title: HV+S-

city: Ithaca

first: Leighton

middle: James

last: Core

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

description: differentiated endoderm

data_processing:
Pass Filter:  Reads that pass filter were selected from fastq files.
Read Trimming: reads were trimmed to 30 bases
rDNA filter: Reads were first mapped to a copy of rRNA gene (GenBank accession #: BK000964.1) including external and interanl spacers, and only reads that were not mapped to the rDNA were kept.
venus and Hex cDNA mapping: To examine the efficiency of the FACS sorting procedure reads were also mapped to the endogenous Hex cDNA and the exogenous Venus cDNA
mapping to the genome: Bowtie was used to map 30mers with up to two mismatches to the mm9 genome.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files are Bedgraphs from both replicates of each sample combined.  Each entry represents the number of reads at each base.

source_name: differentiated endoderm

growth_protocol: Hhex-venus (HV) ES cells (Canham et al., 2010) were used in this study alongside the E14 parental cell line as a control for FACS. ES cells were cultured in standard serum-containing medium with LIF as previously described (Canham et al., 2010).

extract_protocol:
To isolate nuclei, cells were re-suspended in 5 ml LYSO-A buffer (35 mM Tris-Cl, pH7.5, 150 mM sucrose, 80 mM KCl, 5 mM MgCl2, 0.5 mM DTT) and centrifuged for 5 min at 1000 g. They were then re-suspended in 5 ml LYSO-A buffer containing 0.05% Tween-20. Cells were incubated on ice for 1-5 min, with constant checking to ensure that 90% of cells were permeabilised, using a haemocytometer and tryphan blue (Life Technologies). Cells were washed in 5 ml LYSO-A buffer and transferred to siliconized tubes (Eppendorf) in 1 ml LYSO-A. Cells were centrifuged at 900 g for 5 min and re-suspended in 500 μl F80 buffer (50 mM Tris, pH8.3, 40% glycerol, 80 mM KCl, 5 mM MgCl2, 0.1 mM EDTA, 0.5 mM DTT). Cells were counted and then re-suspended at 5 x 106 cells/100 μl before being snap-frozen in liquid nitrogen in aliquots of 100 μl. All steps were carried out at 4°C and using wide-bore pipette tips to minimize the loss of sample.
GRO-seq libraries were prepared as in Core et al. (Core, Waterfall, and Lis, 2008), with the following modifications.  Trizol (invitrogen) was used to stop the reaction instead of DNase I and proteinase K treatment.  The RNA was further extracted once with acid phenol:chloroform, and once with chloroform before precipitating with 2.5 volumes of -20oC ethanol.  Bead binding buffers all contained 4units/ml of SUPERaseIN (ambion) and the following buffers were slightly modified.  Bead blocking buffer: 0.25X SSPE, 1mM EDTA, 0.05% tween, 0.1% PVP, and 1mg/ml ultrapure BSA (Ambion); Binding buffer: 0.25XSSPE, 37.5mM NaCl, 1mM EDTA, 0.05% tween; Low salt wash buffer: 0.2X SSPE, 1mM EDTA, 0.05% Tween.  High Salt wash buffer: 0.25% SSPE, 137.5mM NaCl, 1mM EDTA, 0.05% Tween.  The end repair steps were modified as follows.  Pelleted RNA from the first bead binding was resuspended in 20ul, and heated to 70oC for 5min, followed by incubation on ice for 2min.  1.5ul tobacco acid pyrophosphatase (TAP) buffer, 4.5ul water, 1 ul SUPERaseIn, and 1.5ul TAP (Epicentre) were then added and the reaction incubated at 37oC for 1.5 hours. 1ul 300mM MgCl2 and 1ul T4 polynucleotide Kinase (PNK) were added to the reaction for an additional protocols l 30 min. for phosphorylating the 5’-ends, 20ul T4 PNK buffer, 2ul 100mM ATP, 145ul water, 1ul SUPERaseIn, and an additional 2ul of PNK were added for 30 min at 37oC.  The reaction was then stopped by addition of 20mM EDTA followed by acid phenol extraction and precipitation.

treatment_protocol: To collect differentiated samples, HV ES cells were differentiated for 5 days by LIF withdrawal, as previously described (Morgani et al., 2013).

tag: library strategy

value: GRO-Seq

value: Hhex-venus (HV) ES cells

tag: sample type

value: nascent RNA

tag: gro-seq antibody

value: anti-BrU (sc-32323-ac)


title: HV+S+

status: Public on Jan 03 2022

type: SRA

state: NY

country: USA

description: Primitive endoderm-primed

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Primitive endoderm-primed

tag: cell type


title: HV-S+

description: Epiblast-primed

source_name: Epiblast-primed


title: WT_NoStim_24 [45]

city: Ridgefield

first: Li

last: Li

state: Connecticut

address: PO Box 368

institute: Boehringer Ingelheim Pharmaceuticals, Inc.

data_processing:
Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads
Sequenced reads were examined by fastqc, then mapped to mouse reference genome  Mouse GRCm39/mm39 using STAR, followed by Rsubread to generate raw counts, followed by data normalization by EdgeR. Differentially expressed genes (DEGs) and biological pathway were determined by LIMMA-Voom.
Genome_build: mm39
Supplementary_files_format_and_content: Normalized_data.csv

growth_protocol: Monocytes from NFAM1+/+ and NFAM1-/- mice  were resuspended in cell culture media comprised of RPMI, 10% fetal bovine serum and 1% Penicillin/streptomycin. Monocytes were cultured in a 96 well tissue culture plate  at a concentration of 20,000 cells per well and either left untreated or pretreated for one hour with 100 ug/mL of mouse IFN-γ and subsequently stimulated with MegaCD40L for 6 and 24 hours.

extract_protocol:
RNA was isolated using an RNeasy Plus Mini kit .
Library construction and sequencing were performed at Beijing Genomics Institute as follows. RNA was then fragmented and cDNA was synthesized using the Illumina Truseq polyA mRNA library preparation protocol (non-stranded). RNA-sequencing was performed on an Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads.

treatment_protocol: To better understand the impact of NFAM1 deletion of monocyte activation, monocytes isolated from human PBMCs were nucleofected with CRISPR ribonucleoprotein (RNP) complexes using an Amaxa 4D nucleofection system according to manufacturer’s instructions (Lonza). Knockout efficiency was assessed by western blot detection of NFAM1 protein or sanger sequencing of PCR amplified target genomic loci. We performed whole transcriptome analysis on monocytes that were cultured in the presence or absence of IFN-γ plus CD40L for 6 and 24 hours. NFAM1+/+ and NFAM1-/- monocytes were left unstimulated, or stimulated with IFN-γ plus 1 ug/mL MegaCD40L. 6 or 24 hours later, supernatant was removed, cells were resuspended in RNAlater, and RNA was isolated using an RNeasy Plus Mini kit. Library construction and sequencing were performed at Beijing Genomics Institute as follows. RNA was then fragmented and cDNA was synthesized using the Illumina Truseq polyA mRNA library preparation protocol (non-stranded). RNA-sequencing was performed on an Illumina HiSeq2000 sequencer to generate 101x2 pair-end reads.

tag: strain

tag: agent

value: PBL Monocyte

tag: genotype

value: wild type


title: WT_IFN_CD40L_24 [57]

value: IFN-γ plus 1 ug/mL MegaCD40L


title: RAW CM SCR 4

type: RNA

city: MILANO

first: BIANCA

last: CIONI

state: MI

address: Via Antonio Amadeo 42

department: Research

country: Italy

institute: IRCCS Istituto Nazionale Tumori

description: RAW264.7 cells cultured in conditioned medium of SCR PyMT-41C cells

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol on GeneChip Scanner 3000 7G

data_processing:
Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software
MTA-1_0.r3.pgf
MTA-1_0.na35.mm10.transcript.csv

label: biotin

source_name: RAW264.7  in SCR conditioned medium 4

label_protocol: Total RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

growth_protocol: RAW264.7 cells were grown for 24 hrs in 50:50 normal RPMI supplemented with 10% FBS and conditioned medium of JMDJ6-KO, SCR PyMT-41C cells alone or in combination with CSH.

extract_protocol: Total RNA was extracted using Qiazol reagent and purified with the RNeasy kit on a QIAcube automated station (Qiagen) according to the manufacturers’ instructions

treatment_protocol: not applicable

value: macrophage


title: VL_SkM_12w_RT_SWOLL24

type: genomic

city: Durham

first: Christopher

middle: G.

last: Vann

state: NC

address: 300 N. Duke St

department: Molecular Physiology Institute

institute: Duke University School of Medicine

description: healthy college-aged male

hyb_protocol: DNA was assayed in accordance with manufacturer's specification (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018119_702989_Axiom2_96F_Man_QR.pdf)

data_processing:
Raw data files wire analyzed using Axiom Analysis Suite v4.0.3.3 (Thermo Fisher Scientific).  QC of genotype data was completed using Plink (V. 1.9) controlling for high levels of missingness, minor allele frequency, and violations of the Hardy-Weinberg equilibrium rule.  Genome-wide p-value distribution was evaluated using Q-Q plots of observed versus expected -log10 p-value.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall

label: Streptavidin Phycoerythrin (SAPE)

molecule: genomic DNA

organism: Homo sapiens

source_name: baseline_vastus lateralis_12w_RT_Protein Metabolism Research Laboratory; Stuart M. Phillips, PhD; Department of Kinseiology, McMaster University, Hamilton, Ontario, CAN

label_protocol: As per manufacturer's specificatin (Thermo Fisher)

extract_protocol: Genomic DNA was extracted from vastus lateralis skeletal muscle tissue embedded in OCT.  Tissue samples were equilibrated to room temperature and removed from OCT and rinsed in 1x phosphate buffered saline.  DNA was the extracted using Qiagen DNeasy Blood and Tissue Kits (Qiagen, Venlo, Netherlands; Cat. No: 69506) in accordance with the manufacturers specifications.

tag: age

tag: disease

value: healthy

tag: Sex

value: male

tag: tissue

value: Skeletal Muscle (Vastus Lateralis)


title: VL_SkM_12w_RT_SWOLL34

description: healthy college-aged male

scan_protocol: DNA was assayed in accordance with manufacturer's specification (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018119_702989_Axiom2_96F_Man_QR.pdf)


title: VL_SkM_12w_RT_SWOLL23

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL57

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL35

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL49

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL27

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL43

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL58

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL39

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL40

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL41

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL37

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL38

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL59

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL28

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL47

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL48

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL52

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL32

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL50

description: healthy college-aged male


title: RAW CM SCR 3

source_name: RAW264.7  in SCR conditioned medium 3


title: VL_SkM_12w_RT_SWOLL29

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL51

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL45

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL56

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL33

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL30

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL54

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL20

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL13

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL17

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL16

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL 11

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL 10

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL18

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS84

description: healthy college-aged male

source_name: baseline_vastus lateralis_12w_RT_Molecular and Applied Sciences Laboratory; Michael D. Roberts, PhD, School of Kinesiology, Auburn University, Auburn, AL, USA


