title: 90

description: rawCounts.xlsx

tag: diet


title: hsTPH_Ntermtrunc-1

status: Public on Apr 09 2021

type: SRA

city: La Jolla

first: Wun Kiat Justin

last: Tan

state: California

address: 9500 Gilman Drive #0412, PFBH 414

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
Base calls were made on Illumina's BaseSpace
Sequenced reads were aligned to E. coli MG1655 (NC_000913.3) genome and plasmid sequences using Bowtie 2 ver. 2.1.0 into BAM files
BAM files were processed using HTSeq to generate raw read count files
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-delimited raw read counts for all samples

molecule: total RNA

organism: Escherichia coli

growth_protocol: Gly2 cells transformed with heterologous gene expressing plasmid were grown in M9 with 0.2% w/v glycerol as carbon source

extract_protocol:
Total RNA was isolated using Qiagens RNAProtect Bacteria Reagent kit
Ribosomal RNA was depleted using Illumina's Ribo-Zero rRNA removal kit and libraries were constructed using KAPA RNA-Seq Library Preparation kit

treatment_protocol: At A600 OD = 0.3 rhamnose was added to a final concentration of 1mM for induction of heterologous gene expression. Cells were harvested 2hrs after induction for total RNA extraction.

tag: strain

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: Tumor vs Normal patient ID 007

type: RNA

city: Villejuif

first: Shai

last: Magidi

address: rue Guy Moquet

country: France

institute: WIN Consortium

description:
Tumor vs Normal Lung 007
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

hyb_protocol: Hybridizations were performed as dual-dye-swapped (direct and inversed labeling) experiments with direct cohybridization of equal amounts of labeled tumor and normal probes.

scan_protocol: Microarrays were read using the Agilent 2000 scanner version C.

data_processing: Data was processed with Agilent Feature extractions software

label: Cy5, Cy3

organism: Homo sapiens

source_name: Cancer tissue

label_protocol: Of each tumor and normal tissue, 100 ng total RNA was used to generate double-stranded complementary DNA using MMLV reverse transcriptase and oligo DT primers coupled with the promoter sequence of T7 RNA. Probe labeling and linear amplification were generated using Agilent Technologies reagents and T7 RNA polymerase that generated labeled complementary labeled RNAs (tumor labeled with Cy5 and normal tissue with complementary RNAs with Cy3).

growth_protocol: storage protocol: All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

extract_protocol: The tissue biopsies were lysed with a Polytron, by homogenization in the lysis buffer RLT Plus provided in the kit, and DNA was obtained with a specific affinity silica matrix column, specifically retaining the DNA, whereas RNAs and proteins were collected from the through flow. DNA was washed and eluted. The through flow containing RNAs was mixed with tri-reagent and, subsequently, RNA was obtained by isopropanol precipitation. This procedure enables the collection of all types of RNAs, including mRNAs and small microRNA species. RNAs pelleted through centrifugation were washed with ethanol 75% and solved in nuclease-free water

tag: tissue

value: Lung

tag: gender

value: Male

tag: histology

value: Adenocarcinoma

tag: Stage

tag: age

label: Cy3, Cy5

source_name: Organ-matched normal tissue

value: Bronchial mucosa


title: 04-P054921-S072-R01: cellbender counts

city: Cambridge

first: Caroline

last: Porter

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description: Cellbender remove-background corrected single-cell or single nucleus RNA-Seq (10X) Cellranger counts, stored as an HDF5 file.

data_processing:
sc/snRNA-seq: 3' RNAseq (10x kit V3 chemistry)
sc/snRNA-seq: Demultiplexing is run using Cell Ranger mkfastq.
sc/snRNA-seq: Counts matrix is generated using the Cumulus cellranger_workflow in Terra.
sc/snRNA-seq: Ambient RNA is removed using Cellbender remove-background workflow in Terra.
bulk RNA-seq: Demultiplexing is run using bcl2fastq
bulk RNA-seq: Alignment peformed using STAR
bulk RNA-seq: Counts matrix generated using RSEM
Supplementary_files_format_and_content: Raw count or cellbender count matrices are in the HDF5 Feature Barcode Matrix Format used by 10x, bulk counts matrices are provided as an RSEM counts matrix, and metadata files are comma-delimited text.

source_name: COVID-19 autpsy tissue

extract_protocol:
Dissociated individual cells or isolated individual nuclei from fresh, frozen, or cryopreserved COVID-19 autopsy samples; bulk samples were lysed in RLT buffer + 1% beta mercaptoethanol
3' RNAseq (10x kit V3 chemistry) for sc/snRNA-seq; Smart-seq2 for bulk RNA-seq

value: heart

tag: disease state

tag: sampleID

tag: donor

tag: processing

value: nuclei


title: VT1367_rep_A [RNA-seq]

city: Worcester

first: Ye

last: Duan

state: MASSACHUSETTS

address: 373 Plantation Street, Biotech Two, Suite 306

department: Program of Molecular Medicine

institute: Umass Medical School

description:
WT for U18A
RNA.raw.reads.VT1367_VT3797.csv

data_processing:
Adaptor removal and size filtering by Cutadapt/1.9
rRNA/tRNA/srpR removal by Bowtie2/2.3.4.3
Genome mapping by Star/2.5.3
Gene counting by featureCounts(subread/1.6.2)
Genome_build: WBCel235
Supplementary_files_format_and_content: comma-seperated values of gene counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C.elegans were cultured on nematode growth medium (NGM) and fed with E. coli HB101 unless specified. To obtain populations of synchronized developing worms, gravid adults were collected and washed twice with water. Pellets of centrifuged worms were treated with 5 ml 1N NaOH and 1% (v/v) sodium hypochlorite for 5 min with shaking to obtain embryos, and the embryos were rinsed with M9 buffer three times. The embryos were hatched in 10 ml M9 buffer at 20°C for 16-18 hrs with mild shaking. Hatched L1 larvae were transferred to plates at 30-50 worms per plate and replicate plates were cultured  for defined periods; samples of the population were examined by microscopy to confirm the developmental stage at the time of harvest.

