_counts_mux5708.txt.gz

value: Cholesterol

value: No drug


title: E93_1


title: H37Rv_Cholesterol_8

description:
RBB469
gene_read_counts_mux5708.txt.gz


title: ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 37C, 1

source_name: Spt16-myc ChIP-seq input library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: ChIP-seq input DNA: Spt16-myc background: pob3-E154K, 30C, 2

source_name: Spt16-myc ChIP-seq input library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: LIVER-OMNI-Cess3

city: Baltimore

first: Bongsoo

last: Park

state: Maryland

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

data_processing:
cutadapt
BWA alignment
Python script, peak-level extraction
Genome_build: mm10

organism: Mus musculus

source_name: Liver

extract_protocol:
Wash cells with 50ul cold 1X PBS in epi tube, centrifuge to pellet, discard supernatant
Tn5 treatment, Nextera DNA Library prep kit using standard protocols

value: Liver

tag: treatment

value: Chow diet, PM exposure, PM cessation


title: Genomic DNA from umbilical cord blood buffycoat 82

description:
U94
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 82

value: Female


title: Genomic DNA from umbilical cord blood buffycoat 78

description:
U90
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 78

value: Male


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW, 30C, 1

description:
full genotype name:
MATα SPT16-Myc spt6-YW leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from an spt6-YW strain shifted to 30°C for 80 minutes.

tag: genotype


title: H37Rv_Cholesterol_6

description:
RBB467
gene_read_counts_mux5708.txt.gz


title: E73_1

value: female

value: metabUnHealth


title: Genomic DNA from umbilical cord blood buffycoat 80

description:
U92
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 80

tag: gender

value: Umbilical cord blood buffy coat


title: Genomic DNA from umbilical cord blood buffycoat 79

description:
U91
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 79

tag: tissue


title: ChIP-seq input DNA: Spt16-myc background: wild type, 37C, 2

description:
full genotype name:
MATα SPT16-Myc leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from a wild-type strain shifted to 37°C for 80 minutes.

value: Spt16-myc background wild type


title: E92_1

value: Whole blood

value: 9-11 years


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW, 37C, 1

source_name: Spt16-myc ChIP-seq input library from an spt6-YW strain shifted to 37°C for 80 minutes.


title: ChIP-seq input DNA: Spt16-myc background: spt6-YW, 30C, 2

source_name: Spt16-myc ChIP-seq input library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: E88_2_1

value: male

value: metabHealth


title: Genomic DNA from umbilical cord blood buffycoat 83

description:
U95
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 83

tag: maternal gdm status

value: GDM


title: E82_1


title: Genomic DNA from umbilical cord blood buffycoat 77

description:
U89
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 77

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 75

description:
U87
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 75


title: LIVER-OMNI-Cess2


title: E68_1


title: Genomic DNA from umbilical cord blood buffycoat 74

description:
U86
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 74


title: LIVER-OMNI-FA-22-2

value: Chow diet


title: LIVER-OMNI-Cess1


title: LIVER-OMNI-Cess4


title: Genomic DNA from umbilical cord blood buffycoat 73

description:
U85
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 73


title: LIVER-OMNI-FA-22-1


title: Genomic DNA from umbilical cord blood buffycoat 76

description:
U88
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 76


title: ChIP-seq input DNA: Spt16-myc background: wild type, 37C, 1

source_name: Spt16-myc ChIP-seq input library from a wild-type strain shifted to 37°C for 80 minutes.

tag: strain


title: E69_1

source_name: Whole blood


title: ChIP-seq input DNA: Spt16-myc background: wild type, 30C, 1

description:
full genotype name:
MATα SPT16-Myc leu2Δ1 ura3-52 lys2-128δ
Spt16-myc ChIP-seq input library from a wild-type strain shifted to 30°C for 80 minutes.

tag: rna population


title: ChIP-seq input DNA: Spt16-myc background: wild type, 30C, 2

source_name: Spt16-myc ChIP-seq input library from a wild-type strain shifted to 30°C for 80 minutes.


title: LIVER-OMNI-FA-22-3


title: E106_1


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background spt6-YW pob3-E154K


title: LIVER-OMNI-PM4

value: PM exposure


title: E105_1


title: C99_1


title: LIVER-OMNI-PM2

value: Liver


title: LIVER-OMNI-PM3


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 37C, 1

source_name: Spt6-FLAG ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.


title: E108_1


title: C96_1


title: Genomic DNA from umbilical cord blood buffycoat 70

description:
U82
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 70


title: LIVER-OMNI-PM1

source_name: Liver


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 69

description:
U81
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 69


title: LIVER-OMNI-FA3


title: C90_1


title: Genomic DNA from umbilical cord blood buffycoat 68

description:
U80
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 68


title: ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 37C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from a pob3-E154K strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background pob3-E154K


title: C89_1


title: LIVER-OMNI-FA2


title: Genomic DNA from umbilical cord blood buffycoat 72

description:
U84
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 72


title: Genomic DNA from umbilical cord blood buffycoat 67

description:
U79
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 67


title: LIVER-OMNI-FA1


title: ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 37C, 1

source_name: Spt6-FLAG ChIP-seq input library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 30C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 pob3-E154K lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 71

description:
U83
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 71

value: Female


title: Genomic DNA from umbilical cord blood buffycoat 66

description:
U78
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 66


title: Genomic DNA from umbilical cord blood buffycoat 65

description:
U77
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 65

value: Male


title: LIVER-ATAC-HFD4

value: High-fat diet


title: ChIP-seq input DNA: Spt6-FLAG background: pob3-E154K, 30C, 1

source_name: Spt6-FLAG ChIP-seq input library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: LIVER-ATAC-HFD3


title: C74_2_1


title: C78_1

value: female


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW pob3-E154K, 30C, 1

source_name: Spt6-FLAG ChIP-seq input library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 37C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from an spt6-YW strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background spt6-YW


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 37C, 1

source_name: Spt6-FLAG ChIP-seq input library from an spt6-YW strain shifted to 37°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 64

description:
U76
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 64

value: Umbilical cord blood buffy coat


title: LIVER-ATAC-HFD2


title: C71_1

source_name: Whole blood

value: Whole blood


title: Genomic DNA from umbilical cord blood buffycoat 63

description:
U75
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 63


title: LIVER-ATAC-HFD1


title: Genomic DNA from umbilical cord blood buffycoat 62

description:
U74
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 62


title: C70_1

value: 9-11 years

value: metabUnHealth


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 30C, 2

description:
full genotype name:
MATα spt6-YW-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: ChIP-seq input DNA: Spt6-FLAG background: spt6-YW, 30C, 1

source_name: Spt6-FLAG ChIP-seq input library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: C85_1


title: Genomic DNA from umbilical cord blood buffycoat 61

description:
U73
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 61


title: LIVER-ATAC-PM4

source_name: Liver


title: C67_1

value: male


title: Genomic DNA from umbilical cord blood buffycoat 60

description:
U72
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 60


title: LIVER-ATAC-PM3


title: C28_1


title: ChIP-seq input DNA: Spt6-FLAG background: wild type, 37C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from a wild-type strain shifted to 37°C for 80 minutes.

value: Spt6-FLAG background wild type


title: ChIP-seq input DNA: Spt6-FLAG background: wild type, 37C, 1

source_name: Spt6-FLAG ChIP-seq input library from a wild-type strain shifted to 37°C for 80 minutes.


title: LIVER-ATAC-PM2


title: Genomic DNA from umbilical cord blood buffycoat 59

description:
U71
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 59

value: No GDM


title: C74_1_1


title: ChIP-seq input DNA: Spt6-FLAG background: wild type, 30C, 2

description:
full genotype name:
MATα SPT6-(FLAG)X3 lys2-128δ ura3-52 leu2Δ1
Spt6-FLAG ChIP-seq input library from a wild-type strain shifted to 30°C for 80 minutes.


title: C110_1


title: C107_1


title: LIVER-ATAC-PM1


title: Genomic DNA from umbilical cord blood buffycoat 58

description:
U70
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 58


title: LIVER-ATAC-FA4

value: Chow diet


title: Genomic DNA from umbilical cord blood buffycoat 57

description:
U69
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 57


title: LIVER-ATAC-FA3


title: ChIP-seq input DNA: Spt6-FLAG background: wild type, 30C, 1

source_name: Spt6-FLAG ChIP-seq input library from a wild-type strain shifted to 30°C for 80 minutes.


title: MNase-seq: spt6-YW spt5-QS, 37C, 4

description:
full genotype name:
MATα spt5-QS spt6-YW lys2-128δ ura3-52 leu2Δ1
MNase-seq library from an spt6-YW spt5-QS strain shifted to 37°C for 80 minutes.

data_processing:
Paired-end reads were demultiplexed using fastq-multx (Aronesty, 2011), allowing one mismatch to the barcode. Filtering for the barcode on read 2 and 3′ quality trimming were performed with cutadapt (Martin, 2011). Reads were aligned to the combined S. cerevisiae and S. pombe genome using Bowtie 1 (Langmead et al., 2009), and correctly paired alignments were selected using SAMtools (Li et al., 2009). Coverage of nucleosome protection and nucleosome dyads were extracted using bedtools (Quinlan and Hall, 2010) and shell scripts to get the entire fragment or the midpoint of the fragment, respectively. Smoothed nucleosome dyad coverage was generated by smoothing dyad coverage was generated by smoothing dyad coverage with a Gaussian kernel of 20 bp bandwidth. Due to differences in the proportion of S. pombe DNA added between sequencing runs, coverage was normalized to the total number of correctly paired S. cerevisiae fragments. The quality of raw, cleaned, non-aligning, and correctly paired reads was assessed using FastQC (Andrews, 2014).
Genome_build: S. cerevisiae R64-2-1, S. pombe ASM294v2
Supplementary_files_format_and_content: BigWigs of library-size normalized MNase protection, fragment midpoints, and fragments midpoints smoothed with a Gaussian of 20bp bandwidth.