title: VL_SkM_12w_RT_MPS91

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS74

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL 7

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS75

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS76

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS78

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL 4

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL15

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL19

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL14

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL 8

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS80

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS90

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS86

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS83

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS93

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS89

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL 2

description: healthy college-aged male


title: VL_SkM_12w_RT_SWOLL22

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS87

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS77

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS85

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS73

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS70

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS68

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS67

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS64

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS65

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS62

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS63

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS66

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS52

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS50

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS53

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS60

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS49

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS55

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS59

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS38

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS45

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS46

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS41

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS58

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS48

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS61

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS42

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS40

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS34

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS33

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS36

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS29

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS69

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS28

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS57

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS20

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS25

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS21

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS27

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS23

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS17

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS11

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS14

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS10

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS15

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS04

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS06

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS13

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS12

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS07

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS02

description: healthy college-aged male


title: VL_SkM_12w_RT_MPS08

description: healthy college-aged male


title: BG1030 2

city: New York

first: David

middle: Herman

last: Bechhofer

address: 1 Gustave L. Levy Place

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
base calling and quality scoring conducted via BaseSpace
adaptor trimming and low quality read removal via Trimmomatic v. 0.38 for RNA-seq .fastq dataset
all reads containing custom oligo were extracted via Cutadapt v. 1.16 for Term-seq .fastq dataset
both RNA-seq and Term-seq .fastq files were mapped to B. subtilis genome using bwa-mem v.0.7.12-r1034
sam -> bam, and bam files split by strand via samtools v. 0.1.19-44428cd
coverage files (.cov) for 3' end mapping and .bedgraph files to illustrate coverage were generated using bedtools v. 2.26.0
2 custom python (python v. 3.8.3) scripts were used to identify 3' ends from Term-seq .fastq derived .cov files (located at: https://github.com/zfmandell/Term-seq)
RNA-seq coverage files generated using bedtools v. 2.26.0
Genome_build: Refseq : NC_000964.3
Supplementary_files_format_and_content: bedgraph files, containing a list of called peaks and associated height values

organism: Bacillus subtilis

source_name: bacterial cells

growth_protocol: Cells were plated on LB plates at 37°C with relevant antibiotics when required -> single colonies isolated and grown O/N at 37°C in LB with relevant antibiotics when required  -> next day, cultures were grown in LB at 37°C without antibiotics

extract_protocol:
Total RNA prepared using RNeasy kit,  3' ends treated with CIAP, depleted for rRNA, ligated to unique 5' phosphorylated 2',3' dideoxy 3' end oligo (5’-pAAUGAGACACUGAGAUCCAGUCGAUGAGCUAddC-3')
Standard Illumina library prep by Genewiz using NEBNext Ultra II RNA Library Prep kit

tag: vegetative growth cells

value: PNPase point mutant

value: trpC2 thr-5 pnpAD493A


title: BG1030 3


title: BG1030 1


title: BG838 1

value: CshA deletion mutant

value: trpC2 thr-5 cshA::Nm


title: BG838 3


title: BG838 2


title: BG546 2

value: PNPase deletion mutant

value: trpC2 thr-5 pnpA::Nm


title: BG546 1


title: BG546 3


title: BG1 2

value: Wild type

value: trpC2 thr-5


title: BG1 3


title: BG1 1


title: VL_SkM_12w_RT_MPS18

description: healthy college-aged male


title: WT-input

city: Houston

first: Anthony

last: Flores

state: TX

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

library_source: genomic

data_processing:
Base calls onboard Illumina NextSeq500
Raw data files processed using CLC Genomics Workbench v 21
Reads mapped to reference genome MGAS2221 (CP043530.1) using CLC Genomics Workbench v 21
Peak calls using CLC Genomics Workbench v 21 ChIP-seq analysis tool
Individual peaks enumeratied and normalized [(total reads mapped to peak)/(peak length in bp)*100; reads per kilobase length - RPKL]
Genome_build: MGAS2221 (CP043530.1)
Supplementary_files_format_and_content: Excel tables with peak calls and RPKL

organism: Streptococcus pyogenes

growth_protocol: GAS cells were grown in rich medium (Todd-Hewitt, 0.2% yeast extract) to an OD of 0.5 (mid-exponential phase)

extract_protocol:
Bacterial cell lysates were purified using a CovR-specific antibody
Illumina compatible indexed libraries were prepared from 2-10ng of sheared ChIP or input DNA using the KAPA Hyper Library Preparation Kit (KAPA Biosystems, Inc.)

treatment_protocol: No treatments

tag: replicate

value: Input DNA

tag: growth condition

value: in vitro


title: E281A-input


title: E281A-5

description: processed data file: M1-E281A_GEO-chip_12-2021.xlsx

value: Replicate 5

tag: chip antibody

value: CovR-specific antibody


title: E281A-1

value: Replicate 1


title: WT-6

description: processed data file: M1-WT_GEO-chip_12-2021.xlsx

value: Replicate 6

value: wild type


title: WT-1


title: WT-3

value: Replicate 3


title: WT-5


title: 783236_1

city: Stanford

first: Mira

middle: Noura

last: Moufarrej

state: CA

address: 318 Campus Drive, E300

department: Bioengineering

institute: Stanford University

description:
processed data file:
counts_Stanford_preQC.csv
counts_Discovery_postQC.csv

data_processing:
Raw sequencing reads were trimmed using Trimmomatic (v 0.36)
Mapped to the human reference genome (hg38) with STAR (v 2.7.3a)
Duplicate reads were then removed by GATK’s (v 4.1.1) MarkDuplicates tool
Mapped reads were sorted and quantified using htseq-count (v 0.11.1) generating a counts table (genes x samples)
Gene filtering QC used a basic cutoff that required a given gene be detected at a level of at least 0.5 CPM in at least 75% of discovery samples after removing outlier samples. Following this step, we retain 7,160 genes for differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: preQC csv include counts table for cohort samples (Stanford, Validation2) prior to gene filtering.
Supplementary_files_format_and_content: postQC csv files includes counts table for cohort samples (Discovery, Validation1, Validation2) after gene filtering.

source_name: blood plasma

extract_protocol:
In 96-sample batches, cfRNA from 1-mL plasma samples was extracted in a semi-automated fashion using the Opentrons 1.0 system and Norgen Plasma/Serum Circulating and Exosomal RNA Purification 96-Well Kit (Slurry Format) (Cat No 29500, Norgen). Samples were subsequently treated with Baseline-ZERO DNAse (Cat No DB0715K, Lucigen) for 20 minutes at 37˚C. DNAse-treated cfRNA was then cleaned and concentrated into 12 µL using Zymo RNA Clean and Concentrator-96 kits (Cat No R1080).
cfRNA sequencing libraries were prepared with SMARTer Stranded Total RNAseq Kit v2 - Pico Input Mammalian Components (Cat No 634419, Takara) from 4 µL of eluted cfRNA according to the manufacturer’s instructions. Samples were barcoded using SMARTer RNA Unique Dual Index Kit – 96U Set A (Cat No 634452, Takara), and then pooled in an equimolar fashion.

value: pre-eclampsia

tag: sampling time group

value: ≤12 weeks gestation

tag: cohort

value: Discovery

value: blood plasma


title: 888980_3

value: control

value: ≥23 weeks gestation


title: 960203_4

value: Post-partum


title: 662256_4


title: 737184_2.1

value: severe pre-eclampsia

value: 13-20 weeks gestation


title: 680949_3


title: 809660_1


title: 737184_2


title: 680949_2


title: 550205_3


title: 550205_4


title: 783236_4


title: 787693_3


title: 787693_2


title: 723691_2


title: 723691_4


title: 723691_3


title: 773477_4


title: E281A-3


title: E281A-6


title: 773477_3


title: 773477_2


title: 773477_1


title: 586898_4


title: 549101_3


title: 586898_2


title: 906787_4


title: 698019_1


title: 827529_4


title: 906787_1


title: 334129_1

description:
processed data file:
counts_Validation2_preQC.csv
counts_Validation2_postQC.csv

value: Validation 2


title: 827529_3


title: 549101_1


title: 788006_4


title: 737184_4


title: 809660_3


title: 698019_4


title: 261268_2


title: 788006_2


title: 827529_2


title: 788006_3


title: 434662_2


title: 401187_2


title: 235246_2


title: 108445_1


title: 301419_1


title: 169395_1


title: 339832_2


title: 412304_2


title: 195443_1


title: 349246_1


title: 946772_4


title: 906787_3


title: 464537_2


title: 457230_2


title: 253823_1


title: 159918_2


title: 316949_1


title: 147354_2


title: 331344_2


title: 454195_2


title: 349246_2


title: 406636_1


title: 418624_2


title: 450582_2


title: 946772_3


title: 826701_3


title: 743122_4


title: 939512_3


title: 826701_1


title: 743122_1


title: 743122_3


title: 939512_2.1


title: 384886_2


title: 706816_3


title: 939512_2


title: 161584_1


title: 615064_3


title: 615064_4


title: 615064_1


title: 594098_4


title: 594098_1


title: 594098_2


title: 737046_4


title: 706816_1


title: 737046_2


title: 737046_3


title: 267586_2


title: 737046_1


title: 267586_1


title: 229182_1


title: 293901_1


title: 943952_2


title: 405912_2


title: 295748_1


title: 455648_1


title: 946772_2


title: 393370_2


title: 167961_1


title: 469006_2


title: 330152_1


title: 475571_1


title: 410199_1


title: 262245_1


title: 209564_1


title: 141218_1


title: 615064_2


title: 943952_3


title: 184204_1


title: 133247_1


title: 946772_1


title: 254685_1


title: 121329_2


title: 230843_2


title: 103651_1


title: 346539_1


title: 319860_2


title: 149589_1


title: 692077_4


title: 943952_4


title: 122540_2


title: 265479_2


title: 313204_2


title: 456050_1


title: 490545_1


title: 415120_1


title: 291886_1


title: 253665_1


title: 178534_1


title: 692077_3


title: 443078_1


title: 485310_1


title: 255058_2


title: 328020_1


title: 546738_2.1

description:
processed data file:
counts_Stanford_preQC.csv
counts_Validation1_postQC.csv