extract_protocol:
Harvested worms were washed with M9 medium, centrifuged, and the worm pellets were flash-frozen in liquid nitrogen. The worm pellets were thawed and lysed by adding 4X volumes of QIAzol (Qiagen, Cat: 79306) and shaking vigorously at room temperature for 15 min. The total RNA was extracted by the addition of 0.85X volume chloroform, centrifugation, and recovery of the aqueous phase, which was then re-extracted with 1 volume phenol:chloroform:isoamyl alcohol (25:24:1, pH = 5.5). Total RNA was then precipitated by add 1 volume of isopropanol and 0.5 µl GlycoBlue (Invitrogen, Cat: AM9516), followed by incubation at -80oC for at least 30 min, and recovery by centrifugation at 25,000 rcf for 10 min at 4 °C. The supernatants were then removed, and the RNA pellets were subsequently washed twice by 70% (v/v) ethanol, dried in air for 5 min, dissolved in water, and stored at -80 °C. Worm samples for RNA-seq were aliquoted from the ribosome profiling harvests before the lysis step and frozen separately. The total RNA was extracted as described above. To enrich for mRNA, rRNA was depleted as described in detail elsewhere (Duan et al., 2020b). rRNA-depleted mRNA samples were then purified by RNA Clean & Concentrator-5 Kit (ZYMO, Cat: R1015)
Libraries were constructed by NEBNext Ultra II RNA Library Prep kit (NEB, Cat: E7775, E7335, E7500) and sequenced by Illumina NextSeq 500 system

treatment_protocol: Synchronized populations of developing worms were cultured at 20 °C for 45 hrs after feeding. Harvested worms were washed with water three times and incubated at room temperature for 10 min to allow digestion of intestinal bacteria. Worms were then pelleted by centrifuge at 4,500 rcf for 2 min at room temperature and residual water was removed until the total volumes were twice as the worm pellets. The samples were then flashed frozen by liquid nitrogen and stored at -80 °C.

tag: genotype

value: mid L4

tag: temperature


title: hsTPH_N174trunc-1


title: VT3878_rep_C [RNA-seq]

description:
U13A with lin-41 downstream excluded
RNA.raw.reads.DG3913_VT3878.csv


title: 04-P054921-S024-R01: cellbender counts

value: lung


title: 89

city: Birmingham

first: Martin

last: Young

state: Alabama

address: 703 19th Street S

department: Medicine

institute: University of Alabama at Birmingham

description: rawCounts.xlsx

data_processing:
Basecalling performed using Illumina bcl2fastq version 2.18.0.12.
Raw sequence FASTQ files were aligned using STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM sortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.12.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization was performed using DESeq2 version 1.28.1 using default parameters in their vignette.
Genome_build: Gencode GRCm38 p6 Release M24
Supplementary_files_format_and_content: rawCounts.xlsx: Excel file containing Ensembl ID and raw counts for each gene in each sample.

organism: Mus musculus

source_name: Heart

extract_protocol: RNA was extracted using TriZol.

treatment_protocol: Mice were fed either a control diet or a high fat diet for 20 weeks, after which hearts were isolated at 6 distinct times of the day (ZT1, ZT5, ZT9, ZT13, ZT17, ZT21). Following RNA isolation, RNAseq was performed.

value: Heart

value: High Fat

tag: zietgeber time


title: RFCvar3-2


title: 87

description: rawCounts.xlsx

tag: diet

value: Control


title: VT3878_rep_B [RNA-seq]


title: 04-P006354-S057-R02: cellbender counts

value: cryo


title: 86

description: rawCounts.xlsx


title: 04-P006354-S057-R01: cellbender counts


title: VT3878_rep_A [RNA-seq]


title: RFCvar2-2

tag: strain


title: 83

description: rawCounts.xlsx


title: 02-P348762-S056-R01: cellbender counts


title: 04-P006354-S015-R01: cellbender counts


title: RFCvar1-2

tag: induction concentration


title: 82

description: rawCounts.xlsx


title: RFCvar1-1

tag: induction od


title: 02-P334354-S087-R01: cellbender counts


title: DG3913_rep_C [RNA-seq]

description:
WT for U13A
RNA.raw.reads.DG3913_VT3878.csv


title: DG3913_rep_A [RNA-seq]


title: DG3913_rep_B [RNA-seq]


title: 79

description: rawCounts.xlsx


title: 78

description: rawCounts.xlsx


title: 02-P248880-S086-R01: cellbender counts


title: VT3797_rep_C [Ribo-seq]

description:
U18A
Ribo.raw.reads.VT1367_VT3797.csv

data_processing:
Library strategy: Ribo-seq
Adaptor removal and size filtering by Cutadapt/1.9
rRNA/tRNA removal by Bowtie2/2.3.4.3
Genome mapping by Star/2.5.3
RPF p-offset and monosome periodosity calculation by olastid/0.4.8
Gene counting by plastid_cs/0.4.8
Genome_build: WBcel235
Supplementary_files_format_and_content: comma-seperated values of gene counts

extract_protocol:
Concentrated lysis buffer was add to each frozen sample to final concentration of 20 mM Tris-HCl (pH = 7.4), 150 mM NaCl, 5 mM MgCl2, 0.5X Protease Inhibitor (Sigma, Cat:P2714), 1 mM DTT, 0.1 mg/ml cycloheximide (Millipore, Cat:C4859), 1% (v/v) Triton X100 and 5 U/ml Turbo DNase (Invitrogen, Cat:AM2238), and worm pellets were kept on ice until fully thawed. Suspended worms were transferred to 400 µm silica beads tube (OPS Diagnostic, Cat: PFAW-400-100-04) and lysed in bead beater homogenizer for 3 min at 4 °C. Lysates were then centrifuged at 25,000 rcf for 10 min at 4 °C, and supernatants were collected. To generate monosomes, RNase I (Invitrogen, Cat: AM2294) was added to a final concentration of 0.2 U per µl of harvested worm pellet. The digestion was incubated at room temperature for 40 min with gentle rotation and then quenched by adding SUPERase RNase inhibitor (Invitrogen, Cat: AM2694) at 4 U per RNase I unit. The lysates were then loaded onto 5-40 % (m/v) sucrose gradients prepared with lysis buffer without Triton X100 and centrifuged at 32,000 rpm for 3 hrs at 4 °C in an SW41Ti rotor (Beckman Coulter, Cat:331362). The sucrose gradients were fractionated using BR-188 Density Gradient Fractionation System with 60% (m/v) sucrose as chase solution, and monosome fractions were collected according to OD254 profiles. 3.5 X volumes of QIAzol reagent was added to the gradient fractions containing monosomes, and RNA was extracted and separated by 17.5 % denaturing PAGE. A synthetic RNA oligonucleotide with the length of 30 nt was used as a size marker. The gel was stained by Sybr Gold (Invitrogen, Cat: S11494) at room temperature for 10 min, and a gel slice containing RNA of approximately 30 nt was excised and ground by an RNase-free pellet pestle (Fisher Scientific, Cat: 12-141-364). RNA was extracted from the gel slice by adding 500 µl of 300 mM NaAc (pH = 5.5), 1 mM EDTA, and 0.25% (m/v) SDS and mildly shaking overnight at room temperature. The gel granules were excluded using Spin-X tube filter (Millipore, Cat: CLS8160) and the RNA was then concentrated by ethanol precipitation, dissolved in water, and stored at -80 oC. 5’ phosphorylation and 3’ dephosphorylation were performed with T4 PNK (NEB, Cat: M0201S) following the manufacturer’s instructions, and the products were subjected to phenol/chloroform extraction and ethanol precipitation.
Libraries were constructed using QIAseq miRNA Library Kit (Qiagen, Cat:331505 & 331595) following the manufacturer’s instructions, except that the amplifying PCR was conducted with 9-12 cycles, and sequencing was perform using Illumina NextSeq 500 system.