extract_protocol:
DOI: 10.1016/j.molcel.2018.09.005
At a density of approximately 1 × 107 cells/ml (OD600 = 0.5), cells were crosslinked using 2% formaldehyde for 30 minutes and then treated for 10 minutes with 125 mM glycine before collecting an equal number of cells for each strain. The cells were resuspended in 40 mL of sorbitol buffer (1 M sorbitol, 50 mM Tris pH 7.4, 10 mM ?-mercaptoethanol) and incubated for 30 minutes at 30°C with 10 mg of zymolase 100T (US Biological) per gram of cells. Spheroplasting efficiency was assessed by microscopy and was more than 95% of total cells. The spheroplasts were collected and resuspended in NP buffer (1 M sorbitol, 50 mM sodium chloride, 10 mM Tris pH 7.4, 5 mM magnesium chloride, 1 mM calcium chloride, 0.075% NP-40, 1 mM ?-mercaptoethanol, 500 ?M spermidine). Micrococcal nuclease (MNase; Sigma) was dissolved in Ex50 buffer (10 mM HEPES pH 7.6, 50 mM sodium chloride, 1.5 mM magnesium chloride, 0.5 mM EGTA, 10% glycerol, 1mM dithiothreitol, 0.2 mM phenylmethylsulfonyl fluoride) prepared to produce 500 units per 840 ?l stock as recommended by the manufacturer. The spheroplasts were divided into aliquots and incubated for 20 minutes at 37°C with increasing amounts of MNase, ranging from 2 to 15 ?L of the stock. Digestion was stopped by addition of stop buffer (5% SDS, 100 mM EDTA), samples were subjected to proteinase K digestion and reverse-crosslinking at 65°C overnight, followed by DNA purification. The efficiency of MNase digestion was quantified using DNA fragment size analysis (Agilent Bioanalyzer) to establish an MNase titration curve for each strain. The MNase concentrations which yielded approximately 80% mononucleosomal DNA were selected for library construction. The samples were mixed with the MNase-digested spike-in DNA from S. pombe (strain 972) based on the original cell count (100 ng of spike-in DNA per 7 X 107 S. cerevisiae cells). Mononucleosomal DNA was purified using size-selected gel extraction.

value: spt6-YW spt5-QS


title: C104_1


title: Genomic DNA from umbilical cord blood buffycoat 56

description:
U68
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 56


title: LIVER-ATAC-FA2


title: MNase-seq: spt6-YW spt5-QS, 37C, 3

source_name: MNase-seq library from an spt6-YW spt5-QS strain shifted to 37°C for 80 minutes.


title: KO36_C6

city: Jerusalem

first: Elad

last: Zisman

address: Kalman Ya'akov Man

country: Israel

institute: The Hebrew University

data_processing:
Libraries were created using the Smart-Seq2 protocol as previously described (Sade-Feldman et al., 2018)
Illumina adapters were trimmed from the reads using cutadapt
FASTQ files were aligned to the NCBI Human Reference Genome Build GRCh37 (hg19) using STAR
Genome_build: hg19
Supplementary_files_format_and_content: Count data was normilized vie the Deseq2 library
Supplementary_files_format_and_content: SLAMF6_counts.txt: raw counts

source_name: KO SLAMF6 ISO1 Jurkat cell

growth_protocol: The Jurkat cell line was purchased from ATCC. The cells were cultured in RPMI 1640 supplemented with 10% heat-inactivated fetal calf serum (FCS), 2 mmol/L L-glutamine, and combined antibiotics (all from ThermoFisher Scientific).  The line is regularly tested and was mycoplasma free.

extract_protocol:
lysed in 100Sµl lysis buffer containing TCL buffer (Qiagen, 1031576) containing 1% β-mercaptoethanol. After lysis, plates were imminently frozen and stored in -80C until samples were processed. For RNA purification 10µl of cell lysates for each sample was used. 40µl of Agencourt RNAClean XP SPRI beads (Beckman Coulter, A63987) were added to the cell lysates, and after 10 minutes of incubation in room temperature, plates were place on a DynaMag 96 side skirted magnet (Invitrogen, 12027) for 5 minutes, followed by supernatant removal and 2 cycles of 75% ethanol washes
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1x105 Jurkat cells (either WT or SLAMF6∆17-65 cells) were activated with 200 ng/ml PMA and 300 ng/ml ionomycin for 48h. At the end of the activation, the conditioned medium was collected, and IL-2 or IFN-γ secretion was detected by ELISA (R&D)

tag: cell line

value: Jurkat E6-1

value: Stimulated

tag: time point


title: KO36_C5


title: Genomic DNA from umbilical cord blood buffycoat 54

description:
U66
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 54

value: GDM


title: LIVER-ATAC-FA1

value: Liver


title: LIVER-Cess-4

data_processing:
cutadapt
STAR alignment
featureCount, gene-level extraction
Genome_build: mm10

extract_protocol:
Invitrogen Purelink RNA Minikit, supplemented with the Proteinase K and Rnase-Free Dnaset (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Chow diet, PM exposure, PM cessation


title: MNase-seq: spt6-YW spt5-QS, 37C, 2


title: Genomic DNA from umbilical cord blood buffycoat 53

description:
U63
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 53

value: Male


title: KO36_C4


title: Genomic DNA from umbilical cord blood buffycoat 52

description:
U62
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 52

value: Female


title: KO24_B11


title: Genomic DNA from umbilical cord blood buffycoat 51

description:
U61
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 51


title: MNase-seq: spt6-YW spt5-QS, 30C, 2

description:
full genotype name:
MATα spt5-QS spt6-YW lys2-128δ ura3-52 leu2Δ1
MNase-seq library from an spt6-YW spt5-QS strain shifted to 30°C for 80 minutes.


title: LIVER-Cess-2


title: MNase-seq: spt6-YW spt5-QS, 30C, 1

source_name: MNase-seq library from an spt6-YW spt5-QS strain shifted to 30°C for 80 minutes.


title: KO24_B10


title: LIVER-Cess-1


title: Genomic DNA from umbilical cord blood buffycoat 55

description:
U67
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 55


title: LIVER-FA22-4


title: KO12_B9


title: Genomic DNA from umbilical cord blood buffycoat 50

description:
U59
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 50


title: MNase-seq: spt6-YW pob3-E154K, 37C, 4

description:
full genotype name:
MATα spt6-YW pob3-E154K lys2-128δ ura3-52 leu2Δ1 [pRS316]
MNase-seq library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.

value: spt6-YW pob3-E154K


title: MNase-seq: spt6-YW pob3-E154K, 37C, 3

source_name: MNase-seq library from an spt6-YW pob3-E154K strain shifted to 37°C for 80 minutes.


title: LIVER-FA22-3

source_name: Liver


title: KO12_B8


title: Genomic DNA from umbilical cord blood buffycoat 49

description:
U58
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 49

value: Umbilical cord blood buffy coat


title: MNase-seq: spt6-YW pob3-E154K, 37C, 2


title: KO24_B12


title: LIVER-Cess-3


title: KO12_B7


title: Genomic DNA from umbilical cord blood buffycoat 48

description:
U57
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 48


title: MNase-seq: spt6-YW spt5-QS, 37C, 1


title: Genomic DNA from umbilical cord blood buffycoat 47

description:
U56
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 47


title: MNase-seq: spt6-YW pob3-E154K, 37C, 1


title: Genomic DNA from umbilical cord blood buffycoat 46

description:
U54
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 46


title: LIVER-FA22-1


title: KO6_B6


title: MNase-seq: spt6-YW pob3-E154K, 30C, 4

description:
full genotype name:
MATα spt6-YW pob3-E154K lys2-128δ ura3-52 leu2Δ1 [pRS316]
MNase-seq library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: KO6_B5


title: WAT-Cess-4

source_name: White adipose tissue

value: White adipose tissue


title: Genomic DNA from umbilical cord blood buffycoat 45

description:
U53
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 45


title: MNase-seq: spt6-YW pob3-E154K, 30C, 3

source_name: MNase-seq library from an spt6-YW pob3-E154K strain shifted to 30°C for 80 minutes.


title: KO6_B4

source_name: KO SLAMF6 ISO1 Jurkat cell


title: Genomic DNA from umbilical cord blood buffycoat 44

description:
U52
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 44


title: MNase-seq: spt6-YW pob3-E154K, 30C, 2


title: KO0_B3

value: Unstimulated


title: Genomic DNA from umbilical cord blood buffycoat 43

description:
U51
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 43


title: WAT-Cess-2


title: MNase-seq: spt5-QS, 37C, 4

description:
full genotype name:
MATα spt5-QS lys2-128δ ura3-52 leu2Δ1
MNase-seq library from an spt5-QS strain shifted to 37°C for 80 minutes.


title: KO0_B2


title: Genomic DNA from umbilical cord blood buffycoat 42

description:
U49_rep2
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 42


title: KO0_B1


title: WAT-Cess-1


title: LIVER-FA22-2


title: WAT-FA22-4


title: MNase-seq: spt5-QS, 37C, 3

source_name: MNase-seq library from an spt5-QS strain shifted to 37°C for 80 minutes.


