title: 90 Of2-3

description:
90Of3
processed data file/column: 90 AF2-3 (raw-counts.txt)


title: C-TALE_salt_rep2

status: Public on Jul 20 2021

type: SRA

city: Moscow

first: Arkadiy

last: Golov

address: Vavilova, 34/5

country: Russia

institute: Institute of Gene Biology, RAS

library_source: genomic

data_processing:
Standard Illumina Sequencing Pipeline
C-TALE Processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest was embedded, using Bowtie2 v2.3.5. The data were processed using the hiclib pipeline (https://github.com/mirnylab/hiclib-legacy). Statistics for the C-TALE data processing can be found in the table. 10kb-binned HDF5 files were converted to cool format matrices using cooler v0.8.7. Data from three biological replicates for each experimental condition (control and high salt treated chromatin) were merged in two matrices which were then iteratively normalized using publicly available script (https://github.com/Phlya/C-TALE-Normalization) (“--mult_factor 2” option). Weights in a few poorly covered bins were reduced to NA during the normalization procedure; rhdf5 R package was used to manually replace these NA weights with the values of the highest weight found in each matrix.
ChIP-seq processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest (hg19, chr21: 28,981,189-30,260,402) was embedded, using Bowtie2 v2.3.5. Illumina TruSeq adapters were trimmed with cutadapt. Read pairs with at least one non-uniquely mapped read as well as PCR and optical duplicates were filtered using samtools v1.7. Bedtools v2.25.0 and bedGraphToBigWig utility (from UCSC) were used to generate bigwig coverage files. All bigwig files were scaled to 1 mln uniquely mapped read pairs with deeptools v3.4.3. Corresponding input bigwig files were subtracted from each immunoprecipitation bigwig file and then mean profiles were calculated from pairs of biological replicates. Both operations were performed with deeptools v3.4.3.
Genome_build: hg19 (chr21:27,922,688-32,028,897 region)
Supplementary_files_format_and_content: .cool files contain C-TALE contact matrices in an easy to visualize and access format (see https://cooler.readthedocs.io/en/latest/schema.html)
Supplementary_files_format_and_content: bigwig files are binary files containing ChIP-seq profiles in an easy to visualize and access format

molecule: genomic DNA

organism: Homo sapiens

source_name: HeLa cells

growth_protocol: Human HeLa cells were cultured in a DMEM medium supplemented with 10% FBS, 100 U/ml penicillin and 100 U/ml streptomycin at 37°C in 5% CO2 in a humidified atmosphere. For G1 synchronization, cells were treated with 2 mM thymidine for 20 hours, washed twice with DPBS, and released into a complete medium. After 6 h, nocodazole (Sigma) was added (100 ng/ml) for 8 h. Mitotic cells were collected by shake-off and centrifugation. Cells were washed twice with DPBS and released into a fresh complete medium.Mitotic cells were seeded in poly-L-lysine-coated dishes. For coating, dish bottoms were covered with 0.1 mg/mL solution of poly-L-lysine (Sigma, P6282) in DPBS and incubated for 1 h at room temperature; after the solution was discarded dishes were rinsed twice with DPBS and dried for 45 min under the hood. G1 cells were harvested for experiments after 5 h of release from mitotic arrest.

extract_protocol:
C-TALE was performed as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan). For ChIP-seq experiments, fixed chromatin pellets were resuspended in 600 uL of ice cold RIPA buffer supplemented with protease inhibitors. Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 10 30-sec pulses on “15” power setting, separated with 3 min periods of recovery. Input DNA was isolated from 1/10 aliquots of sonicated samples. Sheared chromatin from approximately 1 mln of cells and 1 ug of antibodies (against either CTCF, Smc3, or Rad21) were used in each immunoprecipitation reaction. Chromatin immunoprecipitation was performed as described in Abcam X-ChIP manual (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor modifications. 25 ul of protein A/G magnetic beads (Thermo Scientific, 26162) was used per reaction instead of agarose beads, thus a magnet was used instead of a centrifuge to reclaim beads. Beads were blocked with 1% BSA solution in RIPA overnight, while chromatin was incubated with antibodies. BSA-blocked beads were mixed with antibody-bound chromatin for 6 h. Immunoprecipitated DNA was separated from beads by overnight treatment with proteinase K (Thermo Scientific, EO0491) in PBS supplemented with 1% SDS at 65C. Solution was then cleared from beads with a magnet and DNA was isolated with standard phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries from 3C-seq material, immunoprecipitated DNA and ChIP inputs were generated as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan).

treatment_protocol: G1 synchronized HeLa cells in 10-cm dishes were washed once with PBS and dishes were cooled on ice for several minutes. 5 mL of ice cold isotonic lysis buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2, 1% NP-40, 1x protease inhibitors) were added to each dish, cells were permeabilized for 10 min on ice, then the buffer was removed. 5 mL of either ice cold isotonic buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1x protease inhibitors) or high salt buffer (10 mM Hepes pH 8.0, 500 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1x protease inhibitors) was added to permeabilized cells. Dishes were incubated at 4°C for 30 min. In one series of ChIP-seq experiments incubation time was shortened to 1 min. After the incubation, permeabilized cells  were rinsed three times with 5 mL of ice cold wash buffer (10 mM Hepes pH 8.0, 145 mM NaCl, 1.5 mM MgCl2). Each washing was performed on ice and lasted for 10 min. After the final portion of wash buffer was discarded, chromatin was fixed for 10 min at room temperature with 9 ml of 2% formaldehyde solution in the wash buffer. Fixation was quenched by adding 1 ml of 2 M glycine for 10 min. Fixed chromatin was washed once with PBS and scraped in 7 mL of ice cold Farnham lysis buffer (5 mM Hepes pH 8.0, 85 mM KCl, 0.5% NP-40 ) supplemented with protease inhibitors. Chromatin was collected with centrifugation at 1,000 g for 5 min at 4°C.

tag: cell line

value: HeLa

tag: cell type

value: cervical carcinoma cells

tag: treatment

value: high salt buffer


title: Primary cancer, AMC-17CT-099

city: Seoul

first: Chang Ohk

last: Sung

address: Song-Pa gu,Pung-nap dong

department: Pathology

country: South Korea

institute: Asan Medical Center

description: gene expression

library_source: transcriptomic

data_processing:
Sequenced reads were removed low quality and adapter sequence before analysis. Then th raw RNA-seq data were analyzed using TCGA RNAseq RSEMv2 pipeline.
Mapping by MapSplice v2.2.1 and gene expression estimation after filtering by RSEM v1.3.0, and fixed upper quartile normalization for gene expression.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file include column head with sample name, and row name with gene symbol, and upper quartile normalized log2 values for each sample.

molecule: total RNA

source_name: colorectal cancer

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen).
cDNA library was constructed using the TruSeq RNA Access Library Prep Kit (Illumina)

treatment_protocol: Formalin-fixed paraffin-embedded tissue

tag: cancer site

value: Large intestine

tag: age

tag: tissue

value: colorectal cancer


title: 30 Of2-3

city: IRAPUATO

first: Alfredo

last: Herrera-Estrella

state: GUANAJUATO

address: Km 9.6 Libramiento Norte Carretera Irapuato-León Irapuato

department: LANGEBIO

country: Mexico

institute: CINVESTAV

description:
30Of3
processed data file/column: 30 AF2-3 (DEG-30Of.txt)

data_processing:
RNA sequencing trought the Illumina NextSeq500 platform in the 1x75 single-end mode
Raw RNA-seq data were first processed with FastQC Version 0.11.6  to clean adapter contamination and quality analysis. Around 14 millions of high-quality reads per library were obtained. After quality analysis read were aligned to the T. atroviride IMI 206040 genome (JAEAGS000000000)  using HISAT2 version 2.1.0 . For mapping reads counting to each gene HTseq version 0.14.1  was used
For differential expression analysis, counted reads were processed with Edge R,  only those with at least two counts in at least five libraries were consider as transcribed
To analyze if there exist differences in gene expression between controls, these were fist compared using contrast between the time point control T0 and control T8 using a cutoff of False Discovery Rate <0.05 and <0.005 using glmQLF Test. Replicate number two of the Time C0 was discarded for the noise at moment to performed differential expresion analysis (DE).
Five libraries of control conditions (T0 and T8) were taken as Control condition for contrasts against injury and fungivory libraries. FDR >0.005 was selected to perform the DE analysis, to find those genes that specifically respond in each condition and time point
After DEG analysis, Gene Ontology (GO) enrichment analysis were performed using topGO from package from R  and a cutoff of Fisher test P>0.05 for significant enriched Biological process
The GO terms before plotting were filter for redundancy using REVIGO
Genome_build: T. atroviride IMI 206040 genome (JAEAGS000000000)
Supplementary_files_format_and_content: A matrix teble "raw-counts.txt" including Counts per million (CPM),  of all conditions and replicates. Counts per gene (rows) and condition (columns) are included. A data datriz containing all Diferential expressed genes against  control condition is included in the file (DEG.txt).  ID Genes (rows) and LogFC values (columns).

organism: Trichoderma atroviride

source_name: 30 min after fungivory by O. folsomi

growth_protocol: 1x10^6 fresh conidia of T. atroviride were inoculated in plates with PDA media and sterile cellophane circles, plates were incubated during 36h in dark at 27C. After treatment, fungi were incubated 30, 90 min, 4 and 8 h.

extract_protocol:
After each incubation times, mycelium was collected and frozen using liquid nitrogen. For the RNA extraction TRIZOL method was performed.
Libraries for RNA sequencing were prepared following the Illumina® TruSeq® Stranded Total RNA Sample Preparation kit instructions.