title: 75

description: rawCounts.xlsx


title: RFC-1

tag: induction time


title: VT3797_rep_B [Ribo-seq]

description:
U18A
Ribo.raw.reads.VT1367_VT3797.csv


title: 02-P248880-S011-R01: cellbender counts

tag: tissue


title: 71

description: rawCounts.xlsx


title: RFCvar3-1


title: VT3797_rep_A [Ribo-seq]

description:
U18A
Ribo.raw.reads.VT1367_VT3797.csv


title: 70

description: rawCounts.xlsx


title: RFCvar2-1


title: VT1367_rep_C [Ribo-seq]

description:
WT for U18A
Ribo.raw.reads.VT1367_VT3797.csv


title: 02-P166169-S117-R01: cellbender counts


title: MBP-1


title: 67

description: rawCounts.xlsx


title: MBP-2


title: 02-P166169-S113-R01: cellbender counts


title: Gly2-WT-2


title: VT1367_rep_B [Ribo-seq]


title: 66

description: rawCounts.xlsx


title: VT1367_rep_A [Ribo-seq]


title: 02-P166169-S109-R01: cellbender counts

value: liver


title: CNTF_belt_2


title: 02-P166169-S099-R02: cellbender counts


title: 61

description: rawCounts.xlsx


title: RFC-2


title: 64

description: rawCounts.xlsx


title: 02-P166169-S099-R01: cellbender counts


title: VT3878_rep_B [Ribo-seq]

description:
U13A with lin-41 downstream excluded
Ribo.raw.reads.DG3913_VT3878.csv


title: VT3878_rep_A [Ribo-seq]


title: 57

description: rawCounts.xlsx


title: 04-P103142-S150-R01: cellranger counts

description: Single-cell or single nucleus RNA-Seq (10X) Cellranger counts, stored as an HDF5 file.

value: fresh


title: CC1-1


title: 02-P240970-S008-R01: cellbender counts


title: 56

description: rawCounts.xlsx


title: DG3913_rep_C [Ribo-seq]

description:
WT for U13A
Ribo.raw.reads.DG3913_VT3878.csv


title: 04-P103142-S149-R01: cellranger counts


title: CC1-2


title: 04-P103142-S148-R01: cellranger counts


title: Gly2-WT-1


title: 53

description: rawCounts.xlsx


title: BRCAvar2-4


title: VT3878_rep_C [Ribo-seq]


title: BRCAvar2-3


title: DG3913_rep_A [Ribo-seq]


title: 49

description: rawCounts.xlsx


title: 48

description: rawCounts.xlsx


title: 04-P079042-S071-R01: cellranger counts


title: 04-P103142-S089-R01: cellranger counts


title: BRCAvar1-1


title: CNTF_belt_1


title: BRCAvar1-2


title: Kp210-2

city: Ulsan

first: Hansol

last: Im

address: UNIST gil 50st

country: South Korea

institute: Ulsan National Institute of Science and Technology

data_processing:
Base-calling using the CLRNASeqTM program (ChunLab, South Korea)
The RNA sequencing reads in each sample were normalized using the RPKM method
Genome_build: NCBI Reference Sequence: NC_005363.1, Bioproject name : PRJNA224116
Supplementary_files_format_and_content: The excel file which include whole information of total reads, RPKM, RLE, TMM normalization. Actual publication would be conducted with RPKM version

organism: Bdellovibrio bacteriovorus HD100

source_name: Bdellovibrio predated Klebsiella pneumoniae

growth_protocol: The predatory bacterium Bdellovibrio bacteriovorus was maintained using Klebsiella pneumoniae clinical isolate as the prey in HEPES buffer with CaCl2 and MgCl2 salts added (3 mM and 2 mM, respectively) , as mentioned at previous report,  'Attack-Phase Bdellovibrio bacteriovorus Responses to Extracellular Nutrients Are Analogous to Those Seen During Late Intraperiplasmic Growth'

extract_protocol:
Overnight cultures of B. bacteriovorus grown on Klebsiella pneumoniae clinical isolate were filtered (0.45 µM) to remove any residual prey or bdelloplasts. These cultures were mixed with Klebsiella pneumoniae clinical isolate (~3X10^9 cells/ml). The mixed culture was collected at 7 different time points (0, 15, 30, 60, 120, 180, 210 min), and they are centrifuged with 2,000xg, 2 min, 2,000xg, 1min, seqeuntially) and the total cellular RNA extracted using ChargeSwitch Total RNA Cell Kits (Invitrogen) and thier manual
After qualification of RNA samples, library was constructed via Hiseq 2500 (Illumina).   Libraries for sequencing were made using the Truseq Standard mRNA sample preparation kit (Illumina, USA). The sequencing was done using single-end 50 bp sequencing on the Illumina Hiseq 2500 platform.

tag: group

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (210 min after predation)


title: Kp210-1


title: 46

description: rawCounts.xlsx


title: BRCA-2


title: 04-P079042-S015-R01: cellranger counts


title: 04-P054921-S072-R01: cellranger counts


title: Kp180-3

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (180 min after predation)


title: BRCA-1

value: 1mM Rhamnose


title: 42

description: rawCounts.xlsx


title: DG3913_rep_B [Ribo-seq]


title: 04-P054921-S024-R01: cellranger counts


title: 52

description: rawCounts.xlsx


title: Kp180-2


title: 04-P006354-S057-R02: cellranger counts


title: Kp210-3


title: 04-P103142-S109-R01: cellranger counts


title: 31

description: rawCounts.xlsx


title: 34

description: rawCounts.xlsx


title: Kp180-1


title: 30

description: rawCounts.xlsx


title: 04-P006354-S057-R01: cellranger counts


title: Kp120-3

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (120 min after predation)


title: 27

description: rawCounts.xlsx


title: Kp120-2


title: AMI/Placebo, rep4

city: Madrid

first: Juan

middle: Carlos

last: Silla-Castro

address: Melchor Fernandez Almagro 3

department: Bioinformatics

country: Spain

institute: CNIC

description: Gene expression data from infarcted heart

hyb_protocol: RNA from tissue samples was hybridized using Affymetrix GeneChip WT Pico Reagent Kit according to the user guide.

scan_protocol: Scan protocol was assessed in an Affymetrix microarray platform.

data_processing: Data were pre-processed for background correction and normalization using Robust Multichip Average (RMA) methodology  implemented in rma function of Bioconductor package oligo.

label: Biotin

organism: Sus scrofa

source_name: Infarcted tissue from animal treated with vehicle

label_protocol: RNA from tissue samples was labelled using Affymetrix GeneChip WT Pico Reagent Kit according to the user guide.

extract_protocol: RNA was isolated with PureLink RNA Mini Kit (Thermo Fisher Scientific, MA, USA) using TRIzol reagent.