title: WT36_C3

source_name: WT Jurkat cell


title: MNase-seq: spt5-QS, 37C, 2


title: WAT-FA22-3


title: MNase-seq: spt5-QS, 37C, 1


title: WT36_C2


title: Genomic DNA from umbilical cord blood buffycoat 41

description:
U48
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 41


title: WAT-FA22-2


title: Genomic DNA from umbilical cord blood buffycoat 40

description:
U47
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 40


title: MNase-seq: spt5-QS, 30C, 2

description:
full genotype name:
MATα spt5-QS lys2-128δ ura3-52 leu2Δ1
MNase-seq library from an spt5-QS strain shifted to 30°C for 80 minutes.


title: WAT-Cess-3


title: WT36_C1


title: Genomic DNA from umbilical cord blood buffycoat 39

description:
U46
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 39


title: WAT-FA22-1


title: MNase-seq: spt5-QS, 30C, 1

source_name: MNase-seq library from an spt5-QS strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 38

description:
U45
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 38


title: WT24_A12


title: WAT-PM3

value: Chow diet, PM exposure


title: Genomic DNA from umbilical cord blood buffycoat 37

description:
U44
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 37


title: Genomic DNA from umbilical cord blood buffycoat 36

description:
U43
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 36


title: WT24_A10


title: Genomic DNA from umbilical cord blood buffycoat 35

description:
U42
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 35


title: WAT-PM1

source_name: White adipose tissue


title: MNase-seq: pob3-E154K, 37C, 2

description:
full genotype name:
MATα pob3-E154K ura3-52 lys2-128δ [pRS316]
MNase-seq library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: WAT-PM2


title: MNase-seq: pob3-E154K, 37C, 1

source_name: MNase-seq library from a pob3-E154K strain shifted to 37°C for 80 minutes.


title: WT24_A11


title: WT12_A9


title: MNase-seq: pob3-E154K, 30C, 2

description:
full genotype name:
MATα pob3-E154K ura3-52 lys2-128δ [pRS316]
MNase-seq library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: WAT-FA4


title: Genomic DNA from umbilical cord blood buffycoat 34

description:
U41
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 34


title: WT12_A8


title: WAT-FA3


title: Genomic DNA from umbilical cord blood buffycoat 33

description:
U40
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 33


title: MNase-seq: pob3-E154K, 30C, 1

source_name: MNase-seq library from a pob3-E154K strain shifted to 30°C for 80 minutes.


title: WAT-FA2


title: WT12_A7


title: Genomic DNA from umbilical cord blood buffycoat 32

description:
U39
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 32


title: Genomic DNA from umbilical cord blood buffycoat 31

description:
U38
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 31


title: MNase-seq: pob3-E154K, 37C, 4


title: WT6_A5


title: WT6_A6


title: MNase-seq: spt6-YW, 37C, 2

description:
full genotype name:
MATα spt6-YW lys2-128δ ura3-52 leu2Δ1 [pRS316]
MNase-seq library from an spt6-YW strain shifted to 37°C for 80 minutes.


title: WAT-HFD4

value: High-fat diet


title: MNase-seq: spt6-YW, 37C, 1

source_name: MNase-seq library from an spt6-YW strain shifted to 37°C for 80 minutes.


title: WAT-FA1


title: MNase-seq: spt6-YW, 30C, 3

description:
full genotype name:
MATα spt6-YW lys2-128δ ura3-52 leu2Δ1 [pRS316]
MNase-seq library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: WT6_A4

source_name: WT Jurkat cell


title: Genomic DNA from umbilical cord blood buffycoat 30

description:
U37
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 30


title: Genomic DNA from umbilical cord blood buffycoat 29

description:
U36
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 29


title: WAT-HFD2


title: Genomic DNA from umbilical cord blood buffycoat 28

description:
U35
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 28


title: WT0_A2


title: MNase-seq: spt6-YW, 30C, 1

source_name: MNase-seq library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: WAT-HFD1


title: Genomic DNA from umbilical cord blood buffycoat 27

description:
U34
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 27


title: WT0_A1


title: QUAD-PM3

source_name: Skeletal muscle

value: Skeletal muscle


title: MNase-seq: spn1-K192N, 37C 2

description:
full genotype name:
MATα spn1-K192N::URA3 leu2D0 lys2-128δ ura3D0
MNase-seq library from a spn1-K192N strain shifted to 37°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 26

description:
U33
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 26


title: Genomic DNA from umbilical cord blood buffycoat 25

description:
U32
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 25


title: MNase-seq: spn1-K192N, 30C 2

description:
full genotype name:
MATα spn1-K192N::URA3 leu2D0 lys2-128δ ura3D0
MNase-seq library from a spn1-K192N strain shifted to 30°C for 80 minutes.


title: Genomic DNA from umbilical cord blood buffycoat 24

description:
U31
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 24

value: No GDM


title: QUAD-PM1


title: QUAD-PM2


title: MNase-seq: spn1-K192N, 30C 1

source_name: MNase-seq library from a spn1-K192N strain shifted to 30°C for 80 minutes.


title: QUAD-FA4

value: Chow diet


title: Genomic DNA from umbilical cord blood buffycoat 23

description:
U30
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 23


title: QUAD-FA3


title: WAT-HFD3

source_name: White adipose tissue


title: WT0_A3


title: MNase-seq: spt6-YW, 30C, 2


title: MNase-seq: wild type, 37C 4

description:
full genotype name:
MATα lys2-128δ ura3-52 leu2Δ1
MNase-seq library from a wild type strain shifted to 37°C for 80 minutes.

value: wild type


title: Genomic DNA from umbilical cord blood buffycoat 22

description:
U28
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 22


title: OSCC SAS siD RIBO-seq

city: Taipei

first: Hung-Hsi

last: Chen

address: N223, IBMS, No. 128, Sec. 2, Academia Rd.

country: Taiwan

institute: Academia Sinica

data_processing:
Library strategy: Ribo-seq
Raw reads were trimmed using Cutadapt version 1.13
Ribosomal RNA reads from trimmed reads were removed using Bowtie 1.30
Filtered reads were alignmed to the human genome assembly (GRch38) using TopHat2, with condition '--no-coverage-search --segment-length 14 --segment-mismatches 1'
Unique reads and multiple-mapped reads were identified, and multiple-mapped reads were removed from the TopHat2 mapped results
Gene expression level, and identification of differentially regulated genes were identified using Cufflinks and Cuffdiff, and Gencode Basic data obtained from Ensembl was used for gene annotation
Genome_build: Human genome GRch38

source_name: OSCC cell line

growth_protocol: SAS cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% (v/v) fetal bovine serum at 37°C with a humidified atmosphere of 5% CO2, 100 U/ml penicillin, 100 μg/ml streptomycin, and 2 mM L-glutamine.

extract_protocol:
For RNAseq, total RNA was extracted using Trizol Reagent (ThermoFisher) according to the manufacturer’s instructions. Ribosomal RNA (rRNA) was depleted using the Ribo-off rRNA Depletion Kit (Vazyme). For Riboseq, cells were lysed with the polysome buffer containing 20 mM Tris-HCl pH7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 200 µg/ml cycloheximide, 1% (v/v) Triton X-100 and 25 U/ml Turbo DNase I (Ambion). The lysates were subsequnetly digested with RNase I (Ambion). After purification, rRNA was depleted using the Ribo-off rRNA Depetion Kit (Vazyme). Ribosome-protected fragments (RPF) were purified with PAGE and dephosphorylated with T4 Polynucleotide Kinase (New England BioLabs).
For RNAseq, library preparation was performed using the NETNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s instructions. For RIBOseq, linkers were ligated to RPFs using T4 RNA ligase 2, truncated K227Q (New England BioLabs) and the cDNA was synthesized using SuperScript III reverse transcriptase (ThermoFisher). The cDNA samples were circularized by CircLigase ssDNA Ligase (Lucigen), amplified by Phusion High-Fidelity DNA Polymerase (New England BioLabs) and purified using AMPure XP for PCR Purification (Beckman Coulter). The quality and quantity of the libraries were respectively analyzed by Fragment Analyzer Automated CE System (Advanced Analytical Technologies) and Qubit Fluorometer (ThermoFisher).

treatment_protocol: Transfection of siRNA was performed using Lipofectamine 3000 (ThermoFisher) according to manufacturer’s instructions.

tag: cell type

value: Patient-derived oral squamous cell carcinoma (OSCC)

value: Transfection of siD


title: OSCC SAS siC RIBO-seq

value: Transfection of siC


title: OSCC SAS siC mRNA-seq

data_processing:
Raw reads were trimmed using Cutadapt version 1.13
Ribosomal RNA reads from trimmed reads were removed using Bowtie 1.30
Filtered reads were alignmed to the human genome assembly (GRch38) using TopHat2, with condition '--no-coverage-search --segment-length 14 --segment-mismatches 1'
Unique reads and multiple-mapped reads were identified, and multiple-mapped reads were removed from the TopHat2 mapped results
Gene expression level, and identification of differentially regulated genes were identified using Cufflinks and Cuffdiff, and Gencode Basic data obtained from Ensembl was used for gene annotation
Genome_build: Human genome GRch38


title: OSCC SAS siD mRNA-seq


title: QUAD-FA2


title: Genomic DNA from umbilical cord blood buffycoat 21

description:
U27
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 21


title: MNase-seq: wild type, 37C 3

source_name: MNase-seq library from a wild type strain shifted to 37°C for 80 minutes.