value: Validation 1


title: 406755_1


title: 501143_2


title: 480303_1


title: 170689_1


title: 197072_2


title: 277408_1


title: 501143_4


title: 915027_1


title: 520109_4


title: 138919_1


title: 525989_4


title: 915027_2


title: 629773_2


title: 525989_2


title: 546738_2


title: 501143_1


title: 637549_4


title: 525989_1


title: 569467_2


title: 569467_2.1


title: 674547_3


title: 629773_1


title: 915027_3


title: 765128_2


title: 765128_4


title: 294171_1


title: 674547_1


title: 597312_2


title: 813805_4


title: 557409_4


title: 520109_2


title: 520109_3


title: 678649_3


title: 765128_1


title: 813805_2


title: 512025_4


title: 813805_1


title: 512025_2


title: 631489_2


title: 597312_3


title: 813805_3


title: 814701_2.1


title: 690247_4


title: 674547_2


title: 631489_3


title: 631489_1


title: 508691_3


title: 678649_2


title: 814701_2


title: 852717_4


title: 690247_2


title: 852717_2


title: 512025_1


title: 505372_3


title: 597312_4


title: 884755_2


title: 625950_1


title: 631489_4


title: 505372_1


title: 740596_3


title: 579493_3


title: 703998_2


title: 740596_2


title: 792176_1


title: 872878_4


title: 988719_4


title: 872878_2


title: 988719_2


title: 872878_3


title: 579493_4


title: 872878_1


title: 695492_2


title: 579493_2


title: 695492_3


title: 664041_2


title: 505372_2


title: 579493_1


title: 792176_4


title: 792176_2


title: 856650_3.1


title: 664041_4


title: 856650_3


title: 988719_1


title: 664041_3


title: 972839_4


title: 852717_3


title: 636361_4


title: 965096_1


title: 856650_2


title: 636361_3


title: 636361_1


title: 972839_1


title: 972839_2


title: 786768_2


title: 534069_2


title: 668974_4


title: 534069_4


title: 534069_1


title: 965096_3


title: 783078_2


title: 668974_3


title: 943952_1


title: 928186_1


title: 668974_2


title: 668974_1


title: 896869_1


title: 977018_3


title: 786768_1


title: 695492_4


title: 668974_4.1


title: 663288_4


title: 625950_3


title: 703998_3.1


title: 782752_4


title: 977018_1


title: 663288_3


title: 783078_1


title: 212444_1


title: 782752_3


title: 692077_2


title: 703998_3


title: 663288_1


title: 786768_3


title: 477841_1


title: 490522_1


title: 339444_1


title: 141956_2


title: 361175_1


title: 250475_1


title: 455697_1


title: 194785_2


title: 166490_1


title: 397120_1


title: 309805_2


title: 205623_2


title: 133532_1


title: 260786_1


title: 406813_1


title: 320238_2


title: 472330_1


title: 739041_3


title: 546738_4


title: 739041_4


title: 902180_4


title: 546738_3


title: 902180_3


title: 902180_2


title: 902180_1


title: 783078_4


title: 582739_4


title: 961389_3


title: 582739_3


title: 888987_4


title: 903837_2


title: 678649_1


title: 888987_2


title: 903837_1


title: 971241_3


title: 971241_2


title: 971241_4


title: 707861_2


title: 752820_4


title: 653512_4


title: 605858_4


title: 692077_1


title: 653512_3


title: 653512_2


title: 709690_4.1


title: 653512_1


title: 709690_3


title: 709690_4


title: 709690_2


title: 709690_1


title: 691160_1


title: 691160_2


title: 605858_3


title: 691160_3


title: 905498_1


title: 905498_2


title: 689440_3


title: 689440_2


title: 689440_4


title: 689440_1


title: 888987_3


title: 982023_3


title: 982023_2


title: 605858_2


title: 500915_3


title: 903837_3


title: 740015_1


title: 997717_4


title: 500915_2.1


title: 997717_3


title: 500915_2


title: 931746_2


title: 997717_2.1


title: 515494_1


title: 637549_3


title: 637580_3


title: 637580_1


title: 835749_3


title: 835749_1


title: trps1:eGFP-enriched

first: Joanna

last: Smeeton

address: 650 W 168TH ST, ROOM 1103A, William Black Building

department: Rehabilitation and Regenerative Medicine

institute: Columbia University Irving Medical Center

data_processing:
Fastq files were aligned using CellRanger v3.0.0 to GRCz11 built with v4.3.2.gtf including GFP and DsRed sequences as additional artificial chromosomes
Genome_build: z11
Supplementary_files_format_and_content: barcodes, features, and matrix files from Cell Ranger alignment

organism: Danio rerio

source_name: Adult Jaw Joint

extract_protocol:
50 micro-dissected jaw joints from 3-month-old sox10:DsRed;trps1:eGFP double transgenic zebrafish were dissociated into single cell suspension then FACS sorted to isolate live DsRed-positive (+/- GFP) and GFP positive populations. Single cells were processed through the 10X chromium controller.
Barcoded single cell cDNA library construction was performed as per 10X Genomics Chromium Single Cell 3' Library and Gel Bead Kit v.2. standard protocol

value: trps1:eGFP-positive joint cell

value: Jaw joint


title: 890932_3


title: sox10:DsRed-enriched

value: sox10:DsRed-positive joint cell


title: 835749_2


title: 931746_1.1


title: 890932_1


title: 825158_3


title: 982023_1


title: 740015_3


title: 825158_1


title: NOR4.fq.gz

city: Changsha

first: Yiwen

last: He

address: num.36 Lu shan road, Yuelu district, Changsha, China

country: China

institute: Hunan normal university

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: excel,expression profiles

organism: Sus scrofa

source_name: feces

growth_protocol: Sixty crossbred piglets (Duroc*Landrace*Yorkshire) weaned at the age of 21 days were maintained for one week and had free access to feed and water. During this week, all the piglets were scored for the severity of diarrhea.

extract_protocol:
Feces were homogenized in sterile PBS for extraction of RNA using a mirVana miRNA isolation kit
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Those piglets with a score of 4 or 5 for three continuous days were designated as diarrhea piglets, while those piglets with a score of 1 or 2 for three continuous days were designated as normal piglets..

tag: breed

value: DLT

value: feces

tag: condition

value: Normal


title: NOR6.fq.gz

tag: sample type


title: NOR5.fq.gz


title: 997717_2


title: NOR3.fq.gz


title: 520587_2.1


title: 520587_2


title: 858366_3


title: 825158_2


title: 858366_1


title: 835749_4

value: pre-eclampsia


title: DIA1.fq.gz

value: Diarrhea


title: DIA3.fq.gz


title: NOR2.fq.gz


title: DIA5.fq.gz


title: 571092_1

value: ≤12 weeks gestation


title: NOR1.fq.gz


title: DIA2.fq.gz


title: 565782_4

value: blood plasma


title: eWAT, WT, replicate 3

city: Berkeley

first: Dongjoo

last: You

state: California

address: 316 Morgan UC Berkeley

department: NST

institute: UC Berkeley

data_processing:
RNA-seq reads were aligned to UCSC mm10 using STAR aligner and uniquely aligned reads were retained for downstream analysis. After filtering rRNA mad mitochondrial reads, gene expression levels were measured using featureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing raw read count and RPKM-normalized count for each gene

source_name: eWAT (epididymal white adipose tissue)

growth_protocol: WT mice or Jmjd8-KO mice were maintained on HFD condition

extract_protocol:
Tissues were removed, flash frozen on liquid nitrogen. For RNA seq, RNA was harvested using Trizol reagent. Qiagen Rneasy mini kit Sample Prep Kit (Cat#74106) was used with 1 ug of total RNA for the construction of sequencing libraries. And sequencing was performed on the BGISEQ.
Libraries were prepared by the genome sequencing facility following manufacturers instructions forBGI Library Preparation Kit for RNA seq.

treatment_protocol: No treatment

value: WT

value: eWAT (epididymal white adipose tissue)


title: eWAT, WT, replicate 1


title: 565782_3

value: control

value: ≥23 weeks gestation


title: 890932_2

value: 13-20 weeks gestation

value: Discovery


title: eWAT, Jmjd8-KO, replicate 3


title: 897309_4

value: Post-partum

value: Validation 1


title: 897309_3


title: eWAT, Jmjd8-KO, replicate 2


title: eWAT, Jmjd8-KO, replicate 1


title: 605858_1


title: 897309_1


title: DIA4.fq.gz


title: 180130-mm18B-D72-lot2 (CEL-seq2)

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Library strategy: CEL-seq2
Extraction of sample barcodes and unique-molecular-identifiers (UMIs) was performed using UMI-tools (T. S. Smith et al., 2017) (version 1.0.1) with the following commands: umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern=NNNNNNCCCCCC --read2-stdout for CEL-Seq2, and umi_tools extract -I r1.fastq --read2-in=r2.fastq --bc-pattern= NNNNNNCCCCCCCCC --read2-stdout for BRB-seq.
The reads were trimmed using Cutadapt (M. Martin, 2011)  (version 2.6) wapper, Trim Galore! (version 0.6.6), with the option:  -a GATCGTCGGACT.
The reads were mapped by the aligning software HISAT2 (D. Kim et al., 2015, M. Pertea et al., 2016, D. Kim et al., 2019) (version 2.1.0) to the reference genome (GRCm38, pre-built HISAT2 index, genome_snp_tran).
Read counts per gene were obtained using featureCounts (Liao Y et al., 2014) (version 2.0.1). Note that UMIs were not used and mitochondrial genes are excluded in the analysis.
DESeq2 software (M. I. Love et al., 2014) (1.28.1) was used to calculate normalized counts.
*.csv files include comma-delimited read count matrices and normalized count matrices.
Genome_build: GRCm38/mm10

source_name: C2C12 cell line

growth_protocol: C2C12 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 20% fetal bovine serum.

extract_protocol:
Total RNA was extracted from cells using Sepasol-RNA I Super G (Nacalai Tesque) and reverse-transcribed with PrimeScript II Reverse Transcriptase (Takara) and either oligo-dT primer or random 6-mer according to the manufacturer’s protocols.
CEL-Seq2 was carried out as described previously (Harada et al. 2017 Nat Commun, Hashimshony et al. 2016 Genome Biol). Sequencing was performed using HiSeq PE Rapid Cluster Kit v2 (Illumina) in an Illumina HiSeq 1500 system with 15 cycles for read 1 and 36 cycles for read 2 in CEL-Seq2.

treatment_protocol: For differentiation, cells were transferred to DMEM containing 2% horse serum upon reaching confluence.

value: C2C12 cell line

tag: cell type

value: Differentiated for 72 hours

tag: sample barcode

value: GTTGCA


title: 897309_2


title: 180122-mm18B-D72-lot2 (CEL-seq2)

value: ACGTAC


title: 180130-mm18B-D72-lot1 (CEL-seq2)

value: GAAGTG


title: 702116_4


title: 180122-mm18B-D72-lot1 (CEL-seq2)

value: GAGTGA


title: 180130-eGFP-D72-lot1 (CEL-seq2)

value: GTCTTC


title: 180130-eGFP-D72-lot2 (CEL-seq2)

value: CACTAG


title: 702116_1

value: ≤12 weeks gestation

value: blood plasma


title: 683266_2


title: 683266_3


title: 180130-eGFP-D72-lot3 (CEL-seq2)

value: CTAGAC


title: 683266_4

value: control


title: 180122-eGFP-D72-lot2 (CEL-seq2)

value: CAGATC


title: 180122-eGFP-D72-lot1 (CEL-seq2)

value: CTTCTG


title: 180403-mm18B-G-lot3 (CEL-seq2)

value: Proliferative


title: 931746_3

value: ≥23 weeks gestation

value: Discovery


title: 683266_1

value: Validation 1


title: 180403-mm18B-G-lot2 (CEL-seq2)

value: C2C12 cell line

value: GATCAC


title: 565782_2

value: 13-20 weeks gestation


title: eWAT, WT, replicate 2

tag: strain

value: WT

value: eWAT (epididymal white adipose tissue)


title: 930841_3


title: 180403-mm18B-G-lot1 (CEL-seq2)

tag: genotype

value: GTTGCA


title: 702116_3


title: 180121-mm18B-G-lot2 (CEL-seq2)

value: CAACCA


title: 930841_2


title: 930841_1

value: ≤12 weeks gestation


title: 180121-mm18B-G-lot1 (CEL-seq2)

value: ACGTAC


title: 839621_3

value: severe pre-eclampsia

value: blood plasma


title: 839621_4

value: Post-partum


title: 180130-mm18B-D72-lot3 (CEL-seq2)

value: Differentiated for 72 hours


title: 180403-eGFP-G-lot2 (CEL-seq2)

value: Proliferative

value: CTAGAC


title: 839621_1

value: Discovery


title: 180403-eGFP-G-lot1 (CEL-seq2)

value: CACTAG


title: 180121-eGFP-G-lot2 (CEL-seq2)

value: C2C12 cell line

value: TGTCGA


title: 565234_2

value: pre-eclampsia

value: 13-20 weeks gestation


title: 662256_3

value: ≥23 weeks gestation


title: 565234_4


title: 862314_4

value: control


title: ct26nlrc5ko

city: shanghai

first: jiale

middle: jia

last: ren

state: shanghai

address: yueyang road 320

department: shanghai institute of nutrition and health

institute: CAS

data_processing:
The 75-nt sequence reads generated by Illumina sequencing  were mapped to the genome using the GALAXY Map with BWA(map short reads(<100bp) against reference genome)
Examine aligned records in BAM datasets to locate duplicate molecules to produce a MarkDuplicates BAM  file
Generates coverage bigWig file from a MarkDuplicates BAM  file
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from indicated cells.
Genomic libraries were prepared according to Vazyme TD501 library prep kit for tagmentation and PCR amplification.

value: BALB/c

tag: genotype/variation

value: Nlrc5 KO


title: ct26p

value: WT


title: 862314_2

tag: disease


title: ct26whsc1ko

value: Whsc1 KO


title: 862314_1

value: ≤12 weeks gestation

value: blood plasma


title: HFD LKO2

city: Chongqing

first: Hong

last: Qin

address: Yuzhong District Medical College Road

institute: ChongQing Medical University

data_processing:
Illumina HiSeq Xten/NovaSeq6000
The raw paired end reads were trimmed and quality controlled by SeqPrep  and Sickle with default parameters.
clean reads were separately aligned to reference genome with orientation mode using HISAT2  software. The mapped reads of each sample were assembled by StringTie in a reference-based approach
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: liver