treatment_protocol: Hearts were extracted by thoracotomy and washed with PBS. Infarcted tissue was minced and collected in Allprotect Tissue Reagent (Qiagen, Hilden, Germany) at -20 °C.

value: Infarcted heart

tag: treatment

value: vehicle

tag: breed

value: Large White pigs


title: 23

description: rawCounts.xlsx


title: Kp120-1


title: 02-P348762-S056-R01: cellranger counts


title: AMI/S-endMSCs*, rep4

source_name: Infarcted tissue from animal treated with S-endMSCs*

value: S-endMSCs*


title: 19

description: rawCounts.xlsx


title: AMI/S-endMSCs, rep4

source_name: Infarcted tissue from animal treated with S-endMSCs

value: S-endMSCs


title: Kp60-3

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (60 min after predation)


title: AMI/S-endMSCs*, rep3


title: 02-P334354-S087-R01: cellranger counts

value: lung

value: nuclei


title: 15

description: rawCounts.xlsx

value: Heart


title: Kp60-2


title: 12

description: rawCounts.xlsx

value: High Fat


title: 02-P248880-S086-R01: cellranger counts


title: 02-P248880-S011-R01: cellranger counts

value: heart


title: Kp60-1


title: AMI/S-endMSCs, rep3


title: 11

description: rawCounts.xlsx


title: Kp30-3

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (30 min after predation)


title: 7

description: rawCounts.xlsx

value: Control


title: AMI/S-endMSCs*, rep1


title: 04-P006354-S015-R01: cellranger counts


title: Kp30-2


title: Kp30-1


title: 3

description: rawCounts.xlsx


title: 02-P166169-S117-R01: cellranger counts


title: AMI/S-endMSCs, rep2


title: AMI/S-endMSCs, rep1


title: 02-P166169-S109-R01: cellranger counts

value: liver


title: 02-P166169-S099-R02: cellranger counts

value: cryo


title: Kp15-2

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (15 min after predation)


title: AMI/Placebo, rep3


title: AMI/S-endMSCs*, rep2


title: WT6

city: Chicago

first: Cambrian

middle: Yangshao

last: Liu

state: IL

address: 5841 S Maryland Ave

department: Department of Medicine

institute: The University of Chicago

data_processing:
Illumina Casava software was used for basecalling.
Abundance measurements (transcripts per million, tpm) were generated from pseudoalignment procedures in kallisto.
Differential expression calls (p values) were made in sleuth using a full linear model (genotype + batch) against a reduced model (batch only), to account for batch-to-batch variability.
Displayed differential expression ratios take into account only the global gene expression values and do not normalize per batch.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file includes tpm levels of individual principal transcripts for each sample and results of differential expression testing.

molecule: polyA RNA

source_name: WT_Bone-marrow macrophage (M1)

extract_protocol:
Bone marrow extracted from mice was treated with 1:20 CMG14-12 conditioned media (containing M-CSF) to generate bone-marrow derived macrophages. Macrophages were treated with 100 U/ml IFNgamma for 16 h followed by 100 ng/ml LPS for 6 hours to induce M1 activation. RNA was prepared using OMEGA Bio-tek EZNA on-column isolation kit.
Libraries were constructed using the Illumina Stranded mRNA library preparation kit to generate single-end reads 1x75bp on NextSeq High Output Runs.

tag: strain background

value: ErbB4-floxxed (WT)

tag: cell type

value: Bone-marrow macrophage (M1)

tag: batch

value: F


title: Input

city: Guangzhou

first: Boyu

last: Yuan

state: Guangdong

address: 24 Dongsha Street

country: China

institute: Zhongkai University of Agriculture and Engineering

library_source: genomic

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the mm10 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using MACS2.2.7.1, in which the total tags are normalized to 1.87e+9.
Peaks are called by using MACS2.2.7.1
Genome_build: mm10

molecule: genomic DNA

source_name: HT22 cells

growth_protocol: HT22 cells were cultured in DMEM medium (Gibco, USA) containing 10% fetal bovine serum (FBS) at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The libraries were constructed following NEB® UltraTM II DNA Library Prep Kit for Illumina (E7645s). Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so adaptors from the NEBNext Adaptor for Illumina with a ‘T’ can ligate on the ends. Then 200–400 bp fragments are beads-isolated and purified. The library was amplified by 15 cycles of PCR.

treatment_protocol: 2mM BHBA was added to the cell culture medium for 24 hours

value: Hippocampal neurons

tag: chip antibody

value: untreated


title: Kp15-1


title: AMI/Placebo, rep2

value: Infarcted heart

value: vehicle

value: Large White pigs


title: WT5

value: E


title: 02-P240970-S008-R01: cellranger counts

value: lung

tag: disease state

tag: sampleID

tag: donor

tag: processing

value: nuclei


title: 02-P166169-S099-R01: cellranger counts


title: KO5

source_name: KO_Bone-marrow macrophage (M1)

tag: genotype

value: LysMCre/ErbB4-floxxed (KO)


title: H4K5bu-B1

tag: strain

value: H4K5bu antibody (PTM-0310, PTM Biolabs)

value: BHBA treatment


title: R7 female heart

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S7

data_processing:
Raw reads were mapped xenopus tropicalis (v9.1) genome using CSBB-v3.0 (https://github.com/praneet1988/Computational-Suite-For-Bioinformaticians-and-Biologists)
CSBB uses RSEM (v1.3) for mapping and quantification and deeptools for bigwig generation
Genome_build: xenopus tropicalis v9.1
Supplementary_files_format_and_content: Counts and TPM matrices

organism: Xenopus tropicalis

value: heart

tag: Sex

value: female

tag: age

value: adult


title: H4K5bu-A1


title: Kp0-2

source_name: Bdellovibrio within HEPES (Attack phase)


title: R5 male testes

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S5

value: testes

value: male


title: H4K5ac-B2

value: H4K5ac antibody (ab51997, Abcam)


title: 02-P166169-S113-R01: cellranger counts


title: Kp0-1

value: Bdellovibrio within HEPES (Attack phase)


title: KO4

value: Bone-marrow macrophage (M1)

value: D


title: WT4

value: ErbB4-floxxed (WT)


title: R4 female lung

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S4


title: H4K5ac-A2

value: Hippocampal neurons

value: untreated


title: Kp15-3

value: Bdellovibrio bacteriovorus HD100 predated on Klebsiella pneumoniae within HEPES (15 min after predation)


title: KO6

value: F


title: R2 male head adult

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S2

value: head


title: W13-Dox Human brain organoid 3

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
At the same time, Q20, Q30 and GC content of the clean data were calculated.
ll the downstream analyses were based on the clean data with high quality
Genome_build: Paired-end clean reads were mapped to the reference genome using HISAT2 software
Supplementary_files_format_and_content: Prcessed data contain up, down and unchanged expression of genes in two groups.

source_name: VPR WTC-iPSCs

growth_protocol: iPSCs-derived brain organoids were routinely generated using neuroectodermal cells derived from iPSCs before embedding these organoids with matrigel. Organoids were maintained in termianl differentiation media (see method in mansucript), media were changed every other day throughout the in vitro culture.