treatment_protocol: Interactions between T. atroviride WT and insects were performed placing the insects on fungus mycelia during 10 minutes in dark. After 10 minutes, insects were immediately carefully withdrawn using a sterile dissection forceps. After fungivory, mycelium was incubated during 30 min, 90 min, 4 h and 8 h. After incubation times, mycelia were collected and frozen using liquid nitrogen. For mechanical injury conditions, mycelium was cut using a sterile scalpel, cuts were performed in all mycelia in the less time possible. After cuts, mycelium was incubated during 30 min, 90 min, 4 h and 8 h. After each incubation times, mycelia were collected and frozen using liquid nitrogen. For control conditions untreated mycelia plates were open for 2 minutes in dark and incubated during 30 min and 8 h

value: mycelia


title: P4_2_R1_RNA

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Using the Kallisto aligner78 v. 0.46, reads were aligned to the hg38 ENSEMBL release 7979 transcripts, with a transcript support level between 1 and 3
Read summation onto genes and differential expression analysis was performed by sleuth v. 0.3080
Differential expression p-values and Bonferroni corrected q-values were calculated using a likelihood ratio test comparing a model containing only participant information (~ Participant) to a model with participant and training status information (~ Participant + Training)
Fold changes were calculated using a Wald-test, as described in the Sleuth manual.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with estimated abundances

source_name: vastus lateralis

extract_protocol:
20-30 mg of human skeletal muscle tissue was used for purification of total RNA. After lysis of muscle tissue in RLT buffer (Qiagen) by the use of a Tissuelyzer II (Qiagen, 30 hertz for 3x30sec), total RNA was purified using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen). The quality of recovered RNA was assessed by the Agilent RNA 6000 Nano Kit (Agilent Technologies) and RNA concentration was determined by spectrophotometry using a NanoDrop 2000 (Thermo Scientific).
For RNA-sequencing, 0.5 microgram of total RNA was depleted of rRNA and subsequently used to generate libraries using the TruSeq standard total RNA with Ribo-Zero Gold kit (Illumina). The PCR cycle number for each library amplification was optimized by running 10% of the library DNA in a real-time PCR reaction using Brilliant III Ultra-fast SYBR Green QPCR Master Mix (AH Diagnostic) and a C1000 Thermal cycler (Bio-Rad)

value: vastus lateralis

tag: participant

tag: training

value: Trained


title: C-TALE_control_rep2

value: isotonic buffer


title: ChIP_input_30min_control_rep1

tag: chip antibody


title: 8h Dm1-1

description:
8Dm1
processed data file/column: 8h AF1-1 (DEG-8hDm.txt)

source_name: 8h after fungivory by D. melanogaster larvae


title: C2C12D_Membrane_Polysome_rep2

city: Philadelphia

first: Bin

last: Tian

state: PA

address: 3601 Spruce Street

department: Program in Gene Expression and Regulation; Center for Systems and Computational Biology

country: USA

institute: Wistar Institute

description:
C2C12D_Membrane_Polysome_rep2
3pREADS_counts_in_pA_sites.txt

data_processing:
Library strategy: 3'READS+
Adpter trimming performed using Cutadapt
3'READs reads were aligned to mm9 using bowtie2
reads with a mapping quality score (MAPQ) ≥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 of each other were clustered.
RNA-seq:  Reads were mapped to the genome using STAR (version 2.5.2) and APAlyzer was used to interrogate APA.
Genome_build: mm9
Supplementary_files_format_and_content: txt files include all cluster sites (chromosome, strand, position) with count values for each sample.
Supplementary_files_format_and_content: RNAseq read counts
Supplementary_files_format_and_content: 3'READS+ clusters with read counts

organism: Mus musculus

source_name: Differentiating C2C12 Cells

extract_protocol:
Phenol/Choloroform
RNAseq libraries: 250 ng of total RNA was used for library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®. 3'READS+ libraries: The READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 0.1 ~ 2.5 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. Both RT primer (5'-GTTCAGAGTTCTACAGTCCGACGATC-3') and PCR primers with indexes have been described previously (Hoque et al., 2013). PCR products were size-selected twice using 0.6 volume of AMPure XP beads (Beckman Coulter) relative to the PCR reaction volume to remove large DNA molecules, followed by an additional 0.4 volume of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The sizes of the libraries eluted from the AMPure beads were examined using a high-sensitivity DNA kit (Agilent) and an Agilent Bioanalyzer. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Equal amounts of libraries were mixed and sequenced using an Illumina NextSeq 500 (1x75 bases).

tag: growth medium

value: DMEM supplemented with 2% horse serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Differentiating

tag: fraction

value: Membrane Polysome


title: 30 Of2-2

description:
30Of2
processed data file/column: 30 AF2-2 (DEG-30Of.txt)


title: C2C12D_Cytosol_Polysome_rep2

description:
C2C12D_Cytosol_Polysome_rep2
3pREADS_counts_in_pA_sites.txt

value: Cytosol Polysome


title: P3_2_R1_RNA


title: 30 Of2-1

description:
30Of1
processed data file/column: 30 AF2-1 (DEG-30Of.txt)


title: C2C12P_Puro30min_Membrane

description:
C2C12P_Puro30min_Membrane
3pREADS_counts_in_pA_sites.txt

source_name: Proliferating C2C12 Cells

extract_protocol:
TRIZol
RNAseq libraries: 250 ng of total RNA was used for library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®. 3'READS+ libraries: The READS+ procedure has been previously described (Zheng et al., 2016). Briefly, polyA+ RNA in 0.1 ~ 2.5 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. Both RT primer (5'-GTTCAGAGTTCTACAGTCCGACGATC-3') and PCR primers with indexes have been described previously (Hoque et al., 2013). PCR products were size-selected twice using 0.6 volume of AMPure XP beads (Beckman Coulter) relative to the PCR reaction volume to remove large DNA molecules, followed by an additional 0.4 volume of beads to remove small DNA molecules. The eluted DNA was selected again with 1 volume of AMPure XP beads to further remove small DNA molecules. The sizes of the libraries eluted from the AMPure beads were examined using a high-sensitivity DNA kit (Agilent) and an Agilent Bioanalyzer. Library concentrations were measured using the Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). Equal amounts of libraries were mixed and sequenced using an Illumina NextSeq 500 (1x75 bases).

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

value: Proliferating

value: 100 microg/ml Puromycin for 30 min

value: Membrane


title: C2C12D_Membrane_Polysome_rep1

description:
C2C12D_Membrane_Polysome_rep1
3pREADS_counts_in_pA_sites.txt


title: 8h Dm1-3

description:
8Dm3
processed data file/column: 8h AF1-3 (DEG-8hDm.txt)


title: P5_1_R1_RNA

value: Untrained


title: C-TALE_control_rep3

value: HeLa

value: cervical carcinoma cells


title: 4h Dm1-2

description:
4Dm2
processed data file/column: 4h AF1-2 (DEG-4hDm.txt)

source_name: 4h after fungivory by D. melanogaster larvae


title: P2_2_R1_RNA


title: MY30

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

institute: University of Illinois Chicago College of Medicine

data_processing:
Image analysis, base calling, and error estimation was performed using Illumina Analysis Pipeline in the HiSeq Control Software version 2.2.38.
Read quality was assessed using FastQC, and adaptor and quality trimming was achieved with Trim Galore using the default settings.
Reads were mapped to the hg38 genome assembly obtained via Illumina iGenomes using TopHat2 version 2.0.14.
Feature counts were generated using samtools version 1.10 and HTseq version 0.11.2.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimted text file of raw (non-normalized) mapped reads.

source_name: Pregnant Myometrium

extract_protocol:
Total RNA was isolated using TRIzol reagent (Life Technologies) according to the instructions of the manufacturer, followed by purification using the RNA Clean-Up and Concentration Kit (Norgen Biotek).
Ribosomal RNA-depleted sequencing libraries were constructed using the TruSeq Stranded Total RNA Sample Prep Kit with Ribo-Zero Gold (Illumina). Sequencing was performed using the Illumina HiSeq 2500 system and HiSeq version 3 sequencing reagents to generate 50 bp single-end reads.

tag: clinical group

value: Group 3 (PTB Intact Mb)

tag: term/preterm

value: Preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: White Non-Hispanic

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Classical

tag: triple i status

value: amniocentesis confirmed Triple I

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

value: Intact, buldging membranes

tag: cesarean indication

value: Breech, protrusion of feet in cervical os

tag: tocolysis (y/n)

value: No

tag: corticosteroids (y/n)

value: Yes

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: P4_1_R1_RNA

tag: tissue

value: vastus lateralis

tag: participant

tag: training


title: 8h Dm1-2

description:
8Dm2
processed data file/column: 8h AF1-2 (DEG-8hDm.txt)

value: mycelia

tag: treatment


title: ChIP_input_30min_salt_rep1

tag: cell line

tag: cell type

tag: chip antibody

value: high salt buffer


title: C2C12P_Puro30min_Cytosol

description:
C2C12P_Puro30min_Cytosol
3pREADS_counts_in_pA_sites.txt

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

value: 100 microg/ml Puromycin for 30 min

tag: fraction

value: Cytosol


title: 90 Dm1-3

description:
90Dm3
processed data file/column: 90 AF1-3 (DEG-90Dm.txt)

source_name: 90 min after fungivory by D. melanogaster larvae


title: P3_1_R1_RNA

value: Untrained


title: C2C12P_Puro60min_Cytosol

description:
C2C12P_Puro60min_Cytosol
3pREADS_counts_in_pA_sites.txt

value: 100 microg/ml Puromycin for 60 min


title: MY27

tag: clinical group

value: Group 3 (PTB Intact Mb)

tag: term/preterm

value: Preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: African American