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent and genomic DNA was removed using DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HFD containing 60 kcal% fat for 16 weeks


title: HFD LKO3


title: HFD LKO1


title: 947956_3


title: HFD CON3

value: wild type


title: HFD CON2


title: 947956_1


title: HFD CON1


title: 702116_2

value: Validation 1


title: 947956_4

value: Post-partum


title: 523257_2

value: Discovery


title: 523257_3


title: 180403-eGFP-G-lot3 (CEL-seq2)

value: Proliferative

value: CTTCTG


title: AAV-GFP-MBNL1∆_3

city: PARIS

first: Denis

last: Furling

state: ILE-DE-FRANCE

address: 52 blv Vincent Auriol

country: France

institute: Centre de Recherche en Myologie

data_processing:
Trimming of low-quality bases of reads with Cutadapt/2.10
Alignment realised with STAR/2.7.5a,
Read-quantification done with HTSeq/0.12.4
Differentially-expressed genes found via DESeq2/1.30.0
Genome_build: mm10
Supplementary_files_format_and_content: .txt= quantification of gene expression

source_name: gastrocnemius muscle

growth_protocol: 2-3 month old FVB mice

extract_protocol:
Gastrocnemius muscles were collected, snap frozen and total RNA was isolated using Trizol reagent then treated with RQ1 RNase-Free DNase (Promega)
RNA quality control realised with Tapestation 2200(Agilent) and libraries were prepared  with the KAPA mRNA hyperprep ROCHE kit from an input of 250ng

treatment_protocol: Gastrocnemius muscles of wild-type FVB mice were injected with saline,  AAV-GFP or AAV-GFP-MBNL1∆. Mice were sacrified 7 weeks after injection

value: gastronemius muscle

value: FVB

tag: treatment

value: treated with AAV-GFP-MBNL1[delta]


title: AAV-GFP-MBNL1∆_1

tag: tissue


title: AAV-GFP_3

value: treated with AAV-GFP


title: 773626_4

value: pre-eclampsia


title: 523257_1


title: AAV-GFP_2


title: 773626_2

value: 13-20 weeks gestation


title: 180121-eGFP-G-lot1 (CEL-seq2)

value: C2C12 cell line

value: CAGATC


title: 773626_3

value: ≥23 weeks gestation


title: AAV-GFP_1


title: 862314_3

value: control


title: 944838_3

value: blood plasma


title: Saline_2

value: saline


title: AAV-GFP-MBNL1∆_2


title: 777827_4

value: severe pre-eclampsia


title: 777827_3


title: 662256_1

value: ≤12 weeks gestation


title: ra-fm1

city: Hamilton

first: Karen

last: Mossman

state: Ontario

address: 1280 Main St West

department: Department of Medicine

country: Canada

institute: McMaster University

data_processing:
Cells were sequenced using a NovaSeq 6000, with a goal of 60 000 reads per cell.
Raw sequencing data (BCL format) processed to FASTQ and demultiplexed using bcl2fastq (Illumina).
FASTQ files processed using 10X Genomics Cell Ranger v3.1.0.
Reads was performed against mouse mm10 genome reference and influenza A/FM/1/47-MA cRNA sequences (PB2 (GenBank: CY087791.1), PB1 (CY087790.1), PA (CY087789.1), NEP/NS1 (CY087788.1), NP (CY087787.1), NA (CY087786.1), M1/M2 (CY087785.1), HA (CY087784.1)
Cells with unique counts over 6,000 or less than 200 were filtered out. Next, cells with mitochondrial counts < 6, 7 and 9% were selected for CS-H1N1, RA-H1N1 and RA-PBS, respectively to best approximate viabilities acquired from input cells by haemocytometry
Raw counts were log-normalized and used for PCA, which was followed by unsupervised clustering analysis and UMAP for dimensionality reduction and visualization (Seurat package in R).
Genome_build: mm10
Supplementary_files_format_and_content: h5 files containing filtered counts (1 file for each sample)

extract_protocol:
Lungs were extracted, minced, and digested with collagenase I (150U/ml, 10ml) for 1h at 37 degrees Celcius. Lungs were pressed through a 40um filter. Cells were centifuged, lysed with ACK buffer, washed twice with PBS, and refiltered at 40um. Cells were then pooled per group and prepared for scRNAseq using 10X Genomics 3'v3.1 chemistry.
Reads were aligned to mm10 mouse genome and A/FM/1/47-MA (+) sense cRNA references.

treatment_protocol: Refer to [Overall Design] and [Characteristics: Treatment]

value: Whole lung cells

value: BALB/c

value: Room air + H1N1


title: ra-pbs

source_name: RA-PBS

value: Room air + PBS


title: 777827_1

value: Discovery


title: cs-fm1

value: Cigarette smoke + H1N1


title: 947956_2


title: M6 CD45-negative cells (QPCTL-KO) tumor bearing

city: Amsterdam

first: Kaspar

last: Bresser

address: Plesmanlaan 125

department: Hematopoeisis

country: Netherlands

institute: Sanquin

description:
all_gene_counts_bulkRNA_QPCTL.tsv
DE_results_tumor.tsv

data_processing:
Reads were aligned to the pre-built GRCm38 genome_snp_tran reference using HISAT2
transcript counts were obtained using in-house generated pipe-line GenSum (https://github.com/NKI-GCF/gensum).
Differential gene expression analysis was performed with the edgeR package
Subsequent analysis was performed using the MetaCell package in the R environment.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: all_gene_counts_bulkRNA_QPCTL.tsv: genecount table for all samples as calculated using GenSum. DE_results_tumor.tsv: Output of EdgeR for the CD45-negative population

molecule: polyA RNA

source_name: CD45-negative cells sorted from B16F10 TMEs

extract_protocol:
RNA was extracted from the indicated frozen tissues using the RNeasy Mini Kit (Qiagen). Flow-sorted cell populations were washed in PBS once, and subsequently lysed in RLT buffer (Qiagen). Whole transcriptome sequencing samples were prepared with the TruSeq Stranded mRNA Kit (Illumina). Paired-end 50 bp sequencing was performed on a NovaSeq 6000 system (S1 flowcell, Illumina), obtaining an average of 18x106 reads per sample.
Whole transcriptome sequencing samples were prepared with the TruSeq Stranded mRNA Kit (Illumina).

value: QPCTL-KO C57/Bl6JR

value: homozygous QPCTL-KO

tag: innoculation

value: B16F10 tumor cells (QPCTL-KO)

tag: time point

value: 14 days post tumor innoculation

value: sorted CD45-negative cells


title: 826701_4

value: Post-partum


title: M5 CD45-negative cells (QPCTL-KO) tumor bearing


title: 662256_2

value: pre-eclampsia

value: 13-20 weeks gestation


title: 944838_4

value: control

value: blood plasma


title: 931746_1

value: ≤12 weeks gestation


title: M4 CD45-negative cells (QPCTL-KO) tumor bearing


title: 944838_1


title: M3 CD45-negative cells (QPCTL-KO) tumor bearing


title: M2 CD45-negative cells (QPCTL-KO) tumor bearing


title: 944838_2


title: M1 CD45-negative cells (QPCTL-KO) tumor bearing


title: M6 CD45-negative cells (QPCTL-WT) tumor bearing

value: wild-type for QPCTL allele (littermate)

value: B16F10 tumor cells (QPCTL-WT)


title: M5 CD45-negative cells (QPCTL-WT) tumor bearing


title: M4 CD45-negative cells (QPCTL-WT) tumor bearing


title: Saline_3

value: gastronemius muscle

value: FVB

value: saline


title: M3 CD45-negative cells (QPCTL-WT) tumor bearing


title: Saline_1


title: HA-FKBP-Gdown1 PRO-Seq 4 h dTAGV1 Rep 1

city: Iowa City

middle: H

last: Price

state: IA

address: 431 Newton Road

department: Department of Biochemistry and Molecular Biology

institute: University of Iowa

data_processing:
Library strategy: PRO-seq
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.2 (PRO-Seq and ChIP-Seq) or hisat2 (RNA-Seq)
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing pileup of normalized RNA-Seq, PRO-Seq, and ChIP-data

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM (Gibco 11965-092) supplemented with 10% FBS.

extract_protocol:
Rapid nuclei isolation steps for PRO-Seq were performed on wet ice using ice-cold buffers as previously described (Nilson et. al. 2017; Ball et. al. 2019). Modifications described in the text were made for harvesting mitotic cells for PRO-Seq. For RNA-Seq, cells were directly lysed in Trizol, and extracted and DNase treated prior to quality control analysis as described in the text.
Details of library construction for each type of assay are provided in the methods.

treatment_protocol: Parental and HA-FKBP-Gdown1 HeLa cells in a T-150 flask were treated with 400 nM dTAGV-1 or DMSO vehicle control for 4 h prior to harvesting nuclei for PRO-Seq.

tag: cell line

value: HeLa

value: 4 h 400 nM dTAGV-1


title: HA-FKBP-Gdown1 PRO-Seq 4 h dTAGV1 Rep 2

tag: chip antibody


title: HA-FKBP-Gdown1 PRO-Seq 4 h DMSO Rep 2

value: 4 h DMSO


title: HA-FKBP-Gdown1 PRO-Seq 4 h DMSO Rep 1


title: 777827_2

value: severe pre-eclampsia

tag: sampling time group

value: Discovery


title: M2 CD45-negative cells (QPCTL-WT) tumor bearing

value: QPCTL-KO C57/Bl6JR

value: 14 days post tumor innoculation

value: sorted CD45-negative cells


title: M1 CD45-negative cells (QPCTL-WT) tumor bearing


title: M6 LN (QPCTL-KO) tumor bearing

source_name: Lymph nodes (from tumor-bearing animal)

value: homozygous QPCTL-KO

value: B16F10 tumor cells (QPCTL-KO)

value: Lymph nodes (from tumor-bearing animal), whole organ


title: Parental PRO-Seq 4 h DMSO Rep 2

value: parental


title: Parental PRO-Seq 4 h DMSO Rep 1


title: HA-ChIP-Seq HA-FKBP-Gdown1 Rep 2

data_processing:
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.2 (PRO-Seq and ChIP-Seq) or hisat2 (RNA-Seq)
Deduplication of fragments based on their unique molecular index tags using awk and bash.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing pileup of normalized RNA-Seq, PRO-Seq, and ChIP-data

value: Untreated

value: HA rabbit pAb (Cell Signaling Technology C29F4)


title: M4 LN (QPCTL-KO) tumor bearing


title: M2 LN (QPCTL-KO) tumor bearing


title: HA ChIP-Seq HA-FKBP-Gdown1 Rep 1


title: M1 LN (QPCTL-KO) tumor bearing


title: HA ChIP-Seq Parental Rep 2


title: M3 LN (QPCTL-KO) tumor bearing


title: HA ChIP-Seq Parental Rep 1


title: M6 LN (QPCTL-WT) tumor bearing

value: wild-type for QPCTL allele (littermate)

value: B16F10 tumor cells (QPCTL-WT)


title: Gdown1 KO 3 Mitotic PRO-Seq Rep 2

value: Gdown1 KO


title: Gdown1 KO 3 Mitotic PRO-Seq Rep 1

value: HeLa


title: M5 LN (QPCTL-WT) tumor bearing


title: M4 LN (QPCTL-WT) tumor bearing


title: M3 LN (QPCTL-WT) tumor bearing


title: Parental Mitotic PRO-Seq Rep 2


title: Parental Mitotic PRO-Seq Rep 1


title: Parental PRO-Seq 4 h dTAGV1 Rep 2

value: 4 h 400 nM dTAGV-1


title: Gdown1 KO 3 Async PRO-Seq Rep 1


title: Gdown1 KO 3 Asycn PRO-Seq Rep 2


title: Parental Async PRO-Sew Rep 2


title: M4 BM (QPCTL-KO)

source_name: Bone marrow

value: No innoculation (baseline)