extract_protocol:
RNA were extract using the Applied Biosystem, Cat. #A25742. RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Doxycycline (1ug/ml) were added daily

value: iPSCs-derived brain organoids

value: WTC-iPSCs


title: KO3

value: LysMCre/ErbB4-floxxed (KO)

value: C


title: Kp0-3


title: R1 female head adult

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S1

value: female

value: adult


title: WT2

value: B


title: KO2


title: W13-Dox Human brain organoid 2


title: R6 female GI tract

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S6

value: GI tract


title: AMI/Placebo, rep1

value: Infarcted heart

value: vehicle

value: Large White pigs


title: R8 male heart

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S8

value: heart

value: male


title: W13+Dox Human brain organoid 2

value: Doxycycline


title: WT1

value: ErbB4-floxxed (WT)

value: Bone-marrow macrophage (M1)

value: A


title: W13+Dox Human brain organoid 3

value: iPSCs-derived brain organoids


title: Control-3

city: Chengdu

first: Yanyun

last: Wang

address: No. 20 Ren Min Nan Lu

institute: West China Second University Hospital, Sichuan University

data_processing:
Raw sequencing data were collected on the basis of image and base recognition, and reads with Q30> 80% were analyzed further.
After 3’ adaptor-trimming and removal of low-quality reads by CUTADAPT software v1.9.3
high-quality reads were aligned to the Genome Reference Consortium GRCm38 /mm10 by Hisat2 software v2.0.4
The expression profiles of the high-quality reads were calculated based on fragments per kilobase of exon per million fragments mapped (FPKM) using Ensembl gtf gene annotation file and cuffdiff software.
m6A methylation regions (peak) on RNAs of each sample were detected by MACS software
Genome_build: GRCm38 /mm10
Supplementary_files_format_and_content: m6A methylation regions (peak)

source_name: Control

extract_protocol:
Total RNA was extracted; Ribosomal RNAs (rRNAs) were removed;Methylated RNA immunoprecipitation (MeRIP) was performed using the GenSeq™ m6A-MeRIP Kit
the immunoprecipitated m6A was used for RNA-seq library construction

tag: gene

value: ApoE-/-

value: Male

tag: mouse group

value: control

value: Abdominal Aorta

tag: molecule subtype

value: m6A Methylated RNA


title: Control-2

tag: tissue


title: Abdominal Aortic Aneurysms -3

source_name: Abdominal Aortic Aneurysms

value: AngII-induced abdominal aortic aneurysm (AAA) model


title: Control-1


title: R3 female ovary adult

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S3

value: ovary

value: female

value: adult


title: Abdominal Aortic Aneurysms -2


title: KO1

value: LysMCre/ErbB4-floxxed (KO)


title: R9 female intestine

description:
Total RNA extracted from indicated tissue using standard Qiagen kits. Kapa mRNA Hyper Prep reagents used for the Illumina library prep
DH6179_S9

value: intestine


title: W13+Dox Human brain organoid 1

value: WTC-iPSCs

tag: treatment


title: Abdominal Aortic Aneurysms -1

tag: strain background


title: WT3

tag: cell type

value: C


title: 899_denervated

status: Public on Apr 08 2021

city: Philadelphia

first: Panteleimon

last: Rompolas

state: PA

address: 421 Curie Blvd., BRB II/III Room 1014

department: Dermatology

institute: University of Pennsylvania

data_processing:
Base calls were converted to FASTQ files using Illunina BaseSpace FASTQ Generation App (v1.0.0)
Sequenced reads were aligned to mm10 genome build using Illumina BaseSpace RNAseq alignment App (v.2.0.2). Briefly, reads were aligned to mouse UCSC mm10 genome build with STAR (v2.6.1a) and quantification of  genes and transcripts was performed using salmon (v.0.11.2)  using UCSC mm10 genome Refseq gene annotation.
Differential gene expression between normal and denervated samples was performed using Illumina BaseSpace RNA-Seq differential expression App (v.1.0.1).
Genome_build: mm10

extract_protocol:
Lgr6-EGFP-Ires-CreERT2; R26loxP-stop-loxP-tdTom mice were administered a single dose of 20 μg, tamoxifen at P42 to activate Cre-recombination. Four weeks after denervation surgery, Lgr6Tom were stained with anti-CD49f-APC (1:300, Biolegend) and isolated from both denervated and control sides of the same mouse. RNA was extracted using RNeasy Mini Kit (Qiagen) following manufacturer's instructions.
Libraries were prepared using NEBNext poly(A) mRNA magnetic isolation module (Cat# E7490S) followed by NEBNext Ultra Directional RNA library preparation kit from Illumina (Cat# E7420L). Library quality was confirmed using an Agilent BioAnalyzer 2100 (Agilent) and library concentration was obtained using NEBNext library quantification kit for Illumina (Cat# E7630L).

treatment_protocol: Dorsal skin peripheral nerves were severed using microsurgery as previously described with minor adaptations69,70. In brief, mice were anesthetized with an intraperitoneal injection of ketamine/xylazine cocktail in PBS (0.1 ml / 20 g body weight; 87.5 mg / kg Ketamine, 12.5 mg / kg Xylazine). Once a surgical plane of anesthesia was verified by absence of pedal reflex responses following physical stimulation, a 4.5-5 cm incision was made along the dorsal midline using surgical scissors to expose cutaneous nerves on the left side of the animal (T3-T12). The nerves on the left side were then removed via blunt dissection at a point close to the anatomical entry site into the skin. All nerves on the right side were left intact. The initial incision was closed with sutures. Mice were always housed individually post-surgery and administered Meloxicam (5 mg/kg) as analgesic every 12 hours for the 2 days following surgery. Mice were closely monitored until full recovery and the resumption of normal behavior.

value: denervated

value: dorsal skin

value: keratinocytes


title: 890_denervated


title: 892_denervated


title: 899_normal

value: normal


title: W13-Dox Human brain organoid 1

value: iPSCs-derived brain organoids

value: untreated


title: 892_normal


title: 890_normal


title: CAF_sc460

city: Houston

first: Chenghang

last: Zong

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
The reads were mapped to the transcriptome using STAR
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: mm10
Supplementary_files_format_and_content: Molecular barcode count for each cell