title: JX12 42127 3uM 12H; second experiment

city: Birmingham

first: Louis

middle: Burt

last: Nabors

state: AL

address: 510 20th Street South, FOT 1020

department: Neurology

institute: University of Alabama at Birmingham

description:
second experiment
SY10

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Sequence reads were aligned to the reference genome using STAR version 2.7.2a with parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-Count version 0.11.1 with paramaters -r pos; -t exon; -i gene_id; -a 10; -s no; -f bam
Normalization and pairwise differential expression was calculated following the DESeq2 vignette
Genome_build: Gencode GRCh38 p7 Release 25
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: PDGx cell line JX12

growth_protocol: The neurospheres were formed and maintained in Neurobasal-A medium (Gibco, Carlsbad, CA, USA) supplemented with a B27 supplement without vitamin A (Gibco), N-2 supplement (Gibco), 2mM L-Glutamine (Media tech, Inc., Manassas, VA, USA), the basal growth factors (EGF, 20 ng/ml and bFGF, 20 ng/ml, were both purchased from Termo Fisher Scientifics (Grand Island, NY, USA)), and 100 U/ml Penicillin/Streptomycin (Media tech, Inc., Manassas, VA, USA).

extract_protocol:
RNA was isolated by using the standard protocol for RNA isolation by using TRIzol Reagent (Invitrogen, Carlsbad, CA). Briefly, neurospheres were collected in growth media, spin down for 5 min at 900 rpm (136 g), neurosphere pellet was washed in PBS, spin down for 5 min at 900 rpm, and the fully aspirated pellet was resuspended in TRIzol Reagent. After RNA purification, the RNA concentration and purity were evaluated by using NanoDrop 1000. The RNA samples were processed, and the sequencing libraries were prepared from RNA samples, which had integrity number higher than 7.0, in the UAB Sequencing Core facility.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Neurospheres were treated in the growth media with SRI-42127 (3uM for 12 hours) or with the corresponding concentration of DMSO (0.012% for 12 hours), as the control.

tag: subtype

value: classic subtype

value: GBM, brain tumor

value: treated with SRI-42127,  3 uM


title: MNase-seq: spn1-K192N, 37C 1

source_name: MNase-seq library from a spn1-K192N strain shifted to 37°C for 80 minutes.


title: QUAD-FA1


title: MNase-seq: wild type, 37C 1


title: Genomic DNA from umbilical cord blood buffycoat 20

description:
U26
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 20

value: Male


title: Genomic DNA from umbilical cord blood buffycoat 19

description:
U25
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 19


title: MNase-seq: wild type, 30C 6

description:
full genotype name:
MATα lys2-128δ ura3-52 leu2Δ1
MNase-seq library from a wild type strain shifted to 30°C for 80 minutes.


title: QUAD-HFD3


title: MNase-seq: wild type, 37C 5


title: QUAD-HFD2


title: X1524 42127 3uM 12H; second experiment

description:
second experiment
SY8

source_name: PDGx cell line X1524

value: proneural subtype


title: MNase-seq: wild type, 30C 2

source_name: MNase-seq library from a wild type strain shifted to 30°C for 80 minutes.


title: X1524 DMSO 12H; second experiment

description:
second experiment
SY7

value: treated with DMSO, 0.012%


title: QUAD-HFD1

source_name: Skeletal muscle


title: Genomic DNA from umbilical cord blood buffycoat 17

description:
U23
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 17

value: Umbilical cord blood buffy coat

value: GDM


title: XD456 42127 3uM 12H; second experiment

description:
second experiment
SY6

source_name: PDGx cell line XD456


title: LIVER-PM3

source_name: Liver

value: Liver

value: Chow diet, PM exposure


title: XD456 DMSO 12H; second experiment

description:
second experiment
SY5


title: PGD1::OsTZF8 rep1

city: Pyeongchang

first: Jae Sung

last: Shim

state: Gangwondo

address: Pyeongchang daero 1447

department: Crop Biotechnology Institute

country: South Korea

institute: Seoul National University

data_processing:
Single-end sequences were obtained using IRGSP (v 1.0) and raw sequence reads were trimmed to remove adaptor sequences, and those with a quality lower than Q20 were removed using the Trimmomatic 0.32 software
Duplicate paired short reads were removed using FastUniq.
To map the reads to reference genome, all reads were assembled with annotated genes from the Rap-DB database [http://rapdb.dna.affrc.go.jp; IRGSP (v 1.0)] using TopHat software (https://ccb.jhu.edu/software/ tophat/index.shtml).
Genome_build: IRGSP-v1.0
Supplementary_files_format_and_content: Abundance measurements

organism: Oryza sativa

source_name: Whole plants

growth_protocol: Rice seeds  were planted on a Murashige–Skoog (MS) solid medium and incubated in the dark for 3 days at 28 °C. After germinating in 28 °C, seedlings were transplanted into soil pots (4 x 4 x 6cm; two plants per pot) and grown for three weeks.

extract_protocol:
Total RNAs were extracted from the whole plants of OsTZF8 overexpressing (T4 generation, line number #20) and non-transgenic (NT) plant using RNeasy plant mini kit (Qiagen, Germany)
The libraries were prepared using the TruSeq RNA sample Prep Kit (v2) (Macrogen).

treatment_protocol: No treatment

tag: cultivar

value: cv. Nakdong

tag: developmental stage

value: three-week-old whole plants


title: non-trasngenic control rep2

value: non-trasngenic control


title: BAL cells - Lung Transplant recipient 1

city: Brisbane

first: Brendan

middle: John

last: O'Sullivan

state: Queensland

address: Level 6, 37 Kent Street Woolloongabba

country: Australia

institute: The University of Queensland Diamantina Institute Translational Research Institute

data_processing:
Processing of the sequencing data into transcript count tables was performed using the Cell Ranger Single Cell Software Suite by 10X Genomics (v2.0.0). Raw base call files from the NextSeq 500 sequencer were demultiplexed, using the Cell Ranger mkfastq pipeline, into sample-specific FASTQ files. These FASTQ files were then processed with the Cell Ranger count pipeline, where each sample was processed independently. First, Cell Ranger count used STAR (Dobin et al., 2013) to align cDNA reads to the GRCh38 human reference transcriptome, which accompanied the Cell Ranger Single Cell Software Suite. Aligned reads were filtered for valid cell barcodes and unique molecular identifiers (UMIs), and observed cell barcodes were retained if they were 1 Hamming distance away from an entry in a whitelist of known barcodes. UMIs were retained if they were not homopolymers and had a quality score >10 (90% base accuracy). The Cell Ranger count corrected mismatched barcodes if the base mismatch was due to sequencing error, as determined by the quality of the mismatched base pair and the overall distribution of barcode counts. A UMI was corrected to another more prolific UMI if it was 1 Hamming distance away and shared the same cell barcode and gene. The Cell Ranger count examined the distribution of UMI counts for each unique cell barcode in the sample and selected cell barcodes with UMI counts that fell within the 99th percentile of the range defined by the estimated cell count value. The expected cell count value of 10,000 was used for this experiment. Counts that fell within an order of magnitude of the 99th percentile were also retained. The resulting data for each sample were then aggregated using the cellranger aggr pipeline, followed by a between-sample normalization step. After aggregation, the count data were processed and analyzed using a comprehensive pipeline assembled and optimized in-house as described below.
Genome_build: Human reference (GRCh38)
Supplementary_files_format_and_content: mtx, genes, barcode

source_name: Lung BAL cells

extract_protocol:
Cryopreserved lung transplant recipient BAL cells were sorted for viable cells
Single-cell suspensions were loaded onto 10X Genomics Single Cell 3′ Chips along with the RT mastermix as per the manufacturer’s protocol for the Chromium Single Cell 3′ Library (v2, PN-120233; 10X Genomics), to generate single-cell gel beads in emulsion.
Sequencing libraries were generated with unique sample indices for each sample. Libraries for samples 1–3 and 4–5 were multiplexed respectively and sequenced on an Illumina NextSeq 500 (NextSeq control software v2.0.2/ Real Time Analysis v2.4.11) using a 150-cycle NextSeq 500/550 High Output Reagent Kit v2 (FC-404-2002; Illumina) in stand-alone mode as follows: 98 bp (read 1), 14 bp (I7 index), 8 bp (I5 index), and 485 10 bp (read 2).

value: BAL cells


title: Genomic DNA from umbilical cord blood buffycoat 15

description:
U20
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 15

value: Female

value: No GDM


title: Genomic DNA from umbilical cord blood buffycoat 16

description:
U22
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 16


title: LIVER-PM1


title: Genomic DNA from umbilical cord blood buffycoat 13

description:
U18
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 13


title: X14P 42127 3uM 12H; second experiment

description:
second experiment
SY4

source_name: PDGx cell line X14p


title: JX12 DMSO 12H; second experiment

description:
second experiment
SY9


title: Genomic DNA from umbilical cord blood buffycoat 18

description:
U24
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 18


title: non-trasngenic control rep1


title: LIVER-FA4

value: Chow diet


title: JX22P 42127 3uM 12H; second experiment

description:
second experiment
SY2

source_name: PDGx cell line JX22p

value: mesenchymal subtype


title: Genomic DNA from umbilical cord blood buffycoat 14

description:
U19
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 14


title: X14P DMSO 12H; second experiment

description:
second experiment
SY3

value: classic subtype

value: GBM, brain tumor


title: LIVER-FA3


title: JX22P DMSO 12H; second experiment

description:
second experiment
SY1


title: PGD1::OsTZF8 rep2


title: Genomic DNA from umbilical cord blood buffycoat 12

description:
U17
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 12


title: Genomic DNA from umbilical cord blood buffycoat 11

description:
U15
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 11

value: Male


title: LIVER-FA2


title: JX12 42127 3uM 12H; first experiment

description:
first experiment
BN10

source_name: PDGx cell line JX12

value: treated with SRI-42127,  3 uM


title: LIVER-PM2


title: JX12 DMSO 12H; first experiment

description:
first experiment
BN9

value: treated with DMSO, 0.012%


title: Genomic DNA from umbilical cord blood buffycoat 9

description:
U12
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 9

value: Umbilical cord blood buffy coat


title: LIVER-FA1


title: LIVER-HFD4

value: High-fat diet


title: LIVER-HFD3

value: Liver


title: X1524 42127 3uM 12H; first experiment

description:
first experiment
BN8

source_name: PDGx cell line X1524

value: proneural subtype


title: Genomic DNA from umbilical cord blood buffycoat 8

description:
U10
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 8


title: X1524 DMSO 12H; first experiment

description:
first experiment
BN7


title: Case3

type: RNA

city: Urumqi

first: Shasha

last: Su

state: Xinjiang

address: 116 Huanghe Road, Shayibake

department: Department of Diestive

country: China

institute: Traditional Chinese Medicine Hospital Affiliated to Xinjiang Miedcal University