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

tag: triple i status

tag: uterine contractions preceding cesarean

value: Absent, abdominal pain present

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

value: Footling breech, vaginal bleeding, buldging membranes with protrusion of feet in cervical os


title: C2C12P_Puro0min_Cytosol

description:
C2C12P_Puro0min_Cytosol
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: treatment

value: 100 microg/ml Puromycin for 0 min


title: 4h Dm1-3

description:
4dm3
processed data file/column: 4h AF1-3 (DEG-4hDm.txt)

tag: tissue


title: 4h Dm1-1

description:
4Dm1
processed data file/column: 4h AF1-1 (DEG-4hDm.txt)


title: 90 Dm1-2

description:
90Dm2
processed data file/column: 90 AF1-2 (DEG-90Dm.txt)


title: P1_2_R1_RNA

tag: participant

tag: training

value: Trained


title: C2C12P_Puro60min_Membrane

description:
C2C12P_Puro60min_Membrane
3pREADS_counts_in_pA_sites.txt

tag: growth medium

tag: status

tag: fraction

value: Membrane


title: MY29

tag: clinical group

value: Group 4 (PPROM)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: Classical

value: amniocentesis confirmed Triple I

value: Absent

tag: membrane status at cesarean

value: Ruptured, PPROM managed expectantly

tag: cesarean indication

value: Cord prolapse

tag: tocolysis (y/n)

value: No

tag: corticosteroids (y/n)

value: Yes

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: C2C12D_Cytosol_Polysome_rep1

description:
C2C12D_Cytosol_Polysome_rep1
3pREADS_counts_in_pA_sites.txt

tag: cell line

value: DMEM supplemented with 2% horse serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

value: Differentiating

value: Cytosol Polysome


title: MY28

value: Preterm

value: African American

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

tag: triple i status

tag: uterine contractions preceding cesarean

value: Occasional on TCG, previously regular, weakened after tocolysis

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

value: Ruptured, PTL on tocolysis, PPROM managed expectantly

value: Non-reassuring fetal status, persistent fever


title: MY25

tag: clinical group

tag: term/preterm

tag: maternal age (y)

value: White Non-Hispanic

value: Low transverse

value: clinical chorioamnionitis, suspected Triple I

value: Occasional, previously regular, weakened after tocolysis

value: Acute clinical chorioamnionitis, breech presentation


title: C2C12P_Puro0min_Membrane

description:
C2C12P_Puro0min_Membrane
3pREADS_counts_in_pA_sites.txt

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

tag: treatment

value: 100 microg/ml Puromycin for 0 min

tag: fraction

value: Membrane


title: MY31

value: Group 3 (PTB Intact Mb)

tag: maternal race/ethnicity

value: amniocentesis confirmed Triple I

tag: membrane status at cesarean

value: Intact, buldging membranes

tag: cesarean indication

value: Breech

tag: tocolysis (y/n)

value: Yes

tag: corticosteroids (y/n)

tag: oxytocin (y/n)

value: No

tag: attempted trial of labor (y/n)


title: P2_1_R1_RNA

tag: tissue

value: vastus lateralis

tag: participant

tag: training

value: Untrained


title: P1_1_R1_RNA


title: MY26

tag: clinical group

value: Group 4 (PPROM)

value: Preterm

value: Hispanic

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Classical

tag: triple i status

value: suspected Triple I

tag: uterine contractions preceding cesarean

value: Present, with sudden onset ~1h prior to CS

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

value: Ruptured, PPROM managed expectantly

value: Breech presentation, sudden onset of contractions, fundal tenderness


title: C2C12P_PuroUntreated_Cytosol

description:
C2C12P_PuroUntreated_Cytosol
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

tag: fraction

value: Cytosol


title: C2C12P_PuroUntreated_Membrane

description:
C2C12P_PuroUntreated_Membrane
3pREADS_counts_in_pA_sites.txt

value: Membrane


title: 30 Dm1-3

description:
30dm3
processed data file/column: 30 AF1-3 (DEG-30Dm.txt)

source_name: 30 min after fungivory by D. melanogaster larvae

value: mycelia

tag: treatment


title: P8_2_K4me1

data_processing:
Reads were aligned using the Subread aligner, against a full index of the main chromosomes of the hg38 reference genome, as genomic DNA and keeping only uniquely mapped reads (-t 1 and -u flags set)
Duplicate reads were removed using Picard tools
Peaks were called using MACS2 with input control and a p-value cutoff of 0.05, this was purely to assess the homogeneity of the samples and highlight poor samples (less than 200.000 peaks, or failure to estimate fragment length), no samples were discarded
For each histone modification, a consensus peak set was generated by pooling all samples, the pooled reads were shuffled and split in two (pseudo replicates).
Peaks were called as above on each of these three samples (pool and two pseudo replicates)
a consensus peak list was generated using the irreproducible discovery rate software with the pseudo replicate peak lists as input and the pooled peak list as oracle peak list. A lenient threshold of 0.05 was used.
For each sample, reads were summarized into consensus peaks using featureCounts
Differentially bound peaks were detected in edgeR as described by (Lun, A.T. and G.K. Smyth. Nucleic Acids Res, 2014), using reads along the entire peak and model of the form ~ Condition + Passage
Genome_build: hg38
Supplementary_files_format_and_content: bed file with peaks and csv file with read-counts in those peaks

extract_protocol:
For library preparation and sequencing, 2-7 ng of immunoprecipitated DNA was used to generate adaptor-ligated DNA libraries using the NEBNext Ultra DNA library kit for Illumina (New England Biolabs, E7370L) and indexed multiplex primers for Illumina sequencing (New England Biolabs, E7335). The PCR cycle number for each library amplification was optimized by running 10% of the library DNA in a real-time PCR reaction using Brilliant III Ultra-fast SYBR Green QPCR Master Mix (AH Diagnostic) and a C1000 Thermal cycler (Bio-Rad). DNA libraries were sequenced on a HiSeq2000 by 50‐bp single‐end sequencing at the National High‐Throughput Sequencing Centre (University of Copenhagen, Denmark)
Human skeletal muscle biopsies before or after training (n=8), frozen biopsies (20-40 mg) were thawed on ice and chopped into small pieces (between 1-3 mm3). The tissue was fixated in 0.5% formaldehyde in PBS for 7.5 min at room temperature followed by quenching with glycine (final concentration of 0.125M). The fixated tissue was washed with PBS before resuspension in 1 ml of IP buffer (67mM Tris-HCl (pH 8), 100mM NaCl, 5mM EDTA (pH 8.0), 0.2% NaN3, 0.33% SDS, 1,67% Triton X-100, 0.5 mM phenylmethylsulfonyl fluoride) and homogenization was performed by douncing until the tissue was completely dissociated. Chromatin was sonicated (Diagenode, Biorupter) to an average length of 200-500 bp (between 20 and 30 cycles; high intensity). Before starting the ChIP experiment, chromatin was cleared by centrifugation for 30 min at 20,000g. For each ChIP, chromatin corresponding to 2 μg DNA was combined with 2.5 μg antibody and incubated with rotation at 4 degrees C for 16 hrs. The following antibodies were used for ChIP: H3K27ac (Ab4729 from Abcam), H3K4me1 (Ab8895 from Abcam). Immunoprecipitation was performed by incubation with Protein G Sepharose beads (GE healthcare) for 4 hrs followed by three washes with low-salt buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA (pH 8.0), 1% Triton X-100, 0.1% SDS, 150 mM NaCl) and two washes with high-salt buffer (20 mM Tris-HCl (pH 8.0), 2 mM EDTA (pH 8.0), 1% Triton X-100, 0.1% SDS, 500 mM NaCl). Chromatin was de-crosslinked in 120 μl 1%SDS and 0.1M NaHCO3 for 6hrs at 65 degrees C, and DNA was subsequently purified using Qiagen MinElute PCR purification kit.

tag: tissue

tag: antibody

value: H3K4me1 (Abcam, Ab8895)

value: Trained


title: MY24

value: Group 3 (PTB Intact Mb)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: White Non-Hispanic

value: amniocentesis confirmed Triple I

value: Receded after tocolysis, previously regular with cervical change

tag: membrane status at cesarean

value: Intact

tag: cesarean indication

value: Acute clinical chorioamnionitis, +IAI, breech presentation

tag: tocolysis (y/n)

value: Yes

tag: corticosteroids (y/n)

tag: oxytocin (y/n)

value: No

tag: attempted trial of labor (y/n)


title: MY23

tag: clinical group

value: Group 4 (PPROM)

value: Preterm

value: African American

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Classical

tag: triple i status

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

value: Ruptured, PPROM managed expectantly

value: Cord prolapse


title: 30Dm1-2

description:
30Dm2
processed data file/column: 30AF1-2 (DEG-30Dm.txt)

tag: tissue

value: mycelia

tag: treatment


title: P8_2_K27ac

value: vastus lateralis

tag: antibody

value: H3K27ac (Abcam, Ab4729)

tag: participant

tag: training

value: Trained


title: P8_1_K27ac

value: Untrained


title: 30Dm1-1

description:
30Dm1
processed data file/column: 30AF1-1 (DEG-30Dm.txt)


title: C2C12P_Membrane_Monosome_rep2

description:
C2C12P_Membrane_Monosome_rep2
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

tag: fraction

value: Membrane Monosome


title: MY22

tag: clinical group

value: Group 5 (PTB_Provider_Initiated)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: Hispanic

tag: maternal parity

value: Low transverse

tag: membrane status at cesarean

value: Intact

tag: cesarean indication

value: Severe preeclampsia, worsening maternal condition

tag: tocolysis (y/n)

tag: corticosteroids (y/n)

value: Yes

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: C2C12P_Membrane_Monosome_rep1

description:
C2C12P_Membrane_Monosome_rep1
3pREADS_counts_in_pA_sites.txt


title: P8_1_K4me1

tag: tissue

tag: antibody

value: H3K4me1 (Abcam, Ab8895)

tag: participant


title: 8hMI-3

description:
8D3
processed data file/column: 8hAI-3 (DEG-8hMI.txt)

source_name: 8h after mechanical injury

tag: treatment

value: Injury


title: C2C12P_Cytosol_Monosome_rep1

description:
C2C12P_Cytosol_Monosome_rep1
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

tag: status

value: Cytosol Monosome


title: 90 Dm1-1

description:
90Dm1
processed data file/column: 90 AF1-1 (DEG-90Dm.txt)

value: mycelia


title: 8hMI-2

description:
8D2
processed data file/column: 8hAI-2 (DEG-8hMI.txt)


title: P7_2_K27ac

value: vastus lateralis

tag: training


title: MY20

tag: clinical group

tag: term/preterm

value: Preterm

tag: maternal age (y)

value: African American

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Classical

tag: triple i status

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

value: Eclampsia, emergent CS

value: No


title: C2C12P_Membrane_Polysome_rep2

description:
C2C12P_Membrane_Polysome_rep2
3pREADS_counts_in_pA_sites.txt

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

value: Proliferating

tag: fraction

value: Membrane Polysome


title: MY21

value: Group 5 (PTB_Provider_Initiated)

tag: maternal race/ethnicity

value: Hispanic

tag: maternal parity

value: Low transverse

tag: membrane status at cesarean

value: Intact

tag: cesarean indication

value: Severe preeclampsia, non-reassuring fetal status

tag: tocolysis (y/n)

tag: corticosteroids (y/n)