source_name: tCAFs from KrasLA1 mice

extract_protocol:
single cell RNA-seq
sonication and ligation

value: lung adenocarcinoma

value: CAFs


title: CAF_sc457


title: CAF_sc458


title: CAF_sc459


title: CAF_sc456


title: CAF_sc455


title: CAF_sc454


title: CAF_sc453


title: CAF_sc451


title: CAF_sc449


title: CAF_sc450


title: CAF_sc446


title: CAF_sc445


title: CAF_sc447


title: CAF_sc442


title: CAF_sc448


title: CAF_sc441


title: CAF_sc440


title: CAF_sc438


title: CAF_sc444


title: CAF_sc443


title: CAF_sc439


title: CAF_sc437


title: CAF_sc436


title: CAF_sc434


title: CAF_sc433


title: CAF_sc435


title: CAF_sc432


title: CAF_sc431


title: CAF_sc430


title: CAF_sc428


title: CAF_sc429


title: CAF_sc425


title: CAF_sc452


title: CAF_sc427


title: CAF_sc423


title: CAF_sc424


title: CAF_sc421


title: CAF_sc426


title: CAF_sc419


title: CAF_sc422


title: CAF_sc420


title: CAF_sc417


title: CAF_sc412


title: CAF_sc413


title: CAF_sc416


title: CAF_sc410


title: CAF_sc408


title: CAF_sc406


title: CAF_sc407


title: CAF_sc405


title: CAF_sc415


title: CAF_sc403


title: CAF_sc404


title: CAF_sc414


title: CAF_sc401


title: CAF_sc411


title: CAF_sc400


title: CAF_sc418


title: CAF_sc398


title: CAF_sc399


title: CAF_sc396


title: CAF_sc397


title: CAF_sc390


title: CAF_sc392


title: CAF_sc409


title: CAF_sc389


title: CAF_sc394


title: CAF_sc395


title: CAF_sc391


title: CAF_sc388


title: CAF_sc393


title: CAF_sc387


title: CAF_sc385


title: CAF_sc384


title: CAF_sc383


title: CAF_sc380


title: CAF_sc379


title: CAF_sc402


title: CAF_sc377


title: CAF_sc381


title: CAF_sc382


title: CAF_sc378


title: CAF_sc373


title: CAF_sc376


title: CAF_sc372


title: CAF_sc371


title: CAF_sc375


title: CAF_sc368


title: CAF_sc370


title: CAF_sc374


title: CAF_sc369


title: CAF_sc386


title: CAF_sc367


title: CAF_sc364


title: CAF_sc365


title: CAF_sc366


title: CAF_sc361


title: CAF_sc360


title: CAF_sc357


title: CAF_sc358


title: CAF_sc352


title: CAF_sc351


title: CAF_sc350


title: CAF_sc354


title: CAF_sc349


title: CAF_sc353


title: CAF_sc348


title: CAF_sc345


title: CAF_sc362


title: CAF_sc343


title: CAF_sc344


title: CAF_sc346


title: CAF_sc341


title: CAF_sc340


title: CAF_sc336


title: CAF_sc335


title: CAF_sc338


title: CAF_sc337


title: CAF_sc342


title: CAF_sc334


title: CAF_sc339


title: CAF_sc333


title: CAF_sc332


title: CAF_sc356


title: CAF_sc363


title: CAF_sc359


title: CAF_sc330


title: CAF_sc331


title: CAF_sc355


title: CAF_sc328


title: CAF_sc329


title: CAF_sc324


title: CAF_sc323


title: CAF_sc325


title: CAF_sc327


title: CAF_sc347


title: CAF_sc326


title: CAF_sc322


title: CAF_sc317


title: CAF_sc318


title: CAF_sc316


title: CAF_sc321


title: CAF_sc319


title: CAF_sc314


title: CAF_sc313


title: CAF_sc311


title: CAF_sc315


title: CAF_sc308


title: CAF_sc309


title: CAF_sc306


title: CAF_sc305


title: CAF_sc304


title: CAF_sc302


title: CAF_sc303


title: CAF_sc299


title: CAF_sc300


title: CAF_sc298


title: CAF_sc301


title: CAF_sc296


title: CAF_sc295


title: CAF_sc294


title: CAF_sc293


title: CAF_sc292


title: CAF_sc291


title: CAF_sc312


title: whole genome-amplified DNA_ref-1

type: genomic

city: Wako

first: Junko

last: Ueda

state: Saitama

address: 2-1 Hirosawa

department: Center for Brain Science

country: Japan

institute: RIKEN

hyb_protocol: According to the standard Affymetrix protocol.

data_processing:
The signal intensity data was analyzed with the MAT Software, using parameters: Bandwith= 300bp, Max Gap= 300, Min Probe= 10.Pvalue = 1e-3.
The resulting mat files are generated by the MAT Software, using parameters: Bandwith= 300bp, Max Gap= 300, Min Probe= 10.Pvalue = 1e-3.

label: biotin

source_name: whole genome-amplified DNA

extract_protocol: Standard phenol–chloroform extraction protocols.

treatment_protocol: fresh-frozen brain samples were separated into neuronal and noneuronal nuclei by NeuN-based cell sorting. Enrichment of methylated DNA was performed using MBD proteins included in the MethylCollector Kit (Active Motif).

tag: individual

value: Reference

tag: fraction

value: reference


title: Postmortem prefrontal cortex, neuron_AM105P2

scan_protocol: According to the standard Affymetrix protocol.

source_name: Postmortem prefrontal cortex, NeuN+, mC+

value: subject 105

tag: disease state

value: Bipolar

value: Postmortem prefrontal cortex

value: neuronal nuclei


title: Postmortem prefrontal cortex, neuron_AM105P1

label_protocol: According to the standard Affymetrix protocol.