value: Baseline, animals aged 10-15 wks

value: Bone marrow, whole organ


title: Parental PRO-Seq 4 h dTAGV1 Rep 1


title: M3 BM (QPCTL-KO)

value: QPCTL-KO C57/Bl6JR


title: M2 LN (QPCTL-WT) tumor bearing

value: 14 days post tumor innoculation


title: M2 BM (QPCTL-KO)


title: M1 BM (QPCTL-KO)


title: Parental Async PRO-Seq Rep 1


title: Pol II ChIP-Seq

value: POLR2A mouse mAb (Santa Cruz sc-55492)


title: K8

city: Maribor

first: Erika

last: Prašnikar

address: Ljubljanska ulica 5

department: Department of Reproductive Medicine and Gynaecological Endocrinology

country: Slovenia

institute: University Medical Centre Maribor

data_processing:
Provided raw fastq files were first evaluated with FastQC v.0.11.9 software to obtain a quality profile of the reads.
Raw paired-end reads were aligned to the UCSC Homo sapiens hg19 reference genome using the Rsubread v.2.2.4 R package.
Mapped reads were counted and assigned to genomic features using featureCounts with the requirement that both ends should be mapped.
Counts per million (CPMs) were calculated using the edgeR v.3.30.3 R package. Genes expressed at low levels were filtered out based on CPMs corresponding to read counts of 10, and retained genes were normalized using the trimmed mean of M values method (TMM)
Mean-variance modelling at the observational level transformation (VOOM) was applied. Differential expression analysis of the adenomyosis group relative to the control group was determined in two RNA-seq datasets using linear models and empirical Bayes implemented in the limma v.3.44.3 R package. RNA-seq datasets were composed of libraries on the basis of the results of endometrial dating of corresponding samples. The first dataset contained all LH-timed samples, while the second dataset contained only samples dated to the receptive phase.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: endometrial biopsy

extract_protocol:
Retrieved endometrial samples were immediately placed in RNAlater solution (Thermo Fisher Scientific Baltics UAB, Vilnius, Lithuania), stored overnight at +4 °C and then transferred to –80 °C. Total RNA was isolated using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s instructions. Each whole-tissue endometrial sample was first disrupted with a Bullet Blender Storm Pro homogenizer (Next Advance, lnc., Troy, NY, USA) using 1 mm zirconium oxide beads in 700 µL of QIAzol Lysis Reagent from the miRNeasy Mini Kit.
Both lncRNA and mRNA 150 bp paired-end libraries were constructed and subsequently sequenced by Novogene Bioinformatics Technology Co., Ltd. (Hong Kong, China). Briefly, a total amount of 2 µg of RNA per sample was used for cDNA sequencing library preparation. Ribosomal RNA (rRNA) was removed using the Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, Brooklyn, NY, USA), and the remaining RNA was used for library generation by the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). First, rRNA-depleted RNA samples were fragmented followed by first- and second-strand cDNA synthesis. The sequencing adaptors were ligated, and library fragments were purified to obtain cDNA fragments 150~200 bp in length. Polymerase chain reaction (PCR) amplification of size-selected, adaptor-ligated cDNA was performed using universal PCR primers and index primers. Index-coded samples were clustered by Illumina TruSeq PE Cluster Kit v3-cBot-Hs. Libraries were sequenced on an Illumina NovaSeq 6000 platform, which generated 150 bp paired-end reads.

treatment_protocol: Endometrial biopsy sampling was conducted in a natural menstrual cycle, and women were scheduled for cycle monitoring by urinary luteinizing hormone (LH) tests (Hangzhou AllTest Biotech Co., Ltd, Hangzhou, P.R. China). Women were scheduled for endometrial sampling conducted by the Pipelle endometrial suction curette (the Probet, Gynetics Medical Products N.V., Lommel, Belgium) in the expected WOI on the day between LH+7 to LH+9 after a participant’s LH surge determination (day LH+0).

tag: study group

value: control

tag: day of biopsy sampling

tag: endometrial dating by the beready test

value: receptive


title: K27


title: K28

value: early-receptive


title: M5 LN (QPCTL-KO) tumor bearing

value: homozygous QPCTL-KO

value: B16F10 tumor cells (QPCTL-KO)

value: Lymph nodes (from tumor-bearing animal), whole organ


title: K26

value: late-receptive


title: M2 BM (QPCTL-WT)

value: wild-type for QPCTL allele (littermate)


title: M1 BM (QPCTL-WT)


title: K22


title: K23


title: K17


title: M3 Spleen (QPCTL-KO)

source_name: Spleen

value: Spleen, whole organ


title: M2 Spleen (QPCTL-KO)


title: K15


title: M1 LN (QPCTL-WT) tumor bearing

value: B16F10 tumor cells (QPCTL-WT)


title: M1 Spleen (QPCTL-KO)


title: M4 Spleen (QPCTL-WT)


title: K11


title: M3 Spleen (QPCTL-WT)


title: M4 Spleen (QPCTL-KO)


title: M2 Spleen (QPCTL-WT)


title: M4 LN (QPCTL-KO)

source_name: Lymph nodes

value: Lymph nodes, whole organ


title: M1 Spleen (QPCTL-WT)

value: No innoculation (baseline)


title: A9

value: adenomyosis case


title: A5


title: A31


title: A29


title: A20


title: M1 LN (QPCTL-KO)

value: Baseline, animals aged 10-15 wks


title: A21


title: M2 LN (QPCTL-KO)

value: QPCTL-KO C57/Bl6JR


title: A18


title: A3


title: M4 LN (QPCTL-WT)


title: M3 LN (QPCTL-KO)


title: M3 BM (QPCTL-WT)

value: Bone marrow, whole organ


title: K24


title: M4 BM (QPCTL-WT)


title: A10


title: M2 LN (QPCTL-WT)


title: M1 LN (QPCTL-WT)


title: KO2_CD11c-IM [12_S26]

city: Indianapolis

first: Mark

last: Kaplan

state: IN

address: 635 Barnhill Dr. MS 420

department: Microbiology and Immunology

institute: Indiana University

data_processing:
Sequence reads were aligned to the mouse reference genome mm10 with STAR v2.5.
featureCounts (subread-1.5.1) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Differential expression analysis was performed using edgeR.
Pathway and functional analysis were performed with IPA (QIAGEN Inc.)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited excel file includes raw counts, log2 fold change values, p-values and FDR for all samples

source_name: Il9r-/-_lung interstitial macrophage

extract_protocol:
cells were stained with surface marker and purified by FACS sorting, RNA was extracted by using RNeasy Micro kit (Qiagen)
RNA-seq libraries were prepared using the Clontech SMART-Seq V4 Ultra Low Input RNA kit.

tag: strain background

value: lung interstitial macrophage


title: M3 LN (QPCTL-WT)


title: RNA-seq sibc DOX rep2

city: Philadelphia

first: Scott

last: Waldman

state: PA

address: 1020 locus st

institute: Thomas Jefferson University

data_processing:
For RNA-seq, low-quality reads containing adapter and poly-N sequences were removed with custom perl scripts by Novogene Corporation. Clean reads were aligned to the human (hg19) reference genome using TopHat (v2.0.12) and reads mapping to each gene were counted with HTSeq (v0.6.1). Genes with counts per million (CPM) >0.5 in at least three samples were included in subsequent analyses (17,728 genes). Differential gene expression (adjusted p value < 0.05) was determined between cells treated with or without respective inducing agents, using the limma (v3.40.6) and edgeR (v3.26.8) packages in R/Bioconductor.
For ChIP-seq, Base-calling: Base call .blc files were generated using the Illumina NextSeq 500 onboard Real Time Analysis (RTA) v2 software. Alignment: sequence read fragments were aligned to the human hg38 reference genome using the BWA-MEM aligner version 0.7.17-r1188 with default parameters. Replicate pooling: Samtools version 1.10 was used to sort the resulting alignments and merge replicate .bam files for consensus peak calling. Peak-calling: Peak calling was performed for each replicate in addition to the merged alignments using macs2 version 2.1.1.20160309 with default parameters for the human genome. Sub-peak calling: sub-peak calling was performed for each replicate in addition to the merged alignments using macs2 version 2.1.1.20160309 by adding the --call-summits parameter. Bigwig generation: deepTools version 3.5.0 bamCoverage was used to generate bigwig files with the following parameters: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads 250 --ignoreDuplicates
Genome_build: hg19 (RNAseq), hg38 (ChIPseq)
Supplementary_files_format_and_content: RNA_seq_results.xlsx: Excel spreadsheet containing read counts and FPKM for each sample
Supplementary_files_format_and_content: Bigwig files: H3K27ac and Pol II ChIP-seq alignments for individual samples and merged replicates
Supplementary_files_format_and_content: Narrowpeak files: H3K27ac and Pol II ChIP-seq peaks from merged replicates
Supplementary_files_format_and_content: Bed files: H3K27ac and Pol II ChIP-seq peak summits from merged replicates

source_name: LS174T (siβ-catenin) cells

growth_protocol: DLD1 and LS174T cells were cultured in DMEM supplemented with 10% FBS, 500 μg/mL zeocin, and 10 μg/mL blasticidin. HT29 cells were cultured in McCoy’s-5A supplemented with 10% FBS and 600 μg/mL hygromycin.

extract_protocol:
For RNA-seq samples, cells were lysed in RLT buffer supplemented with 550 μM 2-Mercaptoethanol, gDNA was removed, and RNA was purified on spin columns using the RNeasy Plus kit (Qiagen, #74134) according to kit directions. Libraries were prepared from 1μg RNA with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB; #E7530L). Briefly, mRNA was purified from total RNA using poly-T oligo magnetic beads, fragmented, and reverse transcribed to double stranded cDNA. Fragments were end-repaired, blunt-ended, 3’adenylated, and ligated to hairpin loop NEBNext Adaptors. 150~200 bp cDNA fragments were selected, PCR-amplified, and sequenced on an Illumina Novaseq 6000 platform, generating 150bp paired-end reads.
For RNA-seq samples, libraries were prepared from 1μg RNA with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB; #E7530L). Briefly, mRNA was purified from total RNA using poly-T oligo magnetic beads, fragmented, and reverse transcribed to double stranded cDNA. Fragments were end-repaired, blunt-ended, 3’adenylated, and ligated to hairpin loop NEBNext Adaptors. 150~200 bp cDNA fragments were selected, PCR-amplified, and sequenced on an Illumina Novaseq 6000 platform, generating 150bp paired-end reads.

treatment_protocol: DLD1 and LS174T cells were induced with 1 μg/mL doxycycline for 24h (DLD1-DNTCF), 48h (LS174T-DNTCF), or 72h (LS174T- shβ-catenin). HT29 cells were induced with 300 μM Zinc chloride for 24h

value: LS174T (siBeta-catenin) cells

tag: transgene

value: Tet-inducible Beta-catenin shRNA

tag: cell source

value: Colorectal adenocarcinoma

value: DOX, 72h


title: RNA-seq sibc DOX rep1


title: RNA-seq sibc DOX rep3


title: RNA-seq sibc rep3


title: KO2_AM [10_S24]

source_name: Il9r-/-_lung aveolar macrophage

tag: cell type

value: lung aveolar macrophage


title: RNA-seq sibc rep2


title: Uninjured spinal cord

city: Solna

first: Moa

last: Stenudd

address: Berzelius väg 25

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

data_processing:
Bcl files were converted to fastq files using cellranger mkfastq (v3.0.1).
Alignment and filtering was conducted with cellranger count (v3.0.1)
Seurat objects were generated from the samples, excluding genes expressed by <3 cells and cells with <500 expressed genes.
Additional filtering was performed to exclude cells expressing  <1% or >20% mitochondrial genes, or >3 standard deviations more genes than in the overall cell population.
Seurat objects from each population (uninjured vs injured) were then integrated into one object.
Genome_build: mm10 supplemented with tdTomato DNA sequence
Supplementary_files_format_and_content: UI_cells_UMI_Matrix.csv - raw count matrix containing all cells in the uninjured sample that express >=500 genes, and all genes expressed in 3 or more cells. SCI_cells_UMI_Matrix.csv - raw count matrix containing all cells in the SCI sample that express >=500 genes, and all genes expressed in 3 or more cells.
Supplementary_files_format_and_content: All_cells_filtered_UMI_Matrix.csv is sampled after filtering (<500 genes, <1%, >20% mitochondrial genes, >3 sd more genes than the overall population removed) and contains all cell types collected from the spinal cords in the the experiment; including ependymal cells, perivascular cells, and contaminating cells. EpA_cells_UMI_Matrix.csv is sampled after filtering, and only includes EpA ependymal cells.