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: The software Agilent feature extraction (v10.7) was used to analyze the hybrid images and extract the data.Then, the data were normalized and analyzed by Agilent genespring

source_name: ascending colon

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

tag: disease state

value: ulcerative colitis

tag: age

value: ascending colon


title: LIVER-HFD2

source_name: Liver


title: Genomic DNA from umbilical cord blood buffycoat 7

description:
U9
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 7


title: Genomic DNA from umbilical cord blood buffycoat 6

description:
U8
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 6


title: XD456 42127 3uM 12H; first experiment

description:
first experiment
BN6

source_name: PDGx cell line XD456


title: Control1

source_name: sigmoid colon

value: healthy

value: sigmoid colon


title: Sample_1201_S24100_5: saracatinib2_RNAseq

city: Los Angeles

first: Jessica

middle: Erin

last: Rexach

state: CA

address: 2506 Gonda Bldg, 695 Charles E. Young Dr. South

institute: UCLA

data_processing:
STAR 2.4.2a alignment + mapping to genome + quantification
filter genes without an assigned ensembl gene identifier
cqn 1.32.0 normalization using transcript lengths from biomaRt, with lengthMethod = "smooth"
batch correction using ComBat from sva (3.6.0)
Genome_build: GRCm38, GencodeM10
Supplementary_files_format_and_content: matrix of gene name x sample counts data in csv format

growth_protocol: Mouse primary embryonic microglial cultures were prepared from P1 C57BL/6J pups as previously described (Saura et al., 2003) and cultured in DMEM-F12 supplemented with 2% heat inactivated FBS, penicillin/streptomycin (100 U/mL) and beta-mercaptoethanol (50 microM) for 24 hours prior to drug treatment.

extract_protocol:
RNA was isolated from primary mouse microglia using NucleoSpin RNA Plus (Takara)
Lexogen QuantSeq 3' Forward kit

treatment_protocol: Saracatinib was purchased from Selleckchem.  Primary microglia were treated with saracatinib  (1μM, 24h) or corresponding DMSO vehicle control as indicated.

value: primary microglia culture

tag: treatment time (hours)

tag: batch


title: Sample_1201_S24100_4: saracatinib2_RNAseq

tag: treatment


title: LIVER-HFD1


title: XD456 DMSO 12H; first experiment

description:
first experiment
BN5


title: Case1

source_name: rectum

value: Female

value: rectum


title: HYPO-PM3

source_name: Hypothalamus

value: Hypothalamus

value: Chow diet, PM exposure


title: Genomic DNA from umbilical cord blood buffycoat 5

description:
U5
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 5

value: GDM


title: HYPO-PM2


title: Control2

value: Male


title: Sample_1201_S24100_2: saracatinib2_RNAseq


title: Genomic DNA from umbilical cord blood buffycoat 3

description:
U3
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 3


title: Sample_1201_S24100_1: saracatinib2_RNAseq


title: Sample_1201_S24100_3: saracatinib2_RNAseq


title: Genomic DNA from umbilical cord blood buffycoat 4

description:
U4
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 4

value: No GDM


title: HYPO-PM1


title: JX22P 42127 3uM 12H; first experiment

description:
first experiment
BN2

source_name: PDGx cell line JX22p

value: mesenchymal subtype

value: GBM, brain tumor

value: treated with SRI-42127,  3 uM


title: X14P 42127 3uM 12H; first experiment

description:
first experiment
BN4

source_name: PDGx cell line X14p

value: classic subtype


title: X14P DMSO 12H; first experiment

description:
first experiment
BN3

value: treated with DMSO, 0.012%


title: Genomic DNA from umbilical cord blood buffycoat 10

description:
U13
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 10

value: Umbilical cord blood buffy coat


title: Sample_1201_CS_5: control2_RNAseq


title: Control3

value: ascending colon


title: JX22P DMSO 12H; first experiment

description:
first experiment
BN1


title: Case2

value: ulcerative colitis


title: Genomic DNA from umbilical cord blood buffycoat 2

description:
U2
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 2


title: Sample_1201_CS_4: control2_RNAseq


title: Genomic DNA from umbilical cord blood buffycoat 1

description:
U1
Umbilical cord blood sample

source_name: umbilical cord blood buffy coat 1


title: HYPO-FA3

value: Chow diet


title: HYPO-FA2


title: Sample_1201_CS_3: control2_RNAseq

value: primary microglia culture


title: TSS-seq: spt6-YW, 37C 2

description:
full genotype name:
MATα spt6-YW lys2-128δ ura3-52 leu2Δ1 [pRS316]
TSS-seq library from an spt6-YW strain shifted to 37°C for 80 minutes.

data_processing:
Library strategy: TSS-seq
Removal of adapter sequences and random hexamer sequences from the 3′ end of the read and 3′ quality trimming were performed using cutadapt (Martin, 2011). The random hexamer molecular barcode on the 5′ end of the read was then removed and processed using a Python script. Reads were aligned to the combined S. cerevisiae and S. pombe reference genomes using Tophat2 (Kim et al., 2013) without a reference transcriptome, and uniquely mapping alignments were selected using SAMtools (Li et al., 2009). Alignments mapping to the same location as another alignment with the same molecular barcode were identified as PCR duplicates and removed using a Python script. Coverage of the 5′-most base, corresponding to the TSS, was extracted using bedtools genomecov (Quinlan and Hall, 2010). Due to high variability in the proportion of S. pombe spike-in alignments among the libraries for certain conditions, coverage was normalized to the total number of alignments uniquely mapping to the S. cerevisiae genome. The quality of raw, cleaned, non-aligning, and uniquely aligning non-duplicate reads was assessed using FastQC (Andrews, 2014).
Genome_build: S. cerevisiae R64-2-1, S. pombe ASM294v2
Supplementary_files_format_and_content: BigWigs of library-size normalized coverage for each strand.

extract_protocol:
DOI: 10.1016/j.molcel.2018.09.005
Total RNA was isolated as previously described (Ausubel, 1991). Poly(A)-enriched RNA was isolated from 300g of total RNA with 300L of Dynabeads oligo(dT)25, using the manufacturers instructions and eluting in water.

tag: genotype

value: polyA RNA


title: HYPO-FA1


title: Sample_1201_CS_2: control2_RNAseq


title: HYPO-HFD4

value: High-fat diet


title: IACSF02

city: la jolla

first: vipul

last: bhargava

address: 9500 gilman drive

institute: ucsd

data_processing:
Raw read quality was evaluated using FastQC. Reads were trimmed for adaptors and sequence quality. Trimmed reads were aligned to human Build 37.3 reference genome using Omicsoft sequence aligner (OSA4). Aligned reads were quantified using EM algorithm with RefSeq transcriptome model accessed on June 6, 2017. Aligned data were evaluated for quality using several quality metrics (e.g. mapping rate, coverage) and visually inspected for samples deviating from the population across multiple metrics and PCA.
Statistical analysis of RNA-seq data was performed in R version 3.3.1 with the limma package version 3.28.14. Limma Voom package was used to normalize and identify DEG from counts data. Transcripts with zero counts in more than two-thirds of the samples were discarded from downstream analysis to reduce noise in the expression data. Gene counts were converted to log2 counts per million (cpm), quantile normalized, and precision weighted. RNA-seq gene features were considered differentially expressed if they satisfied a 2-fold change and FDR <0.05 cut off.

source_name: CD1c+ cells from synovial fluid

extract_protocol:
Total RNA was extracted from CD1c+ DC RA synovial fluid and RA peripheral blood and the quality of all RNA samples evaluated using an Agilent Bioanalyzer.
RNA samples were reverse transcribed, and sequencing libraries were constructed using NuGen Ovation Universal RNA-Seq System (catalogue 0402-A01) according to the manufacturer’s protocol. The resulting sequencing libraries were analyzed using the Caliper LabChip GX and quantified using KAPA qPCR. Libraries were then normalized and pooled in 1 batch of 6 and 1 batch of 5. Each pool was clustered and sequenced on an Illumina NextSeq500 instrument using 2 × 100 bp paired-end reads, following the manufacturer’s protocols.