title: whole genome-amplified DNA_ref-2


title: CAF_sc290


title: CAF_sc307


title: Postmortem prefrontal cortex, nonneuron_AM105N2

source_name: Postmortem prefrontal cortex, NeuN-, mC+

value: non-neuronal nuclei


title: Postmortem prefrontal cortex, nonneuron_AM105N1


title: Postmortem prefrontal cortex, neuron_AM104P2

value: subject 104

value: healthy control


title: CAF_sc288


title: Postmortem prefrontal cortex, neuron_AM104P1


title: Postmortem prefrontal cortex, nonneuron_AM104N2


title: Postmortem prefrontal cortex, nonneuron_AM104N1


title: CAF_sc286


title: Postmortem prefrontal cortex, neuron_AM103P2

value: subject 103


title: CAF_sc285


title: CAF_sc297


title: Postmortem prefrontal cortex, nonneuron_AM103N2


title: CAF_sc282


title: Postmortem prefrontal cortex, neuron_AM103P1


title: CAF_sc284


title: CAF_sc283


title: CAF_sc320


title: Postmortem prefrontal cortex, neuron_AM102P2

value: subject 102


title: CAF_sc281


title: Postmortem prefrontal cortex, neuron_AM102P1


title: CAF_sc310


title: CAF_sc289


title: Postmortem prefrontal cortex, nonneuron_AM102N2


title: Postmortem prefrontal cortex, nonneuron_AM102N1


title: CAF_sc278


title: CAF_sc277


title: CAF_sc287


title: Postmortem prefrontal cortex, nonneuron_AM100N2

value: subject 100


title: CAF_sc275


title: CAF_sc276


title: Postmortem prefrontal cortex, neuron_AM100P2


title: CAF_sc274


title: Postmortem prefrontal cortex, nonneuron_AM100N1


title: CAF_sc280


title: CAF_sc273


title: CAF_sc271


title: Postmortem prefrontal cortex, nonneuron_AM103N1


title: Postmortem prefrontal cortex, nonneuron_AM99N2

value: subject 99


title: CAF_sc270


title: Postmortem prefrontal cortex, neuron_AM99P1


title: CAF_sc272


title: Postmortem prefrontal cortex, neuron_AM98P1

value: subject 98


title: Postmortem prefrontal cortex, nonneuron_AM98N2


title: CAF_sc279


title: CAF_sc269


title: CAF_sc267


title: Postmortem prefrontal cortex, neuron_AM100P1


title: Postmortem prefrontal cortex, nonneuron_AM98N1


title: CAF_sc266


title: Postmortem prefrontal cortex, neuron_AM97P1

value: subject 97


title: CAF_sc268

value: lung adenocarcinoma


title: CAF_sc264

value: CAFs


title: CAF_sc263


title: CAF_sc265


title: Postmortem prefrontal cortex, neuron_AM97P2


title: Postmortem prefrontal cortex, nonneuron_AM97N1


title: CAF_sc262


title: Postmortem prefrontal cortex, nonneuron_AM97N2


title: CAF_sc261


title: Postmortem prefrontal cortex, neuron_AM96P2

value: subject 96


title: Postmortem prefrontal cortex, neuron_AM99P2


title: Postmortem prefrontal cortex, neuron_AM96P1


title: CAF_sc260


title: Postmortem prefrontal cortex, nonneuron_AM99N1


title: Postmortem prefrontal cortex, neuron_AM98P2


title: CAF_sc259


title: CAF_sc258


title: CAF_sc257


title: Postmortem prefrontal cortex, nonneuron_AM96N2


title: Postmortem prefrontal cortex, neuron_AM95P2

value: subject 95


title: Postmortem prefrontal cortex, nonneuron_AM96N1


title: Postmortem prefrontal cortex, nonneuron_AM95N2


title: CAF_sc255


title: CAF_sc254


title: Postmortem prefrontal cortex, nonneuron_AM95N1


title: Postmortem prefrontal cortex, neuron_AM94P2

value: subject 94


title: CAF_sc253


title: CAF_sc251


title: CAF_sc252


title: Postmortem prefrontal cortex, nonneuron_AM94N2

value: Bipolar


title: Postmortem prefrontal cortex, nonneuron_AM94N1

value: Postmortem prefrontal cortex


title: CAF_sc250


title: CAF_sc249


title: CAF_sc248


title: Postmortem prefrontal cortex, neuron_AM92P2

value: subject 92

value: neuronal nuclei


title: Postmortem prefrontal cortex, neuron_AM92P1


title: Postmortem prefrontal cortex, nonneuron_AM92N2

value: non-neuronal nuclei


title: CAF_sc247


title: Postmortem prefrontal cortex, nonneuron_AM92N1


title: CAF_sc245


title: Postmortem prefrontal cortex, neuron_AM91P2

value: subject 91


title: Postmortem prefrontal cortex, neuron_AM91P1


title: CAF_sc243


title: CAF_sc242


title: CAF_sc256


title: Postmortem prefrontal cortex, neuron_AM95P1


title: Postmortem prefrontal cortex, nonneuron_AM91N2


title: Postmortem prefrontal cortex, nonneuron_AM91N1


title: Postmortem prefrontal cortex, neuron_AM94P1


title: Postmortem prefrontal cortex, neuron_AM90P2

value: subject 90


title: Postmortem prefrontal cortex, neuron_AM90P1


title: Postmortem prefrontal cortex, nonneuron_AM90N2


title: Postmortem prefrontal cortex, nonneuron_AM90N1


title: CAF_sc246


title: CAF_sc238


title: CAF_sc237


title: CAF_sc236


title: CAF_sc239


title: CAF_sc234


title: Postmortem prefrontal cortex, nonneuron_AM88N2

value: subject 88


title: Postmortem prefrontal cortex, neuron_AM88P1


title: Postmortem prefrontal cortex, nonneuron_AM88N1


title: Postmortem prefrontal cortex, neuron_AM88P2


title: CAF_sc244


title: Postmortem prefrontal cortex, neuron_AM86P1

value: subject 86

value: healthy control


title: Postmortem prefrontal cortex, neuron_AM86P2


title: CAF_sc232


title: Postmortem prefrontal cortex, nonneuron_AM86N2


title: CAF_sc229


title: CAF_sc230


title: Postmortem prefrontal cortex, nonneuron_AM86N1


title: Postmortem prefrontal cortex, neuron_AM82P2

value: subject 82


title: CAF_sc240


title: CAF_sc241


title: CAF_sc228


title: Postmortem prefrontal cortex, neuron_AM82P1


title: Postmortem prefrontal cortex, nonneuron_AM82N2


title: CAF_sc227


title: Postmortem prefrontal cortex, nonneuron_AM82N1


title: CAF_sc235


title: Postmortem prefrontal cortex, neuron_AM81P2

value: subject 81


title: Postmortem prefrontal cortex, neuron_AM81P1


title: CAF_sc233

value: lung adenocarcinoma


title: CAF_sc225

value: CAFs


title: Postmortem prefrontal cortex, nonneuron_AM81N2


title: CAF_sc223


title: CAF_sc224


title: Postmortem prefrontal cortex, neuron_AM79P2

value: subject 79


title: CAF_sc221


title: CAF_sc222


title: CAF_sc220


title: Postmortem prefrontal cortex, nonneuron_AM81N1


title: Postmortem prefrontal cortex, neuron_AM79P1


title: Postmortem prefrontal cortex, nonneuron_AM79N2


title: CAF_sc231


title: CAF_sc218


title: Postmortem prefrontal cortex, nonneuron_AM79N1


title: CAF_sc219


title: Postmortem prefrontal cortex, neuron_AM78P1

value: subject 78


title: Postmortem prefrontal cortex, nonneuron_AM78N2


title: CAF_sc217


title: CAF_sc216


title: CAF_sc215