source_name: spinal cord EpA ependymal cells

extract_protocol:
Spinal cords were micro dissected and 5 mm segments around the lesion site (or the corresponding regions in uninjured spinal cords) were collected. Collected spinal cord was digested to single cell suspension using the Neural Tissue Dissociation Kit (Miltenyi) with papain digestion enzyme. Cell suspensions were collected in flow cytometry buffer, passed through a 70 µm filter, and myelin debris was reduced by centrifugation through a sucrose solution. Cells were resuspended in cytometry buffer and tdTomato expressing cells were sorted into cold DPBS (supplemented with 0.04% BSA) with an Influx cell sorter with a 100 µm nozzle.
Sorted cells were processed for library preparation using the Chromium Single Cell 3’ Reagent Kit v2, following the manufacturer’s (10X Genomics) instructions.

value: ependymal cells

tag: strain

tag: age

value: Adult (>= 12 weeks)

tag: experimental condition

value: Uninjured spinal cord from Troy-CreERT2+/- x Rosa26-tdTomato

tag: sorting

value: FACS (tdTomato+)


title: RNA-seq sibc rep1

tag: treatment


title: WT2_CD11c+IM [8_S22]

source_name: WT_lung interstitial macrophage

tag: genotype

value: WT


title: Injured spinal cord, 3 dpi

value: Injured spinal cord (3 dpi) from Troy-CreERT2+/- x Rosa26-tdTomato


title: RNA-seq HT29 DOX rep3

source_name: HT29 (APC) cells

value: HT29 (APC) cells

value: Zinc-inducible wild type APC

value: Zinc, 24h


title: Mono_Day02_repC

city: Boulder

first: Stephanie

middle: J

last: Bryant

state: CO

address: 3415 Colorado Ave

department: Chemical and Biological Engineering

institute: University of Colorado

data_processing:
FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17).
Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt.
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 assembly of the mouse genome using gene using gene annotations from Ensembl release 84.
Reads mapping to each gene of the Ensembl 84 annotation were counted with the featureCounts program from the Subread software package (v1.5.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts assigned to each gene of the mouse Ensembl 84 annotation and sample, as tab-separated text table: aggregated by adding different flow-cell lanes for each sample (genecounts.txt)

extract_protocol:
Total RNA was harvested with the RNAeasy kit (Qiagen).
A Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Mountain View, CA, USA) and Nextera XT (San Diego, CA, USA) kit were used. Briefly, library construction started from isolation of total RNA species, followed by SMARTer 1st strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. After that, the samples were taken to the Nextera XT protocol where the sample is simultaneously fragmented and tagged with adapters followed by a limited cycle PCR that adds indexes. Once validated, the barcoded-pooled libraries were sequenced using 1x75bp chemistry on the HiSeq 2500 as routinely performed by the NJH Genomics Facility.

treatment_protocol: PEG hydrogels were implanted subcutaneously in wildtype C57BL/6J mice; Tissue and hydrogels were explanted and digested with Liberase TM for 30 min.

tag: tissue

value: Subcutaneous tissue

value: monocytes

value: PEG hydrogel implant

tag: time point

value: 2 days


title: WT2_AM [7_S21]

source_name: WT_lung aveolar macrophage


title: Mono_Day14_repA

value: 14 days


title: Mono_Day28_repA

value: 28 days


title: Mono_Day28_repB


title: Mono_Day28_repC


title: WT2_CD11c-IM [9_S23]

value: lung interstitial macrophage


title: Mono_Day14_repC


title: KO1_CD11c-IM [6_S20]


title: Mono_Day14_repB


title: Mono_Day02_repB


title: Mono_Day02_repA


title: RNA-seq HT29 DOX rep1

tag: cell line

value: Colorectal adenocarcinoma


title: RNA-seq HT29 DOX rep2


title: Mono_Ctrl_repC

value: control


title: A12

value: adenomyosis case

value: receptive


title: KO1_CD11c+IM [5_S19]


title: Mono_Ctrl_repB


title: RNA-seq HT29 rep3


title: KO2_CD11c+IM [11_S25]


title: KO1_AM [4_S18]

value: lung aveolar macrophage


title: Mono_Ctrl_repA


title: Macro_Day28_repC

value: macrophages


title: Macro_Day28_repB


title: RNA-seq HT29 rep2


title: Macro_Day14_repC


title: WT1_CD11c-IM [3_S17]

value: WT


title: Macro_Day14_repB


title: Macro_Day28_repA


title: Macro_Day14_repA


title: WT1_CD11c+IM [2_S16]


title: WT1_AM [1_S15]


title: Macro_Day02_repC


title: Macro_Day02_repA


title: Macro_Ctrl_repB


title: Macro_Day02_repB


title: RNA-seq L8 DOX rep3

source_name: LS174T (DNTCF) "L8" cells

value: LS174T (DNTCF) "L8" cells

value: Tet-inducible dominant negative TCF7L2

value: DOX, 48h


title: RNA-seq L8 DOX rep2


title: RNA-seq L8 DOX rep1


title: M11_dC34 H3K27ac_ChIP-Seq

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan national university

data_processing:
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the human chromosome 11 (hg19 genome assembly)  using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. Bigwig files generated from BAM files using BamCoverage. ChIP-seq signals were normalized by S3V2-IDEAS method.
Genome_build: Human chromosome 11 (hg19, GRCh37)
Supplementary_files_format_and_content: bigWig

growth_protocol: MEL/ch11 cells were cultured in DMEM medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K27ac and 1 ng for H3K27me3) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. Adaptor-ligated DNA was selected at 175-200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles for H3K27ac and 10-11 cycles for H3K27me3). The fragments are purified using NEBNext sample purification beads.

treatment_protocol: For transcriptional activation of the β-globin gene, MEL/ch11 cells were induced at a concentration of 1.5x10^5 cells/ml with 5 mM HMBA for 72 h.

value: erythroleukemia cells

tag: genotype/variation

value: C3- and C4-deleted (dC34)

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: Macro_Ctrl_repA

value: Subcutaneous tissue


title: J3D Proton 5gy 12hr rep9 [Ger3_J3D_Proton5]

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
Ger3_J3D_Proton5
processed data file: DATASET-J3D_Normalized.xlsx

data_processing:
The FASTQ files were aligned to the human (hg19) or mouse (mm10) genome and transcriptome using TopHat2. From the resulting BAM files, read mapping, expression quantification and differential expression analysis were performed using AltAnalyze version 2.1.0. Prior to differential expression analysis, batch effects were observed by principal component analysis. To correct for batch effects, we explicitly normalized the expression of each gene within each batch relative to its average expression (log2 geometric median normalized). A single-replicate of each cell line RNA-Seq sample was processed in the same manner in each batch, with the same cell lines represented. No batch effects were evident following PCA analysis on the batch corrected data. Differential expression was performed on the batch corrected data.
Differential expression was performed on the batch corrected data using the AltAnalyze supplied empirical Bayes moderated t-test, following Benjamini-Hochberg adjustment for false discovery (FDR), with a cutoff of p<0.05 (FDR) and fold change≥1.3.Gene ontology enrichment analysis was carried out using the ToppFun function of Toppgene64 with the Biological Process database.
Genome_build: hg19 for BL41 samples and mm10 for J3D  samples
Supplementary_files_format_and_content: Differential Expression

source_name: J3D Proton 5gy 12hr

growth_protocol: Human BL41and mouse J3D lymphoma cell lines were maintained in RPMI 1640 media complemented with 10% FBS and Penicillin and Streptomycin.

extract_protocol:
Total RNA was puriﬁed with the SurePrep RNA/DNA/Protein purification kit from samples at 12hr after irradiation.
RNA libraries were prepared for sequencing using standard Illumina protocols by the CCHMC DNA sequencing and genotyping core.

treatment_protocol: Cell lines were re-suspended at 1x106 cells/ml at 6hr before irradiation. For proton irradiation the same SOBP constraints were utilized by energies ranging between 129.3-148.2 MeV/u and median LET: 3.5 keV/µm (ranging from 2.9-7.9 keV/µm) (SuppFig.1). Cells were place in the center area of the SOBP. All proton irradiations were carried out using a raster-scanning technique. Photon Irradiation was performed on a LINAC Artist 6mV system from Siemens. Sham un-irradiated were kept outside incubator at room temperature in parallel of irradiated cells.

tag: tumor type

value: Burkitt lymphoma

tag: passage

tag: irradiation

value: Proton 5Gy

tag: harvest time


title: RNA-seq L8 rep3

tag: transgene

tag: cell source


title: M11_dC5-7 H3K27me3_ChIP-Seq

tag: cell type

value: C5-, C6- and C7-deleted (dC5-7)

value: H3K27me3 (Millipore, 07-449)


title: J3D Proton 5gy 12hr rep8 [Ger2_J3D_Proton5]

description:
Ger2_J3D_Proton5
processed data file: DATASET-J3D_Normalized.xlsx


title: M11_dC5-7 H3K27ac_ChIP-Seq


title: RNA-seq L8 rep1

value: Colorectal adenocarcinoma


title: J3D Proton 5gy 12hr rep7 [Ger1_J3D_Proton5]

description:
Ger1_J3D_Proton5
processed data file: DATASET-J3D_Normalized.xlsx


title: J3D Xray 5gy 12hr rep6 [Ger3_J3D_Xray5]

description:
Ger3_J3D_Xray5
processed data file: DATASET-J3D_Normalized.xlsx

source_name: J3D Xray 5gy 12hr

value: Xray 5Gy


title: J3D Xray 5gy 12hr rep5 [Ger2_J3D_Xray5]

description:
Ger2_J3D_Xray5
processed data file: DATASET-J3D_Normalized.xlsx


title: M11_Con H3K27me3_ChIP-Seq

value: control


title: RNA-seq DLD1 DOX rep3

source_name: DLD1 (DNTCF) cells

value: DLD1 (DNTCF) cells

value: DOX, 24h


title: J3D Xray 5gy 12hr rep4 [Ger1_J3D_Xray5]

description:
Ger1_J3D_Xray5
processed data file: DATASET-J3D_Normalized.xlsx


title: J3D untreated rep3 [Ger3_J3D_Ctrl]

description:
Ger3_J3D_Ctrl
processed data file: DATASET-J3D_Normalized.xlsx

source_name: J3D untreated

value: Sham


title: J3D untreated rep2 [Ger2_J3D_Ctrl]

description:
Ger2_J3D_Ctrl
processed data file: DATASET-J3D_Normalized.xlsx


title: M11_Con H3K27ac_ChIP-Seq


title: RNA-seq HT29 rep1

value: HT29 (APC) cells

value: Zinc-inducible wild type APC


title: ChIP-seq DLD1 DOX input

extract_protocol:
For ChIP-seq samples, cells were fixed in 1% formaldehyde for 10 min at room temperature, quenched with 180mM glycine, and lysed in three steps according a protocol modified from Schmidt. et. al (PMID 19275939). Chromatin was sonicated to an average size of 250-300 bp with a Q800R2 sonicator (QSonica) at 4C. ChIP was performed with 100μg chromatin, 10μg antibody, and protein G Dynabeads (Thermo, #100003D) overnight. IPs were washed, reverse-crosslinked, treated with proteinase K/RNase A, and input and IP DNA was purified MinElute PCR Purification columns (Qiagen #28004).
For ChIP-seq samples, libraries were prepared from input or IP DNA using the Swift Biosciences ACCEL-NGS 2S Plus DNA library kit following the manufacturer’s protocol. Single-end 75-bp sequencing was performed using a high-output flowcell on the Illumina NextSeq 500 at a depth of 40-55M reads per sample

value: Tet-inducible dominant negative TCF7L2

tag: chip antibody vendor

tag: chip antibody catalog#


title: ChIP-seq DLD1 input


title: J3D untreated rep1 [Ger1_J3D_Ctrl]

description:
Ger1_J3D_Ctrl
processed data file: DATASET-J3D_Normalized.xlsx


title: M11_dC34 H3K27me3_ChIP-Seq

value: erythroleukemia cells


title: ChIP-seq DLD1 DOX H3K27ac rep1

description:
PlusDox.H3K27.bw
PlusDox.H3K27_peaks.narrowPeak
PlusDox.H3K27_summits.bed

value: Abcam


title: cervix_healthy_control_12

city: Rotterdam

first: Willem

last: de Koning

state: Zuid-Holland

address: Doctor Molewaterplein 40

institute: Erasmus University Medical Center

hyb_protocol: Hybridization was performed at 65°C for 17 hours using a SimpliAmp Thermal Cycler (Applied Biosystems, Foster City, CA, USA).