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: C2C12P_Cytosol_Polysome_rep2

description:
C2C12P_Cytosol_Polysome_rep2
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

tag: status

value: Cytosol Polysome


title: MY19

tag: clinical group

tag: term/preterm

tag: maternal age (y)

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Severe preeclampsia, transverse lie

value: Yes


title: P7_1_K27ac

tag: tissue

value: vastus lateralis

tag: antibody

value: H3K27ac (Abcam, Ab4729)

tag: participant

tag: training

value: Untrained


title: P7_2_K4me1

value: H3K4me1 (Abcam, Ab8895)

value: Trained


title: 4hMI-3

description:
4D3
processed data file/column: 4hAI-3 (DEG-4hMI.txt)

source_name: 4h after mechanical injury

value: mycelia

tag: treatment

value: Injury


title: MY18

value: Preterm

tag: maternal race/ethnicity

value: White Non-Hispanic

tag: maternal parity

tag: triple i status

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

tag: cesarean indication

value: Severe preeclampsia, breech presentation

tag: tocolysis (y/n)

value: No

tag: corticosteroids (y/n)


title: C2C12P_Membrane_Polysome_rep1

description:
C2C12P_Membrane_Polysome_rep1
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

tag: fraction

value: Membrane Polysome


title: 8hMI-1

description:
8D1
processed data file/column: 8hAI-1 (DEG-8hMI.txt)

tag: tissue


title: C2C12P_Cytosol_Polysome_rep1

description:
C2C12P_Cytosol_Polysome_rep1
3pREADS_counts_in_pA_sites.txt

value: Cytosol Polysome


title: P7_1_K4me1

tag: antibody

tag: participant

tag: training


title: C2C12P_Cytosol_Monosome_rep2

description:
C2C12P_Cytosol_Monosome_rep2
3pREADS_counts_in_pA_sites.txt

value: Cytosol Monosome


title: MY17

tag: clinical group

value: Group 5 (PTB_Provider_Initiated)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Low transverse

value: Intact

value: Severe preeclampsia, active genital HSV infection

value: Yes

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: P6_2_K27ac

value: vastus lateralis

value: H3K27ac (Abcam, Ab4729)

value: Trained


title: MY16

value: Preterm

value: African American

tag: triple i status

tag: uterine contractions preceding cesarean

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

tag: cesarean indication

value: Severe preeclampsia, non-reassuring fetal status

tag: tocolysis (y/n)

tag: corticosteroids (y/n)


title: C2C12P_Membrane

description:
C2C12P_Membrane
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

tag: status

tag: fraction

value: Membrane


title: P6_2_K4me1

tag: tissue

tag: antibody

value: H3K4me1 (Abcam, Ab8895)

tag: participant

tag: training


title: 90MI-3

description:
90D3
processed data file/column: 90AI-3 (DEG-90MI.txt)

source_name: 90 min after mechanical injury

value: mycelia

tag: treatment

value: Injury


title: MY15

tag: clinical group

value: Group 4 (PPROM)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Classical

tag: triple i status

value: amniocentesis excluded Triple I

value: Absent

value: Ruptured, PPROM managed expectantly

value: Non-reassuring fetal status

value: No

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: C2C12P_Cytosol

description:
C2C12P_Cytosol
3pREADS_counts_in_pA_sites.txt

tag: cell line

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

tag: fraction

value: Cytosol


title: 90MI-2

description:
90D2
processed data file/column: 90AI-2 (DEG-90MI.txt)

tag: tissue


title: C2C12P_Insoluble_RNAseq

description:
C2C12P_Insoluble_RNAseq_rep1
RNAseq_counts_in_cUTRs_and_aUTRs.txt

data_processing:
Adpter trimming performed using Cutadapt
3'READs reads were aligned to mm9 using bowtie2
reads with a mapping quality score (MAPQ) ≥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 of each other were clustered.
RNA-seq:  Reads were mapped to the genome using STAR (version 2.5.2) and APAlyzer was used to interrogate APA.
Genome_build: mm9
Supplementary_files_format_and_content: txt files include all cluster sites (chromosome, strand, position) with count values for each sample.
Supplementary_files_format_and_content: RNAseq read counts
Supplementary_files_format_and_content: 3'READS+ clusters with read counts

value: Insoluble


title: 90MI-1

description:
90D1
processed data file/column: 90AI-1 (DEG-90MI.txt)

tag: treatment


title: MY14

tag: clinical group

value: Preterm

value: African American

value: amniocentesis confirmed Triple I

tag: uterine contractions preceding cesarean

value: Absent, forceful contractions following PPROM, receded after magnesium tocolysis

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

tag: cesarean indication

value: Acute chorioamnionitis

tag: tocolysis (y/n)

value: Yes

tag: corticosteroids (y/n)


title: P6_1_K4me1

value: vastus lateralis

tag: antibody

value: H3K4me1 (Abcam, Ab8895)

tag: participant

tag: training

value: Untrained


title: MY13

value: Group 3 (PTB Intact Mb)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: Hispanic

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Classical

tag: triple i status

value: Weak, irregular

value: Intact

value: Acute clinical chorioamnionitis, +IAI, breech presentation

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: P5_2_K27ac

tag: tissue

value: H3K27ac (Abcam, Ab4729)

value: Trained


title: C2C12P_Membrane_RNAseq

description:
C2C12P_Membrane_RNAseq_rep1
RNAseq_counts_in_cUTRs_and_aUTRs.txt

tag: cell line

tag: growth medium

value: DMEM supplemented with 10% fetal bovine serum, 100 IU/ml penicillin, and 100 μg/ml streptomycin.

tag: status

value: Proliferating

tag: fraction

value: Membrane


title: C2C12P_Cytosol_RNAseq

description:
C2C12P_Cytosol_RNAseq_rep1
RNAseq_counts_in_cUTRs_and_aUTRs.txt

value: Cytosol


title: MY11

tag: clinical group

value: Group 4 (PPROM)

value: Preterm

value: African American

value: amniocentesis confirmed Triple I

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

value: Ruptured, PPROM managed expectantly

tag: cesarean indication

value: Acute clinical chorioamnionitis, +IAI

tag: tocolysis (y/n)

tag: corticosteroids (y/n)

value: No


title: P5_2_K4me1

value: vastus lateralis

tag: antibody

value: H3K4me1 (Abcam, Ab8895)

tag: participant

tag: training


title: MY12

value: Group 3 (PTB Intact Mb)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Low transverse

tag: triple i status

value: Present, regular

value: Intact

value: Acute clinical chorioamnionitis, +IAI, non-reassuring fetal status

value: Yes

tag: oxytocin (y/n)

tag: attempted trial of labor (y/n)


title: 30MI-2

description:
30D2
processed data file/column: 30AI-2 (DEG-30MI.txt)

source_name: 30 min after mechanical injury

tag: tissue

value: mycelia

tag: treatment

value: Injury


title: 4hMI-2

description:
4D2
processed data file/column: 4hAI-2 (DEG-4hMI.txt)


title: 30MI-3

description:
30D3
processed data file/column: 30AI-3 (DEG-30MI.txt)


title: 4hMI-1

description:
4D1
processed data file/column: 4hAI-1 (DEG-4hMI.txt)


title: 30MI-1

description:
30D1
processed data file/column: 30AI-1 (DEG-30MI.txt)


title: P5_1_K27ac

value: H3K27ac (Abcam, Ab4729)

value: Untrained


title: UKS

city: Shanghai

first: Guiqin

last: Xu

address: 800 Dongchuan Rd

country: China

institute: Shanghai cancer institute

description: K-rasG12D;Usp16-/-/SV40T (UKS)

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (http://github.com/najoshi/sickle)
Clean reads were mapped to mouse genome (GRCm38.p5) with Hisat2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software
The uniquely mapped fragments of genes were counted by Stringtie(http://ccb.jhu.edu/software/stringtie/index.shtml?t=example).
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

source_name: Usp16 deletion_MEF

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Invitrogen)according the manufacturer’s instructions.Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies)
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA)

tag: strain background

value: embryo

tag: cell type

value: MEF

value: Usp16 deletion


title: CT8-3

description:
C83
processed data file/column: CT8-3 (raw-counts.txt)

source_name: Control 8h

value: Control condition


title: P5_1_K4me1

tag: antibody


title: MY10

tag: clinical group

value: Group 2 (TNL)

value: Term

value: White Non-Hispanic

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

tag: cesarean indication

value: Breech presentation

tag: tocolysis (y/n)

value: No

tag: corticosteroids (y/n)


title: KS

description: K-rasG12D;Usp16+/+/SV40T (KS)

value: control


title: P6_1_K27ac

value: vastus lateralis

tag: participant

tag: training


title: P4_2_K27ac

value: Trained


title: CT8-2

description:
C82
processed data file/column: CT8-2 (raw-counts.txt)

value: mycelia


title: MY08

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: Asian

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Low transverse

tag: triple i status

value: Intact

tag: oxytocin (y/n)


title: P4_2_K4me1

tag: tissue

tag: antibody

value: H3K4me1 (Abcam, Ab8895)


title: 4T1_Stress3_miRNA

city: Chengdu

first: Peixin

last: Du

address: No.37, Guoxue Alley

institute: West china hospital

data_processing:
Basecalls performed using bcl2fastq2 Conversion Software v2.20
miRNA sequencing reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using miRDeep2 v0.0.8 with parameters -e -j -h -l 18 -m
Processed data of miRNA was quantified using miRDeep2 v0.0.8 with parameters -t mmu
For mRNA data, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then aligned to mm10 and quantified using kallisto v0.46.1 with parameters -i transcripts.idx -b 100
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw miRNA counts for every miRNA and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: 4T1 tumor

extract_protocol:
Tumors were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent (Invitrogen, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols. Transcriptome sequencing was performed on an Illumina HiSeq 2500 platform by Shanghai Personal Biotechnology Co. Ltd. Finally, 150-bp paired-end raw reads were obtained.