value: CD1c+ cells from synovial fluid

value: Rheumatoid Arthritis Patient5


title: Sample_1201_CS_1: control2_RNAseq


title: HYPO-FA4

value: Hypothalamus


title: IAC03

source_name: CD1c+ cells from PBMCs

value: CD1c+ cells from PBMCs

value: Rheumatoid Arthritis Patient3


title: HYPO-HFD3


title: Sample_1114_S241_5: saracatinib1_RNAseq


title: IAC02

value: Rheumatoid Arthritis Patient2


title: IACSF01

value: Rheumatoid Arthritis Patient4


title: TSS-seq: spt6-YW, 30C 2

description:
full genotype name:
MATα spt6-YW lys2-128δ ura3-52 leu2Δ1 [pRS316]
TSS-seq library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: TSS-seq: spt6-YW, 37C 1

source_name: TSS-seq library from an spt6-YW strain shifted to 37°C for 80 minutes.


title: TSS-seq: spt6-YW, 30C 1

source_name: TSS-seq library from an spt6-YW strain shifted to 30°C for 80 minutes.


title: HYPO-HFD2


title: TSS-seq: spt6-1004, 37C 2

description:
full genotype name:
MATα spt6-1004 lys2-128δ ura3-52 leu2Δ1
TSS-seq library from an spt6-1004 strain shifted to 37°C for 80 minutes.


title: HYPO-HFD1


title: Sample_1114_S241_4: saracatinib1_RNAseq


title: Sample_1114_S241_3: saracatinib1_RNAseq


title: IAC01

value: Rheumatoid Arthritis Patient1


title: HCC02

value: Healthy Volunteer 2


title: HCC03

value: Healthy Volunteer 3


title: Sample_1114_S241_1: saracatinib1_RNAseq


title: IACSF03

value: Rheumatoid Arthritis Patient6


title: BAT-PM2

source_name: Brown adipose tissue

value: Brown adipose tissue

value: Chow diet, PM exposure


title: Sample_1114_S241_2: saracatinib1_RNAseq


title: TSS-seq: spt6-1004, 30C 1

description:
full genotype name:
MATα spt6-1004 lys2-128δ ura3-52 leu2Δ1
TSS-seq library from an spt6-1004 strain shifted to 30°C for 80 minutes.


title: HCC01

value: Healthy Volunteer 1


title: TSS-seq: spt6-1004, 30C 2

source_name: TSS-seq library from an spt6-1004 strain shifted to 30°C for 80 minutes.


title: TSS-seq: wild type, 37C 2

description:
full genotype name:
MATα lys2-128δ ura3-52 leu2Δ1
TSS-seq library from a wild type strain shifted to 37°C for 80 minutes.

value: wild type


title: KO_P

description:
Analysis of STAU1-binding to APA
fractionation.cluster.all.reads.csv

data_processing:
Library strategy: ribosome profiling
Sequenced reads were trimmed for adaptor sequence, and filtered out low-quality sequence using Cutadaptor
Sequenced reads were masked for 5'-Ts then mapped to hg19 whole genome using STAR. Reads with a mapping quality score (MAPQ) of ≥10 were kept for further analysis.
Reads with ≥2 non-genomic 5'-Ts after alignment were called polyA site supporting (PASS) reads.
pAs within 24 nt from one another were clustered as previously described (Hoque et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: csv files include all cluster sites with count values for each Sample.

source_name: Embryonic kidney

extract_protocol:
RNA was extracted using phenol/chloroform and precipitated using ethanol.
The 3'READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 1 µg of total-cell RNA was captured using 10 µl of oligo(dT)25 magnetic beads (NEB) in 100 µl of 1x Binding Buffer (10 mM Tris-Cl pH 7.5, 150 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20) and fragmented on the beads using 1.5 U of RNase III (NEB) in 30 µl of RNase III Buffer (10 mM Tris-Cl pH 8.3, 60 mM NaCl, 10 mM MgCl2, and 1 mM DTT) for 15 min at 37 °C. After washing away unbound RNA fragments using Binding Buffer, polyA+ fragments were eluted from the beads using TE Buffer (10 mM Tris-Cl, 1 mM EDTA, pH 7.5) and precipitated using ethanol, followed by ligation to 3 pmol of heat-denatured 5'-adapter (5'-CCUUGGCACCCGAGAAUUCCANNNN-3') in the presence of 1 mM ATP, 0.1 µl of SuperaseIn (ThermoFisher Scientific), and 0.25 µl of T4 RNA ligase 1 in a 5 µl reaction at 22 °C for 1 hr. Ligation products were captured using 10 pmol of biotin-T15-(+TT)5 attached to 12 µl of Dynabeads MyOne Streptavidin C1 (ThermoFisher Scientific). After washing with Washing Buffer (10 mM Tris-Cl pH 7.5, 1 mM NaCl, 1 mM EDTA, and 0.05% TWEEN 20), RNA fragments on the beads were incubated with 0.01 U/µl of RNase H (Epicentre) for 30 min at 37 °C in 30 µl of RNase H buffer (50 mM Tris-Cl pH 7.5, 5 mM NaCl, 10 mM MgCl2, and 10 mM DTT). After washing with RNase H Buffer, RNA fragments were eluted from the beads in Elution Buffer (1 mM NaCl, 1 mM EDTA pH7.5, and 0.05% TWEEN 20) at 50 °C, precipitated using ethanol, and then ligated to 3 pmol of heat-denatured 5'-adenylated 3'-adapter (5'-rApp/NNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC-3') using 0.25 µl of T4 RNA ligase 2 (truncated KQ version) for 1 hr at 22 °C in a 5 µl reaction containing 15% PEG 8000 and 0.2 µl of SuperaseIn. Ligation products were precipitated and reverse-transcribed using M-MLV reverse transcriptase, and PCR-amplified using Phusion high-fidelity DNA polymerase (NEB) and bar-coded PCR primers (Sigma-Aldrich) for 15 cycles.

tag: sample treatment

value: STAU1-KO polysome

tag: protocol

tag: rna fraction

value: Polysome Poly(A)+ RNA


title: WT_P

value: WT polysome

value: Wild-type


title: Sample_1114_C24_5: control1_RNAseq

value: primary microglia culture

tag: strain


title: Sample_1114_C24_3: control1_RNAseq


title: BAT-FA3

tag: tissue

value: Chow diet


title: Sample_1114_C24_4: control1_RNAseq


title: KO_C

data_processing:
Sequenced reads were trimmed for adaptor sequence, and filtered out low-quality sequence using Cutadaptor
Sequenced reads were masked for 5'-Ts then mapped to hg19 whole genome using STAR. Reads with a mapping quality score (MAPQ) of ≥10 were kept for further analysis.
Reads with ≥2 non-genomic 5'-Ts after alignment were called polyA site supporting (PASS) reads.
pAs within 24 nt from one another were clustered as previously described (Hoque et al., 2013).
Genome_build: hg19
Supplementary_files_format_and_content: csv files include all cluster sites with count values for each Sample.

tag: cell line

value: STAU1-KO cytoplasm

value: Cytoplasmic Poly(A)+ RNA


title: TSS-seq: wild type, 30C 1

description:
full genotype name:
MATα lys2-128δ ura3-52 leu2Δ1
TSS-seq library from a wild type strain shifted to 30°C for 80 minutes.

tag: rna population

value: polyA RNA


title: TSS-seq: wild type, 37C 1

source_name: TSS-seq library from a wild type strain shifted to 37°C for 80 minutes.


title: WT_C

value: WT cytoplasm


title: TSS-seq: spt6-1004, 37C 1

source_name: TSS-seq library from an spt6-1004 strain shifted to 37°C for 80 minutes.


title: BAT-PM3


title: BAT-HFD2

value: High-fat diet


title: BAT-FA2


title: C6B: control_RNAseq

data_processing:
STAR 2.7.2b alignment + mapping to transcriptome
rsubread 1.34.6 featureCounts gene quantification
filter genes without an assigned ensembl gene identifier
filter genes where 80% of the samples are not > 5
cqn 1.32.0 normalization using transcript lengths from biomaRt, with lengthMethod = "smooth"
Genome_build: GRCm38, GencodeM11
Supplementary_files_format_and_content: matrix of gene name x sample counts data in csv format

treatment_protocol: Fatostatin was purchased from Selleckchem.  Primary microglia were treated with fatotastatin (5μM, 72h)  or corresponding DMSO vehicle control as indicated.

tag: cell type


title: C5B: control_RNAseq


title: BAT-FA1


title: VEH-exposed myometrial progenitor cells

city: AUGUSTA

first: Ayman

last: Al-Hendy

state: Georgia

address: 1120 15th Street

department: Obstetrics and Gynecology

institute: Augusta University

data_processing:
Sequence reads were aligned to the rat reference genome (rn4; version 3.4 by BCM HGSC) using TopHat aligner and aligned read counts were summarized using ShortRead and associated Bioconductor packages.
FastQC was used to ensure overall good quality of data before trimming for further analysis. Read trimming was then performed using BBduk.sh in the BBMap suite. Any reads <20 bp after trimming were discarded. Only Illumina adapters were scanned and trimmed. No Q-scores-based trimming was done as it was not necessary.
rn5 genome build (University of California, Santa Cruz), and annotation files (iGenomes), BBMap aligner indexes were created using the genome.fa file (iGenomes).
Parameters for alignments: maximum indels allowed 100kb, any multi-mapping reads were randomly assigned, and SAM v.1.3 format tags were used in SAM/BAM files. BAM files were then sorted and indexed using Samtools
To estimate expression of genes of interest, featureCounts was used to count reads that map to genomic features, and DESeq2 analysis was completed using the summarized count matrix/gene level
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files and Excel spreadsheet of DES expressions normalized to VEH

organism: Rattus norvegicus

source_name: Myometrial progenitor cells

extract_protocol:
RNeasy RNA isolation kit (Qiagen, Valencia, CA) was used to isolate RNA for RNA-seq analysis. RNA samples were treated with DNase I and the RNA purity and quality was checked by Bioanalyzer prior to cDNA synthesis.
cDNA libraries were constructed using SPRI-works Fragment Library System I (Beckman Coulter, Brea, CA), which were then PCR-enriched and purified. Ten pM DNA was loaded into the paired end flow cell on cBOT for cluster generation and thereafter loaded on the HiSeq2500 platform (Illumina Inc.,San Diego, CA) to generate single 36 bp sequence reads.