scan_protocol: The nCounter FLEX platform was used and genes were counted by scanning 490 Fields-of-view (FOV).

data_processing: Data analysis was performed using the advanced analysis module (version 2.0) of nSolver software (version 4.0, NanoString Technology).

source_name: cervix

extract_protocol: RNA was isolated using the RNeasy® FFPE Kit (Qiagen, Hilden, Q15 Germany) according to the manufacturer’s directions. RNA concentrations and quality were measured using the Agilent 2100 BioAnalyzer (Santa Clara, CA, USA).  To correct for degradation of the RNA, the percentage of fragments of 300-4000 nucleotides was used to calculate the corrected concentrations. For each sample, 300 ng of total RNA, with a maximum of 7 mL (>42.8 ng/mL), was used.

value: cervix

tag: stage at last follow-up


title: ChIP-seq DLD1 H3K27ac rep1

description:
MinusDox.H3K27.bw
MinusDox.H3K27_peaks.narrowPeak
MinusDox.H3K27_summits.bed

tag: treatment


title: ChIP-seq DLD1 DOX PolII rep2

description:
PlusDox.PolII.bw
PlusDox.PolII_peaks.narrowPeak
PlusDox.PolII_summits.bed

value: RNA Polymerase II


title: RNA-seq DLD1 rep2


title: RNA-seq DLD1 DOX rep1


title: RNA-seq DLD1 DOX rep2


title: RNA-seq DLD1 rep3


title: cervix_healthy_control_11


title: ChIP-seq DLD1 DOX PolII rep1


title: ChIP-seq DLD1 PolII rep2

description:
MinusDox.PolII.bw
MinusDox.PolII_peaks.narrowPeak
MinusDox.PolII_summits.bed


title: RNA-seq L8 rep2

value: LS174T (DNTCF) "L8" cells


title: cervix_healthy_control_10


title: NCCLu-283

city: Goyang-si

first: namhee

last: yu

state: Gyeonggi-do

address: 323, Ilsan-ro, Ilsandong-gu

institute: National cancer center

data_processing:
Quality filtering and adapter trimming: FASTQC and Trimmomatic(Version 0.39) (standard parameters)
Mapping with STAR(version 2.7.0a)
Quantification with RSEM (v1.2.31 )
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

source_name: Lung cancer patient derived cells

growth_protocol: Pleural effusions, pericardium effusions, ascites and tissues were obtained by lung cancer patients at National Cancer Center. All experiments utilizing human material were approved by NCC IRB. For liquid samples, effusions were transferred to conical tube and centrifuged at 120 x g for 10 min. The cell pellet was resuspended in RPMI and carefully layered onto LSM (Lymphocyte Separation Medium, #091692249 MP Biomedicals, France). After centrifugation at 400 x g for 30 min at room temperature, interphase layer between RPMI and LSM including tumor cells was harvested and washed with RPMI. For tissue sample, tumor tissues were minced finely and washed with RPMI. After washing, cells from effusion or tissue were cultured in AR-5 medium (5% FBS, 1 X GlutaMAX (Thermo Fisher Scientific), 1 X ITS (Insulin-Transferrin-Selenium, Thermo Fisher Scientific), 1% Penicillin/streptomycin, 50 nM hydrocortisone, 1 mM Sodium Pyruvate and 1 ng/ml EGF in RPMI) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Total RNA was purified from cultured cell using RNeasy® mini kit, and AllPrep DNA/RNA Mini kit (Qiagen, German) and handled by QIAcube automatic instrument (Qiagen, German).
For RNA-seq analysis, we prepared mRNA sequencing libraries as paired-end reads with a length of 100 bases using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) according to the manufacturers’ protocols. Briefly, mRNA molecules were purified and fragmented from 2 μg of total RNA. The libraries were sequenced as paired-end reads (2 × 150 bp) using the NovaSeq 6000 (Illumina).

treatment_protocol: non-treatment

value: Pleural fluid

tag: disease

value: Lung cancer

tag: histopathology

value: Adenocarcinoma


title: RNA-seq DLD1 rep1

value: Colorectal adenocarcinoma


title: ChIP-seq DLD1 PolII rep1


title: SNI 7dpi 2

city: Palo Alto

first: Gregory

last: Scherrer

address: 1050 Arastradero Rd

department: Anesthesiology

institute: Stanford University

data_processing:
Reads were mapped to the UCSC mouse reference genome mm10 via the Galaxy platform (http://usegalaxy.org) using HISAT2 version 2.0.5.1.
FPKM (fragments per kilobase of transcript sequence per million mapped fragments) values were obtained using Cufflinks version 2.2.1.
Reads were quantified using featureCounts version 1.4.6.p5
Differential expression analysis was conducted in R with DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM for all samples
Supplementary_files_format_and_content: excel spreadsheet with Deseq2 output for all groups

source_name: Lumbar spinal cord microglia

extract_protocol:
Mice were perfused with ice cold PBS, caudal lumbar cord was dissection and manually dissociated then subjected to MACS myelin removal and CD11b selection. Total RNA was extracted from CD11b-positive cells using the RNeasy Micro Kit
Libraries were prepared using Smart-Seq2 and modified for sequencing using the Nextera XT DNA Sample Preparation Kit (Illumina)

treatment_protocol: Mice received one of 2 chronic morphine dosing strategies (fixed or escalating) or one of three peripheral nerve injuries - sciatic nerve transection (SNT), chronic constriction injury (CCI), or spared nerve injury (SNI). Controls received saline or no treatment/injury

tag: tissue

value: Lumbar spinal cord microglia

tag: strain

tag: condition

value: SNI

tag: timepoint or dose


title: SNI 7dpi 1


title: cervix_healthy_control_14


title: cervix_healthy_control_13


title: Control 6

value: saline

value: fixed


title: cervix_healthy_control_9


title: Control 5


title: NCCLu-278


title: Control 1


title: NCCLu-276

value: Miscellaneous


title: ChIP-seq DLD1 H3K27ac rep2

tag: cell line

value: DLD1 (DNTCF) cells

tag: chip antibody


title: ChIP-seq DLD1 DOX H3K27ac rep2

value: DOX, 24h


title: NCCLu-272


title: NCCLu-269


title: NCCLu-267


title: DM1cl6_2

data_processing:
Trimming of low-quality bases of reads with Cutadapt/2.10
Alignment realised with STAR/2.7.5a,
Read-quantification done with HTSeq/0.12.4
Differentially-expressed genes found via DESeq2/1.30.0
Genome_build: GRCh37 ,hg19
Supplementary_files_format_and_content: .bam = aligned sequenced reads

source_name: Immortalized myoblasts

growth_protocol: DM1 immortalized myoblasts were transduced with a lentiviral vector containing a Tet-On GFP-tagged MBNL1∆ construct allowing its expression only in the presence of doxycycline. Immortalized DM1 and WT myoblasts were differentiated for 3 days

extract_protocol:
Total RNAs were isolated using TRI-Reagent according to the manufacturer’s protocol, and treated with RQ1 RNase-Free DNas according manufacturer’s protocol (Promoga)
RNA quality control done using RNA6000 Nano LabChip analysis on Bioanalyzer(Agilent),and libraries were prepared with TruSeq Stranded Total RNA with Ribo-Zero Kit (Illumina),with an input of 1μg.

treatment_protocol: MBNL1∆ expression was induced in differentiated DM1 myoblasts  by adding Doxycylin to the culture medium. 3 days later, MBNL1∆-treated DM1 cells were compared to untretad DM1 and WT differentiated myoblasts.

value: Differentiated myoblasts

value: untreated

tag: genotype/variation


title: DM1cl6_MBNL1Δ_1

value: Treated with MBNL1[delta]


title: DM1cl6_MBNL1Δ_3


title: C25cl48_3

value: WT


title: DM1cl6_1


title: C25cl48_2


title: DM1cl6_MBNL1Δ_2


title: NCCLu-264


title: NCCLu-280


title: C25cl4_3


title: C25cl48_1


title: C25cl4_1


title: C25cl4_2


title: NCCLu-263


title: NCCLu-262

value: Small cell lung cancer


title: DM1cl6_3


title: cervix_no_recurrence_12

value: cervix

value: Alive

tag: age

tag: surgical approach

value: Robot

tag: histological subtype

value: adeno

tag: lvsi

tag: tnm-stage

tag: hpv

tag: adjuvant therapy

value: Follow up


title: cervix_healthy_control_8

tag: stage at last follow-up


title: cervix_healthy_control_3


title: cervix_healthy_control_2


title: cervix_healthy_control_6


title: cervix_healthy_control_7


title: cervix_healthy_control_5


title: cervix_healthy_control_4


title: cervix_healthy_control_1


title: NCCLu-254

value: Pericardial fluid

tag: disease

value: Lung cancer

value: Adenocarcinoma


title: NCCLu-256

value: Pleural fluid

tag: histopathology


title: NCCLu-266

tag: tissue


title: cervix_no_recurrence_11


title: Cbx8_LOVO_UNC7040_rep1

city: Los Angeles

first: Oliver

last: Bell

address: 1450 Biggy St, NRT6510

institute: USC

data_processing:
Processing and mapping of raw reads: The raw reads of ChIP-seq were mapped to the custom concatenated human (hg38) and spike-in mouse (mm10)  genome sequences using bowtie 2 with “–no-mixed” and “no-discordant” options  (Langmead and Salzberg, 2012). Subsequently, low quality reads were removed using SAMtools (Li et al., 2009), duplicated reads were discarded with the Picard toolkit (http://broadinstitute.github.io/picard/) and only unique mapped reads were retained for subsequent analysis.
For visualization uniquely mapped human reads were normalized by random subsampling using calibration factors calculated from the corresponding mm10 spike-in reads as described previously (Fursova et al., 2019) using samtools. High correlation between replicates was confirmed using multiBamSummary and plotCorrelation functions from deepTools (Ramírez et al., 2016) before merging for visualization and downstream analysis. Genome coverage tracks (bigWig files) were generated with MACS2’ pileup function (Zhang et al., 2008)
Raw paired RNA-seq reads were aligned to the hg38 genome sequences using STAR-2.6.1c (Dobin et al., 2013). Overlap of aligned reads in bam format with genes was performed using HTSeq count function (Anders et al., 2015) with stranded=no option and the GRCh38 version 101 GTF file. The HTseq count matrix was pre-filtered to remove any genes with less than 10 reads. Differential gene expression analysis was performed using DESeq2 (Love et al., 2014) using “apeglm” method (Zhu et al., 2019) for LFC shrinkage.
Genome_build: hg38