tag: strain

value: Balb/c

tag: age

value: 35 days post inoculation

value: 4T1 tumor

tag: treatment

value: treated with restraint stress 2 hours/ day for consecutive 28days


title: CT8-1

description:
C81
processed data file/column: CT8-1 (raw-counts.txt)

value: Control condition


title: 4T1_Stress2_miRNA


title: 4T1_Stress1_miRNA


title: P4_1_K27ac

value: H3K27ac (Abcam, Ab4729)

value: Untrained


title: MY06

tag: clinical group

value: Group 2 (TNL)

value: Term

value: White Non-Hispanic

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

tag: cesarean indication

value: History of shoulder dystocia

tag: tocolysis (y/n)

tag: corticosteroids (y/n)

tag: attempted trial of labor (y/n)


title: CT0-3

description:
CT03
processed data file/column: CT0-3 (raw-counts.txt)

source_name: Control Time 0

value: mycelia


title: 4T1_Control3_miRNA

value: untreated


title: P4_1_K4me1

value: vastus lateralis

tag: participant

tag: training


title: 4T1_Control2_miRNA


title: MY05

value: Group 1 (TL)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

value: African American

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

tag: cesarean incision type

value: Low transverse

tag: triple i status

value: Present, regular

value: Ruptured in labor

value: Failure to descend

value: No

tag: oxytocin (y/n)

value: Yes


title: CT0-2

description:
CT02
processed data file/column: CT0-2 (raw-counts.txt)

tag: tissue

tag: treatment

value: Control condition


title: MY04

tag: clinical group

tag: uterine contractions preceding cesarean

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

tag: cesarean indication

value: Failure to progress


title: CT0-1

description:
CT01
processed data file/column: CT0-1 (raw-counts.txt)


title: 4T1_Control1_miRNA

tag: strain

value: Balb/c

tag: age

value: 35 days post inoculation

value: 4T1 tumor


title: P3_2_K4me1

tag: antibody

value: H3K4me1 (Abcam, Ab8895)

tag: participant

tag: training

value: Trained


title: MY09

value: Group 2 (TNL)

tag: term/preterm

value: Term

tag: maternal age (y)

tag: maternal race/ethnicity

value: White Non-Hispanic

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: birthweight (g)

value: Absent

value: Intact

value: Fetal macrosomia

tag: tocolysis (y/n)

tag: corticosteroids (y/n)

tag: attempted trial of labor (y/n)


title: P3_2_K27ac

tag: tissue

value: vastus lateralis

value: H3K27ac (Abcam, Ab4729)


title: MY03

tag: clinical group

value: Group 1 (TL)

value: Hispanic

tag: cesarean incision type

value: Low transverse

tag: triple i status

tag: uterine contractions preceding cesarean

value: Present, regular

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

value: Ruptured in labor

value: Failure to descend

value: No

tag: oxytocin (y/n)


title: mbl-1 rep3

city: Helsinki

first: Olli

last: Matilainen

address: Viikinkaari 9C

country: Finland

institute: University of Helsinki

data_processing:
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of WBcel235 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.

organism: Caenorhabditis elegans

source_name: whole animal lysate

growth_protocol: N2 and mbl-1(tm1563) strains were synchronized by bleaching and plated as L1 larvae on RNAi plates seeded with HT115 bacteria carrying empty vector (control vector for RNAi). To prevent the hatching of the progeny, worms were transferred to plates containing 10 μM of 5-fluorouracil (Sigma) at the L4 stage. Worms were collected at day 2 of adulthood (three biological replicates for both strains) and freezed in liquid nitrogen.

extract_protocol:
Total RNA was extracted with TRIzol Reagent (Ambion) and assessed for degradation using Agilent 2100 Bioanalyzer.
Illumina Truseq stranded polyA-mRNA library was prepared following the manufacturer's protocol. Libraries were sequenced by using the Illumina NextSeq 500 following the manufacturer's protocol.

tag: genotype

tag: growth temperature

value: 20 degree Celsius

tag: age

value: day 2 adult (5th day from hatch)


title: MY02

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

tag: maternal parity

tag: gestational age at delivery (weeks.days)

tag: cesarean indication

value: Failure to progress

value: Yes


title: P3_1_K27ac

source_name: vastus lateralis

tag: tissue

tag: antibody

tag: participant

tag: training

value: Untrained


title: 4T1_Stress3_mRNA

tag: strain

value: Balb/c

value: 35 days post inoculation

value: 4T1 tumor

tag: treatment

value: treated with restraint stress 2 hours/ day for consecutive 28days


title: MY07

tag: clinical group

value: Group 2 (TNL)

value: Term

value: White Non-Hispanic

tag: birthweight (g)

tag: cesarean incision type

tag: triple i status

tag: uterine contractions preceding cesarean

value: Absent

tag: contractions semi-quantitative scale (0-2)

tag: cervical dilation before cesarean (cm)

tag: membrane status at cesarean

value: Intact

value: Breech presentation

tag: tocolysis (y/n)

tag: corticosteroids (y/n)

tag: attempted trial of labor (y/n)


title: mbl-1 rep1

tag: genotype

tag: growth temperature

tag: age


title: MY01

value: Group 1 (TL)

tag: term/preterm

tag: maternal age (y)

tag: maternal race/ethnicity

tag: maternal parity

tag: gestational age at delivery (weeks.days)

value: Low transverse

value: Present, regular

value: Ruptured in labor

tag: cesarean indication

value: Failure to descend

tag: oxytocin (y/n)


title: N2 rep3

value: N2 (wild-type)

value: 20 degree Celsius

value: day 2 adult (5th day from hatch)


title: 4T1_Stress1_mRNA

tag: strain

value: Balb/c

value: 35 days post inoculation

tag: tissue

tag: treatment


title: P2_2_K27ac

value: vastus lateralis

tag: antibody

value: H3K27ac (Abcam, Ab4729)

tag: participant

tag: training

value: Trained


title: 4T1_Stress2_mRNA

value: 4T1 tumor

value: treated with restraint stress 2 hours/ day for consecutive 28days


title: 4T1_Control3_mRNA

value: untreated


title: P2_2_K4me1

value: H3K4me1 (Abcam, Ab8895)


title: NCI-H23-siUSP16-2

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to homo genome (hg38) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V2 Library Prep Kit for Illumina

value: lung

tag: cell line

tag: cell type

value: Human lung tumor cells

value: USP16 knockdown by siRNA


title: NCI-H23-siUSP16-1


title: 4T1_Control2_mRNA


title: N2 rep2

tag: genotype

tag: growth temperature


title: P2_1_K27ac

value: Untrained


title: NCI-H23-NC

value: control


title: N2 rep1

value: N2 (wild-type)

tag: age


title: 4T1_Control1_mRNA


title: P2_1_K4me1


title: ChIP_input_1min_salt_rep2

source_name: HeLa cells

value: HeLa

value: cervical carcinoma cells

tag: chip antibody

value: high salt buffer


title: mbl-1 rep2

value: 20 degree Celsius

value: day 2 adult (5th day from hatch)


title: P1_2_K27ac

value: vastus lateralis

value: H3K27ac (Abcam, Ab4729)


title: P1_2_K4me1

value: Trained


title: P3_1_K4me1


title: ChIP_input_1min_salt_rep1


title: cKO NK-3

city: Hefei

first: Zhigang

state: Anhui

address: Huangshan Road，number 443

institute: Univerity of Science and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling. Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Differential expression analysis of two groups (three biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression txt file

molecule: polyA RNA

source_name: Splenic NK cell

extract_protocol:
NK cells were lysed in TRIZOL, followed by total mRNA extraction using Direct-zol RNA Miniprep kit (Zymo Research)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: NK

value: Spleen


title: ChIP_input_1min_control_rep2

value: isotonic buffer


title: cKO NK-2


title: cKO NK-1


title: WT NK-3

value: Mettl3fl/fl (WT)


title: P1_1_K27ac


title: P1_1_K4me1

value: H3K4me1 (Abcam, Ab8895)


title: WT NK-2


title: ChIP_Rad21_30min_salt_rep1

value: Rad21 (Abcam, ab992)


title: 10-16_low in the number of fine MPs

first: Seok-Hyeon

last: Beak

address: 1, Gwanak-ro

institute: Seoul National University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Bos taurus (NCBI) whole genome using Bowtie2
Read count extraction using bedtools.
Genome_build: Bos taurus
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Bos taurus

source_name: Longissimus thoracis muscle

growth_protocol: The steers were raised using conventional manner and fed commercial feeds.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

value: Longissimus thoracis muscle

tag: breed

value: Hanwoo (Korean native cattle)

tag: sample type

value: steer

value: 35.4 months

tag: group

value: low in the number of fine MPs


title: ChIP_Rad21_30min_salt_rep2

value: HeLa

value: cervical carcinoma cells

value: high salt buffer


title: 3-3_low in the number of fine MPs

value: 33.7 months


title: ChIP_input_1min_control_rep1


title: HL60_day4_replicate3

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Illumina novaSeq base call (BCL) files are converted in fastq file through bcl2fastq (version v2.17)
Sequence reads were trimmed using cutadapt software (v. 1.18).
Alignment was performed with STAR 2.6.1a on GrCh38.89.
The expression levels of genes were determined with RSEM (v. 1.3.0)
Normalization and filtration was performed using EdgeR (v. 3.24.3)
Genome_build: GrCh38.89
Supplementary_files_format_and_content: Tab-delimited normalized and filtered count per million (CPM)

source_name: HL60 human cell line

growth_protocol: RPMI (ThermoScientific, USA)+ 10% FBS (ThermoScientific, USA), cells were passaged every 2 days at a 100'000 cells/ml density.