value: myometrium

value: VEH-exposed myometrial progenitor cells

tag: passages


title: DES-exposed myometrial progenitor cells

value: DES-exposed myometrial progenitor cells


title: BAT-PM1

value: Brown adipose tissue

value: Chow diet, PM exposure


title: dmeros1_VN

city: Lyon

first: Daniel

last: Bouyer

address: 46 Allée d'Italie

department: ENS-Lyon/RDP

country: France

institute: CNRS

data_processing:
Reads were preprocessed with Trimmomatic to remove adaptors, and Bismark was used to map filtered reads to the Arabidopsis TAIR10 genome reference, in order to calculate methylation at each individual cytosine
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files containing the cytosine methylation level for each sample and each context (CG; CHG and CHH) seperately

organism: Arabidopsis thaliana

source_name: pollen vegetative cell

growth_protocol: plants were grown at 23°C with 16h light/ 8h dark

extract_protocol:
Pollen nuclei of wild-type (Col-0) and mutant dme/+, ros1 and dme/+,ros1 plants were purified by FACS using SYBR Green staining. open flowers were collected into a 50 ml falcon tubes, and vortexed in 10 ml of Galbraith buffer (45 mM MgCl2, 30 mM Sodium Citrate, 20 mM MOPS, 1% Triton-100, pH to 7.0) for 3 minutes, at room temperature. This crude fraction was then filtered through Miracloth (Calbiochem) and centrifuged for 1 minute at 2600 g to concentrate the pollen fraction. The pollen was then transferred to a 1.5 ml eppendorf tube containing approximately 100 μl of acid-washed glass beads (425–600 μm, Sigma), and vortexed continuously at maximum speed for 3 minutes in order to break the pollen cell wall. The fraction containing the released nuclei was then filtered through a 10μm mesh (Celltrics, Sysmex-Partec) to exclude pollen debris, and stained with SYBR Green dye (Lonza). FACS was performed using a FACSAria IIU cell sorter (BD Biosciences), with 70µ nozzle at 70psi. A 488-nm laser was used for SYBR Green excitation, which was detected by a 530/30 nm band-pass filter. Approximately 500,000 nuclei from each cell type were purified, and genomic DNA was extracted using the Masterpure kit (Epicenter).
Genomic DNA was fragmented by Covaris to approximately 300bp, and fragments were end-repaired, A-tailed, and ligated to methylated Illumina adaptors (Bioo Scientific). Ligated fragments were bisulfite treated with the EZ DNA Methylation-Gold Kit (Zymo) and PCR-enriched with KAPA high-fidelity Uracil+ polymerase (Roche).

tag: ecotype background

tag: genotype/variation

value: dme/+;ros1 mutant

value: pollen

value: vegetative cell

tag: molecule subtype

value: bisulfite-converted DNA


title: dmeros1_SC

source_name: sperm cell

value: sperm cell


title: dme_VN

value: dme/+ mutant


title: TSS-seq: wild type, 30C 2

source_name: TSS-seq library from a wild type strain shifted to 30°C for 80 minutes.

value: wild type


title: C3B: control_RNAseq

value: primary microglia culture


title: dme_SC


title: C4B: control_RNAseq


title: Sample_1114_C24_2: control1_RNAseq


title: scRNA_MEF_batch10

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description:
barcodes_and_annotations.xlsx.gz
MEF_to_XEN_countMatrix.csv.gz

data_processing:
Single-cell data were cleaned up to remove cells in which a few kinds of spike-in RNA were detected and then normalized with the R package RUVSeq to remove batch effects. The mean value and dispersion were considered when variable genes were picked up for principal component analysis and t-distributed stochastic neighbor embedding. The transcriptional factor gene correlation network was constructed by calculating the correlations between gene pairs, and only edges with correlations less than –0.4 (negatively correlated) or greater than 0.4 (positively regulated) were retained.
Genome_build: mm9
Supplementary_files_format_and_content: MEF_to_XEN_countMatrix.csv.gz: comma-delimited text file of count matrix ; barcodes_and_annotations.xlsx.gz: Excel data file including sequences of barcodes used in scRNA-seq and annotations of cells.

source_name: Chemically-induced mouse embryonic fibroblasts

growth_protocol: MEFs were cultured with high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% GlutaMAX, 1% nonessential amino-acids (NEAAs), 0.055 mM 2-mercaptoethanol, and 1% penicillin-streptomycin.

extract_protocol: Individual cell was manually picked after digestion, lysed and subjected to cDNA synthesis. Single-cell cDNA was then amplified and fragmented as published steps. The sequencing library was constructed and sequenced with paired-end 150-bp reads on an Illumina HiSeq X-Ten platform. Raw reads were firstly separated by cell barcodes, then trimmed, and aligned to the mm9 mouse transcriptome and de-duplicated by UMIs information as described previously.

treatment_protocol:
For XEN induction, the medium was changed to
XEN reprogramming medium the next day, and it was changed every 4 days for 12 days.


title: scRNA_MEF_batch9


title: BAT-HFD3


title: Sample_1114_C24_1: control1_RNAseq


title: ros1_VN

value: ros1 mutant


title: scRNA_MEF_batch8


title: C2B: control_RNAseq


title: Control_2

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

data_processing:
Basecalls performed using CASAVA version 1.8, FASTQ files are generated using the appropriate bcl2fastq software (Illumina Inc.)
Tophat aligns the sequencing reads to the rat reference genome using the sequence aligner Bowtie2
Cufflinks takes the alignment results from Tophat to assemble the aligned sequences into transcripts, constructing a map or a snapshot of the transcriptome.
The Cufflinks assembles aligned reads into different transcript isoforms based on exon usage and also determines the transcriptional start sites (TSSs).
Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output.
Genome_build: Ensembl (Rattus norvegicus)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

source_name: Control undifferentiated MSCs (Untreated), Replicate 2

growth_protocol: Group A and Group B MSCs-derived NPCs were maintained in their respective microenvironment for 3 days prior to RNA extraction.

extract_protocol:
Total RNA of each sample was extracted using miRNeasy mini kit (Qiagen) according to manufacturer's protocol. Starting material (300 ng) of total RNA was used the construction of sequencing library.
The library preparation was done using TruSeq® Stranded mRNA Sample preparation kit (Illumina Inc).

value: bone marrow

tag: passage

value: Passage 3

value: Untreated

value: Mesenchymal stem cell


title: Group B_3

source_name: Group B MSCs-derived NPCs (EGF+bFGF+IGF1), Replicate 3


title: scRNA_MEF_batch7


title: C1B: control_RNAseq

tag: treatment time (hours)


title: ros1_SC


title: Group B_2

source_name: Group B MSCs-derived NPCs (EGF+bFGF+IGF1), Replicate 2


title: BAT-HFD1

data_processing:
cutadapt
STAR alignment
featureCount, gene-level extraction
Genome_build: mm10

value: High-fat diet


title: Control_3

source_name: Control undifferentiated MSCs (Untreated), Replicate 3


title: scRNA_MEF_batch6


title: Col_VN


title: F5B: fatostatin_RNAseq


title: Group B_1

source_name: Group B MSCs-derived NPCs (EGF+bFGF+IGF1), Replicate 1


title: Col_SC


title: F4B: fatostatin_RNAseq


title: Group A_3

source_name: Group A MSCs-derived NPCs (EGF+bFGF), Replicate 3

value: EGF+bFGF


title: Control_1

source_name: Control undifferentiated MSCs (Untreated), Replicate 1


title: scRNA_MEF_batch4


title: F3B: fatostatin_RNAseq


title: F2B: fatostatin_RNAseq


title: Old (9 months old) oocytes - rep 2

city: Tzur Hadassa

first: Michael

last: Klutstein

state: Other

address: Yasmin 273 Tzur Hadassa

department: Institute of Dental Sciences

institute: Hebrew University

description: small RNAs

data_processing:
The first 3 bases of R1 reads were discarded (positions for template switching), the reads were quality-trimmed at both ends, poly-G sequences (NextSeq’s no signal), adapter sequences, and poly-A sequences were removed from the 3' end, and finally low quality reads were filtered out. Paired-end libraries were similarly processed for R2 and re-paired by read name after trimming and filtering was done. Trimming adapters and other technical bases was done with cutadapt, v2.10, and parameters -O 1, --match-read-wildcards and -m 15. Quality filtering was performed using the fastq_quality_filter program of the FASTX package, v0.0.14, with parameters -q 20 and -p 90.
Processed reads were aligned with TopHat, v2.1.1, using parameters -G genes_extended.gtf, --read-gap-length 5, --read-realign-edit-dist 1, --no-coverage-search, -g 1000, --library-type fr-secondstrand, for both single-end and paired-end libraries, and -N 2, --read-edit-dist 7, --segment-length 18, for paired-end libraries, or -N 5, --read-edit-dist 10, --segment-length 23, for single-end libraries. All libraries were aligned to the mouse genome GRCm38, supplemented with the 45S pre-rRNA (NR_046233.2), and annotations from Ensembl release 99 with additional annotations for rRNA, tRNAs (from tRNAscan) and repeat sequences (from UCSC genome browser rmsk table).
Raw counts were obtained with htseq-count, v0.12.4, with -s 'yes' and -a 0, counting all primary alignments. The annotations file was based on the Ensembl release 99 annotations, but was modified: all 5S rRNA genomic locations were treated as one gene, tRNAs (from tRNAscan predictions) were counted according to the tRNA type, and repeats (from the rmsk table) were counted by their name.
Normalization and differential expression analysis were done with the DESeq2 package, v1.22.2, using default parameters (except setting independentFiltering to FALSE), after removing genes with a sum of counts less than 10 over all samples. The model included both a batch factor, for single-end or paired-end sequencing, and the age factor.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with a header row and a row for each gene. Columns A-I, general gene details, multiple values are separated with ';'. Columns J-M, raw counts. Columns N-Q, normalized counts. Column R, the baseMean value. Columns S-W, the results of comparing old vs. yound samples. A '?' denotes missing value.