source_name: LOVO cells

growth_protocol: SUDHL4 (ATCC #CRL-2957), were cultured in RPMI-1640 complemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin.  LoVo (ATCC #CCL-229) were maintained in F-12K medium supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
For RNA-seq sample preparation, 5-10x10^6 SUDHL-4 or LoVo cells (untreated, UNC7263 or UNC7040 treated at least in duplicate) were trypsinized and collected by centrifugation for 5 min at 500 g. Subsequently, cell pellets were washed 1× with PBS and collected in 1X DNA/RNA protection reagent (Monarch Total RNA Miniprep Kit, NEB). Cells were lysed and total RNA was isolated following the mammalian cell protocol inlcuding on-column DNase I treatment. Total RNA samples were submitted to Novogene Co. for quality control and library preparation, applying poly-A enrichment and using the NEBNext Ultra II RNA Library Prep kit (NEB), indexed using NEBNext Multiplex Oligos (NEB). Final libraries were sequenced as 150 bp paired-end reads on the Illumina HiSeq platform. ChIP-seq Library PreparationLibraries were prepared using the NEXTflex ChIP-Seq kit (Bio Scientific) following the “No size-selection cleanup” protocol. Each sample of ChIPed DNA was end-repaired and ligated to unique barcoded adaptors to produce individual libraries. Libraries corresponding to samples to be directly compared to each other (e.g. DMSO vs UNC7040) were pooled together and purified using 1 volume of Agencourt AMPure XP (Beckman Coulter). The pooled libraries were eluted with 23 µL of elution buffer (NEXTflex ChIP-Seq kit) and amplified using the KAPA Real-Time Library Amplification Kit (KAPABiosystems) following the kit instructions. Finally, the amplified libraries were size-selected and purified using 0.9x volume of Agencourt AMPure XP (Beckman Coulter). Library quality control including determination of average size and concentration was performed prior to sequencing by commercial Next Generation Sequencing providers. NGS libaries were eventually sequenced as 150 bp paired-end reads on the Illumina HiSeq platform.
NGS libaries were eventually sequenced as 150 bp paired-end reads on the Illumina HiSeq platform.

tag: treatment

value: Cbx8 (Bethyl Laboratories, A300-882A)


title: Cbx8_LOVO_UNC7040_rep2


title: Cbx8_LOVO_UNC7263_rep2


title: Cbx8_LOVO_UNC7263_rep1


title: Ring1B_LOVO_UNC7263_rep2

value: Ring1B (Cell Signaling, D22F2)


title: Ring1B_LOVO_UNC7263_rep1


title: cervix_no_recurrence_10

value: squamous


title: cervix_no_recurrence_9

value: Open


title: NCCLu-245


title: H3K27me3_LOVO_DMSO_rep1

value: DMSO


title: H3K27me3_LOVO_DMSO_rep2


title: cervix_no_recurrence_8

value: radiotherapy


title: Ring1B_LOVO_UNC7040_rep1


title: Cbx8_SUDHL4_UNC7040_rep2

source_name: SUDHL4 cells


title: NCCLu-251


title: NCCLu-244


title: NCCLu-241


title: Cbx8_SUDHL4_UNC7263_rep1


title: Cbx8_SUDHL4_UNC7263_rep2


title: Cbx8_SUDHL4_UNC7040_rep1


title: cervix_no_recurrence_6


title: cervix_no_recurrence_7


title: cervix_no_recurrence_5


title: Ring1B_LOVO_UNC7040_rep2


title: NCCLu-234


title: Ring1B_SUDHL4_UNC7040_rep2


title: Cbx8_SUDHL4_DMSO_rep1


title: Ring1B_SUDHL4_UNC7040_rep1


title: Ring1B_SUDHL4_UNC7263_rep1


title: Ring1B_SUDHL4_DMSO_rep2


title: NCCLu-233


title: Ring1B_SUDHL4_DMSO_rep1


title: NCCLu-230


title: H3K27ac_SUDHL4_DMSO_rep2

value: H3K27ac (Abcam, ab4729)


title: NCCLu-229


title: H3K27ac_SUDHL4_DMSO_rep1


title: H3K27me3_SUDHL4_DMSO_rep2


title: H3K27me3_SUDHL4_DMSO_rep1


title: NCCLu-228


title: LOVO_UNC7040_rep1


title: LOVO_UNC7040_rep2


title: Cbx8_SUDHL4_DMSO_rep2


title: NCCLu-227


title: LOVO_UNC7263_rep2


title: cervix_no_recurrence_3


title: cervix_no_recurrence_4


title: cervix_local_recurrence_14

value: Death

value: no

tag: time to recurrence


title: cervix_no_recurrence_1

value: cervix

value: Alive


title: cervix_no_recurrence_2

value: adeno


title: NCCLu-225


title: Ring1B_SUDHL4_UNC7263_rep2


title: SUDHL4_UNC7040_rep2


title: LOVO_UNC7263_rep1


title: SUDHL4_UNC7040_rep3


title: cervix_local_recurrence_11

value: Follow up


title: cervix_local_recurrence_13


title: cervix_local_recurrence_12

value: yes


title: NCCLu-240

value: Lung cancer


title: NCCLu-220

value: Adenocarcinoma


title: SUDHL4_UNC7263_rep2


title: SUDHL4_UNC7040_rep1


title: cervix_local_recurrence_10


title: cervix_local_recurrence_9

value: no HPV


title: NCCLu-217

value: Pleural fluid


title: SUDHL4_UNC7263_rep1


title: SUDHL4_DMSO_rep1

description:
DeSeq2_SUDHL4_UNC7263vsDMSO.csv
DeSeq2_SUDHL4_UNC7040vsDMSO.csv


title: SUDHL4_DMSO_rep3


title: LMNB1_ctrl_EN_rep2

city: Beijing

first: Ran

last: Li

address: Yiheyuan Road No.5

institute: Peking University

data_processing:
The RNA-seq reads were initially performed adaptor removal by our own script with phred quality score over 33. The reads were then mapped using hisat2 (v2.1.0) to the human genome assembly GRCh38 (hg38) with Homo_sapiens.GRCh38.87.gtf annotations (http://ftp.ensembl.org/pub/release-87/gtf/homo_sapiens), using the following command: hisat2 -p 8 -x ~/genome/Homo_sapiens/hisat2_index/Homo_hisat2 -1 $clean_file1 -2 $clean_file2|samtools view -b > $output.bam
The mapped reads were then sorted by name using samtools: samtools sort -n $output.bam -o $output.sortname.bam
The sorted reads were counted by HTSEQ (v0.7.2): htseq-count -s no -f bam $output.sortname.bam ~/genome/Homo_sapiens/Homo_sapiens.GRCh38.87.chr.gtf > $output.txt
The mapped data was visualized using WashU Epigenome Browser or Integrative Genomics Viewer. The mapped reads were generated from mapped BAM file to BigWig file using bamCoverage (v2.5.3) and normalized all mitochondrial counts to 2,000,000 for MITO MERR APEX-seq samples or and normalized all mitochondrial counts to 200,000 for LMNB1 MERR APEX-seq samples: bamCoverage -b $out.bam -o $out.bw --scaleFactor
The BigWig files of two biological replicates were merged into one bedGraph file using bigWigMerge (v2): bigWigMerge $input1.bw $input2.bw $out.bedGraph
BedGraph files were converted to BigWig files using bedGraphToBigWig (v4): bedGraphToBigWig $input.bedGraph ~/genome/Homo_sapiens/chromosome.sizes $output.bw
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-deliminted text files include count data from Hisat2 and HTSEQ; quantified expression values in TPM (Transcripts Per Million); or DESeq2 log2foldchanges and P-value or Padjusted values for each gene.
Supplementary_files_format_and_content: BigWig files contain normalized expression signal merged by 2 replicates.

source_name: human embryonic kidney 293T cells

growth_protocol: HEK293T cells (passages < 25) were cultured in DMEM supplemented with 10% fetal bovine serum at 37℃ under 5% CO2.

extract_protocol:
HEK293T cells under labeling and unlabeling in 6-well plate were extracted by 1 mL TRIzol reagent following the manufacture protocol after MERR APEX labeling. The extracted total RNA was eluted into ultrapure water.  Total RNA was treated 1 µL DNase I (NEB) to remove residual DNA and incubated at 37℃ for 15 min. Then, RNA was purified by RNA clean and concentrator kit (Zymo). RNA integrity was analyzed by Fragment Analyzer (Agilent). Only RNA with a RQN (RNA quality number) > 8.0 was used for subsequent experiments as INPUT. INPUT samples were enriched by 10 µL Dynabeads MyOne Streptavidin C1 (Invitrogen). RNA afer enrichment was purified by TRIzol reagent and dissolved in 20 µL ultrapure water as ENRICH samples.
cDNA libraries for RNA-seq were constructed from ~300 ng INPUT samples and 5 µL ENRICH samples (enriched from 6.5 μg INPUT) using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) with Poly(A) mRNA Magnetic Isolation Module (NEB) selection. PolyA RNA was fragmented at 94℃ for 12 min. cDNA was amplified 11 cycles for INPUT and 15 cycles for ENRICH samples. The prepared libraries were quality-controlled by Fragment Analyzer (Agilent). Good libraries with most cDNA range from 250 bp to 350 bp were sequenced on the Illumina HiSeq X Ten platform at ~10 million paired (2 x 150) reads per library.

treatment_protocol: HEK293T cells at 60-70% confluency were treated with 100 µM s6G or 100 µM s4U for 4.5 hr as described at 37℃ under 5% CO2. Then, cells were performed APEX labeling by adding 0.5 mM biotin-phenol in culture medium for 30 min incubation. After that, 1 mM H2O2 was added and gently rotated for 1 min. The reaction was quenched with 10 mM NaAsc, 5 mM trolox and 10 mM NaN3 in PBS by replacing medium three times before further cell fixation or RNA extraction. Negative controls were processed identically, except s6G, s4U or BP addition steps were omitted.

tag: cell compartment

value: nuclear lamina

value: untreated


title: SUDHL4_DMSO_rep2


title: LMNB1_ctrl_EN_rep1

tag: cell line


title: NCCLu-216


title: LMNB1_RNA_EN_rep2


title: NCCLu-221


title: LMNB1_RNA_IN_rep1


title: cervix_local_recurrence_7

value: Open

value: squamous


title: cervix_local_recurrence_8

value: radiotherapy


title: LMNB1_ctrl_IN_rep2


title: LMNB1_ctrl_IN_rep1


title: NCCLu-201


title: cervix_local_recurrence_6


title: NCCLu-211

value: Miscellaneous


title: LMNB1_RNA_EN_rep1


title: LMNB1_RNA_IN_rep2


title: NCCLu-218


title: cervix_local_recurrence_5

value: Death


title: NCCLu-204


title: SUDHL4_UNC7263_rep3


title: NCCLu-199


title: LMNB1_s6G_IN_rep2

value: treated with 100 µM s4U for 5 hr


title: LMNB1_s6G_IN_rep1


title: LMNB1_s6G_EN_rep1


title: cervix_local_recurrence_3

value: cervix

value: no


title: NES_s6G_EN_rep2

value: cytosol

value: treated with 100 µM s6G for 5 hr


title: cervix_local_recurrence_4

value: Alive

value: yes

value: Follow up


title: NCCLu-197

value: Lung cancer

value: Adenocarcinoma


title: NCCLu-215

value: Pleural fluid


title: NES_s6G_EN_rep1


title: NES_s6G_IN_rep2


title: cervix_local_recurrence_2


title: NCCLu-195


title: NES_s6G_IN_rep1


title: NCCLu-190


title: ERM_s6G_EN_rep3

value: endoplasmid reticulum membrane


title: ERM_s6G_EN_rep4


title: cervix_distant_recurrence_8

value: Open

value: chemoradiation


title: LMNB1_s6G_EN_rep2

value: nuclear lamina


title: ERM_s6G_EN_rep1


title: NCCLu-185


title: cervix_distant_recurrence_7

value: squamous

value: radiotherapy