extract_protocol:
Trizol (ThermoScientific, USA) reagent extraction followed by Qiagen spin column purification
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For differentiation cells were passaged 200'000 cell/ml and treated with 5uM ATRA. Cells were passaged at day 2 1:5

tag: passage

tag: colletion time


title: HL60_day4_replicate4


title: ChIP_Rad21_30min_control_rep2


title: 3-1_low in the number of fine MPs

value: 37.8 months


title: HL60_day4_replicate2


title: 10-9_high in the number of fine MPs

value: 34.5 months

value: high in the number of fine MPs


title: ChIP_Rad21_30min_control_rep1


title: DsRed_oht_4

city: Neuherberg

first: Pawel

last: Smialowski

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
Sixteen bases were sequenced within the first read to obtain cellular and molecular barcodes, and 50 bases were sequenced in the second read into the cDNA fragment
An additional eight bases were sequenced to obtain the i7 barcode
Gene-based transcripts counts were obtained by running the zUMI pipeline (Parekh et al., 2018) (version 0.0.2) using Ensembl annotation release 81
Supplementary_files_format_and_content: NormCount

source_name: SC-Astro

growth_protocol: Cells were maintained in DMEM/F12 2%B27, 10% FBS, P/S

extract_protocol:
RNA was extracted from FACS-sorted cells using PicoPure kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with hydroxyl-tamoxifen (100nM final concentration) for 24 hours prior the FACS sorting

tag: tf

value: dsred

value: oht

tag: barcode

value: CCGGAC


title: Pooled_slow_type_muscle_fibers

type: RNA

city: Tsukuba

first: Mika

last: Oe

state: Ibaraki

address: Ikenodai 2

country: Japan

institute: Institute of Livestock and Grassland Science, NARO

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE v2 8 x 60K Microarray (Agilen) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: slow type muscle fibers isolated from soleus muscles

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug Total RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: The total RNAs were isolated from the pooled 4,447 fast and 1,659 slow type fibers using Qiagen RNeasy mini kit (Qiagen).

treatment_protocol: The extensor digitorum longus (EDL) and soleus muscles were dissected from 8 male GFP-Myh7 heterozygous (G/+) mice aged 6-8 weeks to isolate single myofibers. Fast type fibers which were not indicated by GFP were collected from EDL muscles, while slow type fibers with GFP fluorescence were collected from soleus muscles. The total RNAs were isolated from the pooled 4,447 fast and 1,659 slow type fibers.

tag: strain

value: GFP-Myh7 heterozygous (G/+) mice

tag: gender

value: male

value: 6-8 week

tag: tissue

value: extensor digitorum longus (EDL)

tag: tissue subtype

value: slow type muscle fibers


title: Pooled_fast_type_muscle_fibers

source_name: fast type muscle fibers isolated from EDL muscles

value: fast type muscle fibers


title: DsRed_oht_3

tag: treatment

value: CCCCGT


title: HL60_day4_replicate1


title: ChIP_Smc3_30min_salt_rep2

data_processing:
Standard Illumina Sequencing Pipeline
C-TALE Processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest was embedded, using Bowtie2 v2.3.5. The data were processed using the hiclib pipeline (https://github.com/mirnylab/hiclib-legacy). Statistics for the C-TALE data processing can be found in the table. 10kb-binned HDF5 files were converted to cool format matrices using cooler v0.8.7. Data from three biological replicates for each experimental condition (control and high salt treated chromatin) were merged in two matrices which were then iteratively normalized using publicly available script (https://github.com/Phlya/C-TALE-Normalization) (“--mult_factor 2” option). Weights in a few poorly covered bins were reduced to NA during the normalization procedure; rhdf5 R package was used to manually replace these NA weights with the values of the highest weight found in each matrix.
ChIP-seq processing: Reads were mapped to the 4 Mb fragment of the genome (hg19, chr21:27,922,688-32,028,897), in which the region of interest (hg19, chr21: 28,981,189-30,260,402) was embedded, using Bowtie2 v2.3.5. Illumina TruSeq adapters were trimmed with cutadapt. Read pairs with at least one non-uniquely mapped read as well as PCR and optical duplicates were filtered using samtools v1.7. Bedtools v2.25.0 and bedGraphToBigWig utility (from UCSC) were used to generate bigwig coverage files. All bigwig files were scaled to 1 mln uniquely mapped read pairs with deeptools v3.4.3. Corresponding input bigwig files were subtracted from each immunoprecipitation bigwig file and then mean profiles were calculated from pairs of biological replicates. Both operations were performed with deeptools v3.4.3.
Genome_build: hg19 (chr21:27,922,688-32,028,897 region)
Supplementary_files_format_and_content: .cool files contain C-TALE contact matrices in an easy to visualize and access format (see https://cooler.readthedocs.io/en/latest/schema.html)
Supplementary_files_format_and_content: bigwig files are binary files containing ChIP-seq profiles in an easy to visualize and access format

extract_protocol:
C-TALE was performed as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan). For ChIP-seq experiments, fixed chromatin pellets were resuspended in 600 uL of ice cold RIPA buffer supplemented with protease inhibitors. Chromatin was sheared on ice with a VirSonic 100 cell disrupter with 10 30-sec pulses on “15” power setting, separated with 3 min periods of recovery. Input DNA was isolated from 1/10 aliquots of sonicated samples. Sheared chromatin from approximately 1 mln of cells and 1 ug of antibodies (against either CTCF, Smc3, or Rad21) were used in each immunoprecipitation reaction. Chromatin immunoprecipitation was performed as described in Abcam X-ChIP manual (https://www.abcam.com/protocols/cross-linking-chromatin-immunoprecipitation-x-chip-protocol) with minor modifications. 25 ul of protein A/G magnetic beads (Thermo Scientific, 26162) was used per reaction instead of agarose beads, thus a magnet was used instead of a centrifuge to reclaim beads. Beads were blocked with 1% BSA solution in RIPA overnight, while chromatin was incubated with antibodies. BSA-blocked beads were mixed with antibody-bound chromatin for 6 h. Immunoprecipitated DNA was separated from beads by overnight treatment with proteinase K (Thermo Scientific, EO0491) in PBS supplemented with 1% SDS at 65C. Solution was then cleared from beads with a magnet and DNA was isolated with standard phenol-chloroform extraction and ethanol precipitation.
Sequencing libraries from 3C-seq material, immunoprecipitated DNA and ChIP inputs were generated as described previously (Golov AK, Ulianov SV, Luzhin AV, Kalabusheva EP, Kantidze OL, Flyamer IM, Razin SV, Gavrilov AA. C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries. Methods. 2020 Jan).

tag: cell line

value: HeLa

tag: cell type

value: Smc3 (Abcam, ab9263)


title: DsRed_oht_2

value: CCCACG


title: HL60_day2_replicate4


title: Ngn2ERT2_no_3

value: no

value: CCAACC


title: 10-8_high in the number of fine MPs

value: Longissimus thoracis muscle

value: Hanwoo (Korean native cattle)

value: steer

value: 33.8 months


title: ChIP_Smc3_30min_salt_rep1

value: cervical carcinoma cells

value: high salt buffer


title: HL60_day2_replicate3


title: AOPH-12_SwB9_CAM_3: PDA plate containing 50µM camalexin rep1

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Trimmomatic v0.36 was employed to trim raw reads with settings for single- or paired-end sequencing and the following settings for paired-end: ILLUMINACLIP:TruSeq2-PE.fa:5:30:10 SLIDINGWINDOW:3:18 LEADING:6 TRAILING:6 MINLEN:90
FastQC v0.11.5 (Brabham bioinformatics) was used to perform quality control of the trimmed reads. Mapping was conducted with HISAT2 (Kim et al., 2015) with --max-intronlen 500 -k 1 against the S. sclerotiorum isolate 1980 reference genome
Sorted BAM files and indices were generated with samtools v1.7
FPKM (fragments per kilobase of transcript per million mapped reads) tables were generated using the Cufflinks function cuffnorm with --compatible-hits-norm --library-norm-method classic-fpkm
Genome_build: S. sclerotiorum 1980 version 2 (GCA_001857865.1); S. trifoliorum SwB9 v1 (PRJEB36746/ERZ1667436 at https://www.ebi.ac.uk/ena)
Supplementary_files_format_and_content: tab-delimited text files include total count of uniquely mapped reads per gene for each Sample

organism: Sclerotinia trifoliorum

source_name: ~20mm wide mycelium colony

growth_protocol: Plants were  grown in Jiffy pots under controlled conditions at 23°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
The edge and center of developed mycelial colonies (~20 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

value: Mycelium from in vitro culture

value: in vitro (Stcam)


title: WT NK-1

value: NK

value: Spleen

tag: genotype

value: Mettl3fl/fl (WT)


title: ChIP_Smc3_30min_control_rep2

value: isotonic buffer


title: DsRed_no_3

value: dsred

value: GTTCGA


title: HL60_day2_replicate2


title: AOPH-11_SwB9_CAM_2: PDA plate containing 50µM camalexin rep1


title: Ascl1ERT2_no_3

value: GGGATT


title: ChIP_Smc3_30min_control_rep1

value: HeLa

value: Smc3 (Abcam, ab9263)


title: ChIP_CTCF_30min_salt_rep2

value: CTCF (Active Motif, 61311)


title: HL60_day0_replicate4


title: AOPH-10_SwB9_CAM_1: PDA plate containing 50µM camalexin rep1


title: AOPH-9_SwB9_DMSO_3: PDA plate containing DMSO rep3

value: in vitro (Stdmso)


title: Ngn2ERT2_no_2

value: no

value: TTAGTT


title: Ascl1ERT2_oht_4

value: oht

value: TGTTTA


title: HL60_day0_replicate3


title: ChIP_CTCF_30min_salt_rep1

value: cervical carcinoma cells

value: high salt buffer


title: ChIP_CTCF_30min_control_rep1


title: HL60_day0_replicate2


title: ChIP_CTCF_30min_control_rep2


title: AOPH-8_SwB9_DMSO_2: PDA plate containing DMSO rep2

value: Mycelium from in vitro culture


title: 3-8_high in the number of fine MPs

value: Longissimus thoracis muscle

value: Hanwoo (Korean native cattle)

value: steer

tag: age

value: 32.5 months

value: high in the number of fine MPs


title: Ngn2ERT2_oht_4

value: TACTAT


title: ChIP_Smc3_1min_salt_rep2

value: HeLa

tag: chip antibody


title: AOPH-7_SwB9_DMSO_1: PDA plate containing DMSO rep1


title: ChIP_Smc3_1min_salt_rep1

value: Smc3 (Abcam, ab9263)