source_name: pool of 50 oocytes

growth_protocol: Ovaries were collected and dissected in M2 medium (M7167). GV oocytes were collected under a binocular using a Stripper and washed in hyaluronidase (H4272-30MG) to remove granulosa cells and acidic Tyrode's Solution (T1788) to remove the Zona Pellucida.

extract_protocol:
RNA extraction was done according to the TRIzol reagent user guide, into  10 ul of nuclease-free water.
Amplification was performed using the SMARTer® smRNA-Seq Kit for Illumina®-12 Rxns, TAKARA 635029.

value: oocyte

tag: age

value: 9 months


title: Group A_2

source_name: Group A MSCs-derived NPCs (EGF+bFGF), Replicate 2

tag: treatment


title: Old (9 months old) oocytes - rep 1

description: small RNAs


title: scRNA_MEF_batch3


title: Group A_1

source_name: Group A MSCs-derived NPCs (EGF+bFGF), Replicate 1


title: scRNA_MEF_batch2


title: Young (8 weeks old) oocytes -rep 2

description: small RNAs

value: 8 weeks


title: WT mESCs - RCOR2 ChIP-seq negative control rep2

city: Clayton

first: Monika

last: Mohenska

state: VIC

address: 15 Innovation Walk

institute: Monash University

data_processing:
TINC-seq data processing:    Raw FASTQ files were quality trimmed with Trimmomatic v0.36, parameters SE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to a GENCODE’s GRCm38 with default parameters. Following this, sambamba was used to convert the mapped .sam files into .bam files. The .bam files which were then sorted and indexed with sambamba using default parameters. Unlike conventional DNA-pull down techniques such as ChIP or genome wide sequencing experiments, TINC-seq targets a very small fraction of the genome (in theory only one region). Due to the low input fraction and the fact that mostly similar sequences should be pulled down, the method is prone to more noise than experiments which include a vast proportion of the genome. For this reason reads were then quality filtered for blacklisted regions as well as repeat masker regions. Peak calling was then performed with macs2 v2.1.1.20160309 on pooled (by macs2) TALE1 or TALE2 replicates over the input, with the --no-model parameter, reads of MAPQ>10 were considered, and a FDR cut-off of 0.01 was applied. HOMER’s (v3.2) mergePeaks function was applied to calculated overlapping peaks with the parameter -d given. Motif enrichment analysis was performed on peaks called for each TALE sample with meme v5.0.1. The bedtools2 v2.25.0, function getfasta was used to convert the enriched peak regions of each TALE into fasta files. These were then utilised for the motif enrichment analysis with the parameters -dna -revcomp -minw 8 -maxw18.
ChIP-seq data processing:    Data was first quality trimmed with Trimmomatic v0.36 (Bolger, Lohse, and Usadel 2014) with the parameters SE (single-end) or PE (paired-end) -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTtQ files were then mapped to a customized GENCODE’s GRCm38, which included the RCOR2-HA, and mCherry ORF sequences (Rcor2 (C-3xHA-tag; VectorBuilder), mCherry (ORF:IRES:mCherry:T2A:puromycin)) with Bowtie2 v2.3.4.1, with default mapping parameters. Sambamba was used to convert mapped .sam files into .bam files, then sort and index them with default parameters. Reads were then quality filtered for blacklisted regions, and reads with MAPQ>10 were retained using samtools v1.8 and GNU parallel. This was followed by peak calls macs2 v2.1.1.20160309, using the parameters --keep-dup 1 -g 1.87e9. Biological replicates of samples and negative controls were pooled with  macs2, and then using HOMER’s mergePeak function, peaks within 700bp of their peak centre were merged. HOMER’s mergePeak function was then used to determine all variations of co-occupancy between RCOR2 and published (OCT4, SOX2, NANOG, LSD1, NuRD complex, REST/CoREST complex and ESC enhancers) data sets using the parameter -d dist, followed by genomic annotation of all regions using HOMER’s annotatePeaks.pl function (default parameters). This provided the final RCOR2 ChIP-seq peak set.
ATAC-seq data processing:    Data was first quality trimmed with Trimmomatic v0.36, with the parameters PE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to GENCODE’s GRCm38 with Bowtie2 v2.3.4.1, with default mapping parameters. Sambamba was used to convert mapped .sam files into .bam files, and then sort and index them with default parameters. Reads were then quality filtered for blacklisted regions, and reads with MAPQ>10 were retained using samtools v1.8 and GNU parallel. No peak calling was required for the study.
RNA-seq data processing:    Raw RNA-seq reads in the form of FASTQ format were demultiplexed with sabre using parameters pe -c -u -m 1 -l 8 -n -a 1, for the multiplexing indexes. Trimmomatic v0.36 was ised for quality trimming, with the parameters SE -phred 33 SLIDINGWINDOW:3:15 MINLEN:36. FASTQ files were then mapped to a customized GENCODE’s GRCm38, which included the RCOR2-HA, and mCherry ORF sequences (Rcor2 (C-3xHA-tag; VectorBuilder), mCherry (ORF:IRES:mCherry:T2A:puromycin)), with STAR v2.5.2b, using the parameters --outSAMattributes All --alignIntronMax 1000000 --alignEndsType EndToEnd, samples were sorted with Sambamba, and default parameters. Read counts were then generated with Subread’s featureCount function, using default parameters.
bigWig files were generated using deeptools2. Library size normalised (CPM) BigWig files were generated for all samples with parameters -bs 1 --minMappingQuality 10 --exactsScaling --ignoreDuplicates. For TINC-seq and ChIP-seq samples, the step was followed by generation of mean BigWig samples between the replicates and removal of the input sample (TINC-seq) or negative control (ChIP-seq). The parameters used were --scaleFactors 1:1 -bs 1.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; raw counts

growth_protocol: ESCs were cultured in gelatin coated dishes at 37°C, 5%  CO2 in ESC media (KnockOutTM DMEM (Life Technologies) containing 15% Fetal Bovine Serum (Thermo Scientific), GlutaMAX Supplement, MEM Non-Essential Amino Acids Solution , Penicillin-Streptomycin, 0.1% (v/v) 2-Mercaptoethanol, 1000 U/mL Leukemia Inhibitory Factor, and 2i (1mM PD0325901 (StemMACS) and 3mM CHIR99021 (StemMACS)).

extract_protocol:
Approximately 30 x 10^6 cells were used per ChIP. The samples were pre-cleared with 100 μL of Pierce Control Agarose Resin (Thermo Fisher Scientific) for 1 h  at 4 °C and immunoprecipitations were performed with 30 μL of Pierce Anti-HA Agarose (Thermo Fisher Scientific) per sample rotating overnight at 4 °C.
Libraries were prepared using the ThruPLEX DNA-seq 12S kit (Rubicon Genomics, Cat#R400429). After limited PCR amplification, libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, Cat#A63880), according to the manufacturer’s recommendations. 75 bp paired end sequencing was performed on an Illumina HiSeq 3000.

tag: strain background

tag: genotype

value: mCherry expressing

value: embryonic stem cells (ESCs)

tag: antibody


title: Young (8 weeks old) oocytes -rep 1

description: small RNAs


title: NET-seq: spt6-YW, 37C 2

city: Boston

first: Fred

last: Winston

address: 77 Avenue Louis Pasteur, Room 239

institute: Harvard Medical School

description:
full genotype name:
MATα RPB3-(FLAG)x3::NatMx spt6-YW ura3-52 his4-912δ lys2-128δ
NET-seq library from an spt6-YW strain shifted to 37°C for 80 minutes.

data_processing:
Library strategy: NET-seq
Removal of adapter sequences from the 3′ end of the read and 3′ quality trimming were performed using cutadapt (Martin, 2011). Reads were aligned to the S. cerevisiae genome using Tophat2 without a reference transcriptome (kim2013), and uniquely mapping alignments were selected using SAMtools (Li et al., 2009). Coverage of the 5′-most base of the read, corresponding to the 3′-most base of the nascent RNA and the active site of elongating RNA polymerase, was extracted using bedtools genomecov (Quinlan and Hall, 2010), and normalized to the total number of uniquely mapping alignments. The quality of raw, cleaned, non-aligning, and uniquely aligning reads was assessed using FastQC (Andrews, 2014).
Genome_build: S. cerevisiae R64-2-1, S. pombe ASM294v2
Supplementary_files_format_and_content: BigWigs of library-size normalized coverage for each strand.

extract_protocol:
DOI: 10.1038/nature09652
RNA was extracted as previously described (Churchman, 2011).

value: nascent RNA