title: Ngn2ERT2_oht_3

value: TAAAGT


title: AOPH-5_Ss1980_CAM_2: PDA plate containing 125µM camalexin rep2

organism: Sclerotinia sclerotiorum 1980 UF-70

value: in vitro (Sscam)


title: HL60_day2_replicate1


title: Ascl1ERT2_oht_5

value: TTTACA


title: DsRed_no_2

value: dsred

value: ATTTCA


title: HL60_day0_replicate1


title: ChIP_Smc3_1min_control_rep2

value: isotonic buffer


title: AOPH-4_Ss1980_CAM_1: PDA plate containing 125µM camalexin rep1


title: Ascl1ERT2_oht_3

value: oht

value: ATTCTA


title: Ascl1ERT2_oht_2

value: ATTACT


title: AOPH-3_Ss1980_DMSO_3: PDA plate containing DMSO rep3

value: Mycelium from in vitro culture

value: in vitro (Ssdmso)


title: ChIP_Smc3_1min_control_rep1

value: cervical carcinoma cells


title: MCS4

city: Hangzhou

first: Huizeng

last: Sun

state: Zhejiang

address: 866 Yuhangtang Road

department: College of Animal Sciences

institute: Zhejiang University

data_processing:
Low-quality bases and adapter sequence was trimmed and quality of reads was filtered using fastq-mcf with parameters quality score > 20 and length > 75 bp
The cleaned reads were then aligned to the reference bovine genome UMD3.1 (http://bovinegenome.org/?q=umd_downloads) and assembled with TopHat2 (v2.0.9) software package
Samtools (v1.1) was then applied to generate BAM alignment files and convert them into SAM format
HTSeq-count (v0.6.1) was used to quantify the number of mapped reads per each bovine gene
Genome_build: bovine genome UMD3.1 (http://bovinegenome.org/?q=umd_downloads)
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample

source_name: mammary gland

extract_protocol:
Approximately 100 mg of frozen tissue samples were ground to fine powder in a sterilized mortar and then liver and mamamry gland tissue samples were applied to isolate the total RNA using a mirVana total RNA Isolation Kit (Ambion, Carlsbad, CA, USA) while backfat tissue was applied to isolate total RNA using RNeasy Lipid Tissue Mini Kit (Qiagen, Germany) following the manufacturer’s instructions. The RNA was quantified using the Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA) and checked for purity and integrity using the Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). RNA with the ration of 28S/18S ranging from 1.7 to 2.4 and the RNA integrity number greater than 7.0 was used for RNA-Seq library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diets

value: corn stover based diet

value: mammary gland

tag: milk production (kg/d)

tag: parity

tag: dry matter intake (kg/d)

tag: day in milk


title: MCS6


title: MCS3


title: MCS5


title: ChIP_CTCF_1min_salt_rep2

value: CTCF (Active Motif, 61311)

value: high salt buffer


title: DsRed_no_1

tag: tf

value: no

value: ATGAAT


title: AOPH-6_Ss1980_CAM_3: PDA plate containing 125µM camalexin rep3

value: in vitro (Sscam)


title: ChIP_CTCF_1min_salt_rep1

value: HeLa


title: Ngn2ERT2_oht_2

tag: barcode

value: ATATAG


title: AOPH-1_Ss1980_DMSO_1: PDA plate containing DMSO rep1


title: HWG39_PVU_NEC_3: Common bean infected by S. sclerotiorum rep3

source_name: Center of ~20mm wide disease lesion on leaves

value: Mycelium from leaves of 5-week old plants

value: in planta (Pvu)


title: MCS1


title: ChIP_CTCF_1min_control_rep2

value: isotonic buffer


title: Ngn2ERT2_oht_1

value: oht

value: AATCTT


title: Ascl1ERT2_no_1

value: AATACA


title: ChIP_CTCF_1min_control_rep1


title: MethylC-Capture Sequencing (MCC-seq) 7

city: Ste Anne-de-Bellevue

first: Romain

last: Lambrot

state: QC

address: 21111 Lakeshore road

department: Animal Science

country: Canada

institute: McGill University

data_processing:
Library strategy: MCC-seq
ChIP-seq processing: Raw reads were trimmed from the 3' end to have a phred score of at least 30. Illumina sequencing adapters were removed from the reads. Trimming and clipping were performed using Trimmomatic version 0.36 (Bolger et al., 2014).
Each read was mapped against the Feb. 2009 assembly of the human genome (hg19, GRCh37 Genome Reference Consortium Human Reference 37 (GCA_000001405.1) downloaded from UCSC genome browser (Haeussler et al., 2019) using Bowtie 2 version 2.3.4.1 (Langmead and Salzberg, 2012).
We excluded reads that exhibited more than 3 mismatches. SAMtools version 1.9 (Li et al., 2009) was then used to sort and convert SAM files.
Targeted sperm panel MCC-Seq HiSeq reads were aligned using the Genpipes pipeline (Bourgey et al. 2019). Specifically, the MCC-Seq paired-end fastq reads were first trimmed for quality (phred33 >= 30), length (n>50bp) and Illumina adapters using Trimmomatic (version 0.36) (Bolger et al. 2014).
Trimmed reads were aligned, per sequencing lane, to the bisulfite-converted hg19/GRCh37 reference genome using Bismark (version 0.18.1) (Krueger and Andrews 2011) with Bowtie 2 (version 318 2.3.1)(Langmead and Salzberg 2012) in pair-end mode using the non-directional protocol setting and other default parameters. Methylation calls were obtained using Bismark  to record counts of methylated and unmethylated cytosines at each cytosine position in the  genome. A methylation level  of each  CpG was calculated by the number of methylated reads over the total number of sequenced reads. CpG sites with less than 20x read coverage were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, coverage tracks were generated from aligned reads using deepTools2 (Ramirez et al., 2016). The coverage was calculated as the number of reads extended to 150bp fragment size per 25 bp bin and normalized using Reads Per Kilobase per Million mapped reads (RPKM) not located in chromosome X. MCC-seq track files were prepared by converting methylation call files returned by Bismarck into bigwig files.

source_name: human sperm individual 7

extract_protocol:
Semen samples were collected by masturbation after at least 3 days of abstinence. Following semen liquefaction (20-30min at room temperature), an aliquot was used for sperm count and the remaining sample was immediately frozen.
ChIP-seq libraries were prepared using the Kapa HTP Library Preparation Kit (Roche) as per the manufacturer's recommendations except that the size selection was performed after the PCR step. For MCC-seq, bisulfite DNA was quantified with OliGreen® (Life Technology) and amplified with 9–12 PCR cycles using the KAPA® HiFi HotStart Uracil+ DNA Polymerase kit. SeqCap® Epi Enrichment System protocol (Roche NimbleGen®) was used to capture the regions of interest. Equal amounts of multiplexed libraries were combined to obtain 1μg of total input library, which was hybridized to the capture panel at 47°C for 72 h. Washing, recovery, and PCR amplification of the captured libraries, as well as final purification were conducted as recommended by the manufacturer (Roche/KAPA® Biosystems) according to suggested protocols.

value: sperm

value: spermatozoa


title: spinal cord-culture-6 [TTTAGT]

data_processing:
Sixteen bases were sequenced within the first read to obtain cellular and molecular barcodes, and 50 bases were sequenced in the second read into the cDNA fragment
An additional eight bases were sequenced to obtain the i7 barcode
Gene-based transcripts counts were obtained by running the zUMI pipeline (Parekh et al., 2018) (version 0.0.2) using Ensembl annotation release 81
Genome_build: Ensembl annotation release 81
Supplementary_files_format_and_content: Gene-based transcripts counts

source_name: astrocytes

growth_protocol: Astrocytes were isolated via ACSA2-MACS-sorting and either immediately processed with PicoPure klt or seeded in grown for 7 days in astro medium (DMEM/F12, 10% FBS, 2% B27, P/S, Egf, Fgf, 10ng/ml). Cells were then trypsinized, seeded in 6-well plates and collected the subsequent day.

extract_protocol:
Cells were trypsinized, collected by centrifugation, and lyzed with lysis buffer from PicoPure kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: isolation

value: MACS-sorted

tag: cultured

value: culture


title: HWG38_PVU_NEC_2: Common bean infected by S. sclerotiorum rep2

tag: tissue


title: HWG37_PVU_NEC_1: Common bean infected by S. sclerotiorum rep1


title: spinal cord-culture-5 [TTGAAT]


title: HWG36_PVU_FRT_3: Common bean infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM4097183 in GSE138039

source_name: Periphery of ~20mm wide disease lesion on leaves


title: MAH4

value: alfalfa hay based diet

value: mammary gland


title: MAH5


title: MethylC-Capture Sequencing (MCC-seq) 5

source_name: human sperm individual 5


title: AOPH-2_Ss1980_DMSO_2: PDA plate containing DMSO rep2

value: Mycelium from in vitro culture

value: in vitro (Ssdmso)


title: MCS2

value: corn stover based diet


title: MethylC-Capture Sequencing (MCC-seq) 4

source_name: human sperm individual 4


title: MAH2


title: HWG35_PVU_FRT_2: Common bean infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM4097182  in GSE138039


title: MethylC-Capture Sequencing (MCC-seq) 6

source_name: human sperm individual 6


title: MAH3


title: HWG34_PVU_FRT_1: Common bean infected by S. sclerotiorum rep1 [re-analysis]

description: re-analysis of GSM4097181 in GSE138039


title: MethylC-Capture Sequencing (MCC-seq) 3

source_name: human sperm individual 3


title: MAH1


title: MAH6


title: spinal cord-acute-4 [TGTAAA]

value: acute


title: LCS6

source_name: liver

value: liver


title: MethylC-Capture Sequencing (MCC-seq) 2

source_name: human sperm individual 2


title: HWG30_RCO_NEC_3: Castor bean infected by S. sclerotiorum rep3

value: Mycelium from leaves of 5-week old plants

value: in planta (Rco)


title: LCS5


title: HWG29_RCO_NEC_2: Castor bean infected by S. sclerotiorum rep2


title: MethylC-Capture Sequencing (MCC-seq) 1

source_name: human sperm individual 1


title: HWG28_RCO_NEC_1: Castor bean infected by S. sclerotiorum rep1


title: spinal cord-culture-4 [TAGTTT]


title: LCS4


title: spinal cord-culture-3 [TACTTA]


title: LCS3


title: HWG27_RCO_FRT_3: Castor bean infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM4097177 in GSE138039


title: spinal cord-acute-6 [TTCAAT]


title: airway-differentiated_lung_progenitors_3

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

institute: Kyoto University

description:
CF_TPM.txt
processed data header: CF_air-3_1

data_processing:
Sequenced reads from fasq files were mapped to GRCh37/hg19 whole genome using HISAT2.
Transcripts Per Kilobase Million (TPM) value of each gene was calculated using Stringtie.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample .

source_name: 201B7 iPS cells

growth_protocol: Human iPS cell-derived lung progenitors were maintained under 5% CO2 at 37°C. Please refer to our manuscript about the medium in detail.

extract_protocol:
Total RNA was extracted using PureLink RNA mini kit (Thermo Fisher Scientific) or NucleoSpin RNA Plus XS (Takara Bio) according to manufacturer's protocol.
Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

tag: compound


title: cortex-culture-5 [TAATTC]


title: airway-differentiated_lung_progenitors_2

description:
CF_TPM.txt
processed data header: CF_air-2_1


title: airway-differentiated_lung_progenitors_1

description:
CF_TPM.txt
processed data header: CF_air-1_1


title: LCS2


title: spinal cord-acute-5 [TTAAAG]


title: spinal cord-acute-3 [GTTTTA]


title: HWG25_RCO_FRT_1: Castor bean infected by S. sclerotiorum rep1 [re-analysis]

description: re-analysis of GSM4097175 in GSE138039

tag: treatment


title: alveolar-differentiated_lung_progenitors_3

description:
CF_TPM.txt
processed data header: CF_3i-3

tag: cell line


title: HWG26_RCO_FRT_2: Castor bean infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM4097176 in GSE138039


title: cortex-culture-4 [GTATAA]


title: cortex-acute-5 [TATGTT]


title: alveolar-differentiated_lung_progenitors_2

description:
CF_TPM.txt
processed data header: CF_3i-2


title: HWG20_BVU_NEC_2: Beetroot infected by S. sclerotiorum rep2

value: in planta (Bvu)


title: cortex-culture-3 [GAAATT]


title: LAH6


title: HWG21_BVU_NEC_3: Beetroot infected by S. sclerotiorum rep3


title: LAH5


title: cortex-culture-2 [CAATAA]


title: LAH4


title: HWG19_BVU_NEC_1: Beetroot infected by S. sclerotiorum rep1


title: 3D_culture_lung_progenitors_3

description:
CF_TPM.txt
processed data header: CF_4w-3


title: cortex-acute-4 [ATTTGT]


title: LAH3


title: 3D_culture_lung_progenitors_2

description:
CF_TPM.txt
processed data header: CF_4w-2


title: spinal cord-acute-2 [ATATCT]


title: HWG18_BVU_FRT_3: Beetroot infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM4097171 in GSE138039


title: HWG17_BVU_FRT_2: Beetroot infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM4097170 in GSE138039


title: LAH1


title: HDX45_HAN_NEC_3: Sunflower infected by S. sclerotiorum rep3

value: in planta (Han)


title: cortex-culture-1 [ACTTTA]


title: Lung_progenitors_B2-3_3

description:
CF_TPM.txt
processed data header: MACS-3

value: Lung_progenitors_B2-3 hiPSC line


title: LCS1


title: HDX42_HAN_NEC_2: Sunflower infected by S. sclerotiorum rep2


title: HWG16_BVU_FRT_1: Beetroot infected by S. sclerotiorum rep1 [re-analysis]

description: re-analysis of GSM4097169 in GSE138039


title: cortex-acute-3 [ATACTT]


title: spinal cord-culture-2 [AATTGA]


title: Lung_progenitors_B2-3_1

description:
CF_TPM.txt
processed data header: MACS-1


title: cortex-acute-2 [AATGAT]


title: 3D_culture_lung_progenitors_1

description:
CF_TPM.txt
processed data header: CF_4w-1


title: HDX39_HAN_NEC_1: Sunflower infected by S. sclerotiorum rep1


title: tRIP-seq_SRSF3_C2C12

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

institute: Nagoya University Graduate School of Medicine

data_processing:
Library strategy: tRIP-seq
For paired-end read data, only P5 reads were used for analysis.
After standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10).
Mapping was first performed against the mouse repetitive elements in RepBase with STAR (v2.5.2b).
Repeat-mapped reads were removed, and all others were then mapped against the mouse genome (mm10) with STAR (v 2.5.2b).
Multiply mapped reads were filtered out. Duplicates of reads uniquely mapped to the human or mouse genome were removed by Picard (v2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with a "--binsize 1" parameter.

source_name: Myoblast

growth_protocol: C2C12 cells were grown in DMEM with 10% fetal bovine serum at 37°C in 5% CO2.

extract_protocol:
C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells
tRIP was performed as previously described: Masuda et al. (2020):tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly.  EMBO Rep PMID: 32189459

value: no treatment

tag: cell type

value: Myoblast


title: alveolar-differentiated_lung_progenitors_1

description:
CF_TPM.txt
processed data header: CF_3i-1


title: transplanted_cells_3


title: HDX44_HAN_FRT_3: Sunflower infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM4097165 in GSE138039


title: Lung_progenitors_B2-3_2

description:
CF_TPM.txt
processed data header: MACS-2


title: transplanted_cells_2


title: LAH2


title: HDX41_HAN_FRT_2: Sunflower infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM4097163 in GSE138039


title: transplanted_cells_1


title: tRIP-seq_CPSF6_C2C12


title: HDX38_HAN_FRT_1: Sunflower infected by S. sclerotiorum rep1 [re-analysis]

description: re-analysis of GSM4097161 in GSE138039


title: Lung_progenitors_mB2-3_2

value: Lung_progenitors_mB2-3 hiPSC line


title: HDX51_SLY_NEC_2: Tomato infected by S. sclerotiorum rep2

value: in planta (Sly)


title: Lung_progenitors_mB2-3_1


title: HDX48_SLY_NEC_1: Tomato infected by S. sclerotiorum rep1


title: spinal cord-acute-1 [AATAGT]

value: MACS-sorted


title: Single-cell RNA-seq assay (scRNA-seq) of the coronal suture at E18.5, replicate 1

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
Preprocessing of 10X Genomics scRNA-seq data, clustering and cell type identification was performed using Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files consist of barcode, feature and matrix files.

source_name: Murine coronal suture at E18.5

extract_protocol:
Coronal sutures, encompassing the SM, OFs, and frontal and parietal bones in the region of overlap, were dissected from C57BL/6J mice. Ectocranial and endocranial membranes were removed to the extent possible, and frontal and parietal bones were separated with forceps to expose the SM. Pooled E16.5 sutures were digested at 37ºC in αMEM (Gibco, 32571-036) with 0.2% collagenase type II (Worthington, LS004176), 0.2% dispase II (Sigma-Aldrich, 4942078001), and 1U/μl DNase (Qiagen, 79254). Sutures were serially digested with agitation five times for 10 minutes each in a shaking incubator. Successive fractions were pooled on ice with the addition of FBS to 2%. Cell suspensions were strained through a 40 μm filter (Falcon, 352340), pelleted at 400g for 7 minutes, washed in PBS/1% BSA, and resuspended in PBS/1% BSA.
scRNA-seq 3’ expression libraries were prepared on a Chromium instrument (10X Genomics, model GCG-SR-1) using the Chromium Single Cell Gene Expression kit (version 3 for E16.5 libraries; version 2 for E18.5 libraries).

tag: strain

tag: developmental stage

tag: suture

value: coronal

tag: region

value: complete suture


title: Single-cell RNA-seq assay (scRNA-seq) of the coronal suture at E18.5, replicate 2


title: HDX53_SLY_FRT_3: Tomato infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM2850653 in GSE106811


title: Single-cell RNA-seq assay (scRNA-seq) of the coronal suture at E16.5, replicate 2

source_name: Murine coronal suture at E16.5


title: PD_3 decidual leukocytes-scRNA-seq

city: Beijing

first: Yan-Ling

last: Wang

state: Beijing

address: Beichen West Rd., Chaoyang, Beijing

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
scRNA-Seq: We checked the quality of raw sequencing data by FastQC software.  We used 10x genomics cellranger count pipeline 2.0.0 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were merged together by cellranger aggr pipeline and normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

source_name: CD45+ leukocytes

extract_protocol:
RNA were prepared for sequencing
Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared  for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v2 (10X Genomics)

treatment_protocol: The fresh tissue samples were gently triturated with GentelMACS Dissociator (Miltenyi Biotec, Germany) in the RPMI-1640 medium (Invitrogen) and enzymatically digested twice for 30 minutes in 37℃ shaker with 1.6 mg/ml type IV collagenase (9001121, Gibco) and 10U/ml type I DNase (DN25, Sigma). the suspended cells were subsequently passed through 60 mesh and 200 mesh cell strainers, and centrifuged at 1000rpm for 10 min. After the supernatant was removed, the pelleted cells diluted 1:1 by PBS, followed by Ficoll-Paque Plus (17-1440-02, GE Healthcare,) separation, after washing with 1x PBS, then the lymphocytes were centrifuged at 1000rpm for 10 min. the cell pellets were resuspended in PBS, The lymphocytes were stained with eFluor 506-viability dye (65-0866-14, ebioscience) and FITC-labeled anti-CD45 antibody (11-0459-42, ebioscience), then subjected to FACS sorting to obtain CD45+ lymphocytes.

tag: ethnicity

value: Chinese

value: Uterus

tag: age

tag: disease

value: recurrent spontaneous abortion (RSA) patient


title: Single-cell RNA-seq assay (scRNA-seq) of the coronal suture at E16.5, replicate 1


title: cortex-acute-1 [AAGTAT]

value: acute


title: PD_2 decidual leukocytes-scRNA-seq


title: HDX50_SLY_FRT_2: Tomato infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM2850652 in GSE106811