title: Postmortem prefrontal cortex, nonneuron_AM78N1


title: Postmortem prefrontal cortex, neuron_AM78P2


title: CAF_sc226


title: CAF_sc214


title: CAF_sc213


title: Postmortem prefrontal cortex, neuron_AM77P2

value: subject 77


title: Postmortem prefrontal cortex, neuron_AM77P1


title: Postmortem prefrontal cortex, nonneuron_AM77N2


title: CAF_sc212


title: Postmortem prefrontal cortex, nonneuron_AM77N1


title: CAF_sc211


title: CAF_sc209


title: CAF_sc210


title: CAF_sc208


title: Postmortem prefrontal cortex, neuron_AM76P2

value: subject 76


title: Postmortem prefrontal cortex, neuron_AM76P1

value: Postmortem prefrontal cortex


title: Postmortem prefrontal cortex, nonneuron_AM76N2


title: CAF_sc206


title: Postmortem prefrontal cortex, nonneuron_AM76N1


title: CAF_sc205


title: Postmortem prefrontal cortex, neuron_AM75P2

value: subject 75

value: Bipolar


title: Postmortem prefrontal cortex, neuron_AM75P1

value: neuronal nuclei


title: CAF_sc204


title: Postmortem prefrontal cortex, nonneuron_AM75N2

value: non-neuronal nuclei


title: Postmortem prefrontal cortex, neuron_AM74P2

value: subject 74


title: Postmortem prefrontal cortex, nonneuron_AM75N1


title: CAF_sc203


title: CAF_sc201


title: CAF_sc199


title: Postmortem prefrontal cortex, neuron_AM74P1


title: Postmortem prefrontal cortex, nonneuron_AM74N2


title: CAF_sc198


title: CAF_sc200


title: Postmortem prefrontal cortex, neuron_AM72P2

value: subject 72


title: CAF_sc197


title: Postmortem prefrontal cortex, nonneuron_AM72N2


title: Postmortem prefrontal cortex, nonneuron_AM74N1


title: Postmortem prefrontal cortex, neuron_AM72P1


title: CAF_sc196


title: CAF_sc207


title: CAF_sc202


title: Postmortem prefrontal cortex, nonneuron_AM72N1


title: Postmortem prefrontal cortex, neuron_AM71P2

value: subject 71


title: CAF_sc195


title: CAF_sc191


title: CAF_sc193


title: CAF_sc190


title: CAF_sc192


title: CAF_sc194


title: CAF_sc189


title: Postmortem prefrontal cortex, neuron_AM69P2

value: subject 69

value: healthy control


title: CAF_sc188


title: Postmortem prefrontal cortex, nonneuron_AM69N2


title: CAF_sc187


title: Postmortem prefrontal cortex, nonneuron_AM71N1


title: Postmortem prefrontal cortex, nonneuron_AM71N2


title: CAF_sc186


title: Postmortem prefrontal cortex, nonneuron_AM69N1


title: CAF_sc185


title: Postmortem prefrontal cortex, neuron_AM68P2

value: subject 68


title: Postmortem prefrontal cortex, neuron_AM68P1


title: CAF_sc184

value: lung adenocarcinoma


title: CAF_sc183

value: CAFs


title: Postmortem prefrontal cortex, neuron_AM71P1


title: CAF_sc182


title: CAF_sc181


title: Postmortem prefrontal cortex, nonneuron_AM68N2


title: CAF_sc180


title: Postmortem prefrontal cortex, nonneuron_AM68N1


title: Postmortem prefrontal cortex, neuron_AM67P1

value: subject 67


title: Postmortem prefrontal cortex, neuron_AM67P2


title: Postmortem prefrontal cortex, nonneuron_AM67N1


title: CAF_sc178


title: CAF_sc179


title: Postmortem prefrontal cortex, neuron_AM65P2

value: subject 65


title: CAF_sc177


title: Postmortem prefrontal cortex, neuron_AM69P1


title: Postmortem prefrontal cortex, nonneuron_AM65N2


title: Postmortem prefrontal cortex, neuron_AM65P1


title: CAF_sc176


title: CAF_sc174


title: CAF_sc175


title: Postmortem prefrontal cortex, nonneuron_AM65N1


title: Postmortem prefrontal cortex, neuron_AM64P2

value: subject 64


title: CAF_sc173


title: CAF_sc172


title: Postmortem prefrontal cortex, nonneuron_AM64N2


title: CAF_sc171


title: Postmortem prefrontal cortex, neuron_AM64P1


title: CAF_sc170


title: Postmortem prefrontal cortex, nonneuron_AM64N1


title: CAF_sc169


title: Postmortem prefrontal cortex, neuron_AM62P2

value: subject 62


title: CAF_sc167


title: Postmortem prefrontal cortex, nonneuron_AM67N2

value: Postmortem prefrontal cortex


title: CAF_sc165


title: Postmortem prefrontal cortex, nonneuron_AM62N1


title: Postmortem prefrontal cortex, neuron_AM62P1


title: Postmortem prefrontal cortex, nonneuron_AM62N2


title: CAF_sc168


title: CAF_sc163


title: CAF_sc164


title: CAF_sc162


title: Postmortem prefrontal cortex, nonneuron_AM61N2

value: subject 61


title: Postmortem prefrontal cortex, neuron_AM61P1

value: Bipolar


title: CAF_sc161


title: Postmortem prefrontal cortex, neuron_AM59P2

value: subject 59

value: neuronal nuclei


title: Postmortem prefrontal cortex, nonneuron_AM59N2

value: non-neuronal nuclei


title: Postmortem prefrontal cortex, neuron_AM59P1


title: Postmortem prefrontal cortex, nonneuron_AM61N1


title: CAF_sc160


title: CAF_sc159


title: CAF_sc158


title: Postmortem prefrontal cortex, nonneuron_AM59N1


title: CAF_sc156


title: Postmortem prefrontal cortex, neuron_AM58P1

value: subject 58


title: CAF_sc155


title: CAF_sc157


title: Postmortem prefrontal cortex, nonneuron_AM58N2


title: CAF_sc166


title: Postmortem prefrontal cortex, neuron_AM61P2


title: CAF_sc154


title: Postmortem prefrontal cortex, nonneuron_AM58N1


title: CAF_sc153


title: Postmortem prefrontal cortex, neuron_AM58P2


title: Postmortem prefrontal cortex, neuron_AM56P2

value: subject 56


title: Postmortem prefrontal cortex, neuron_AM56P1


title: Postmortem prefrontal cortex, nonneuron_AM56N1


title: CAF_sc149


title: CAF_sc150


title: CAF_sc148


title: Postmortem prefrontal cortex, neuron_AM53P2

value: subject 53


title: Postmortem prefrontal cortex, nonneuron_AM53N2

value: healthy control


title: Postmortem prefrontal cortex, neuron_AM53P1


title: CAF_sc146


title: CAF_sc147


title: Postmortem prefrontal cortex, nonneuron_AM53N1


title: CAF_sc145


title: Postmortem prefrontal cortex, neuron_AM51P2

value: subject 51


title: Postmortem prefrontal cortex, neuron_AM51P1


title: CAF_sc144

value: lung adenocarcinoma


title: CAF_sc143

value: CAFs


title: Postmortem prefrontal cortex, nonneuron_AM51N2


title: Postmortem prefrontal cortex, nonneuron_AM51N1


title: Postmortem prefrontal cortex, neuron_AM50P2

value: subject 50


title: Postmortem prefrontal cortex, neuron_AM50P1


title: CAF_sc142


title: CAF_sc152


title: CAF_sc140


title: CAF_sc139


title: CAF_sc151


title: CAF_sc138


title: Postmortem prefrontal cortex, nonneuron_AM50N1


title: Postmortem prefrontal cortex, nonneuron_AM50N2


title: CAF_sc137


title: Postmortem prefrontal cortex, nonneuron_AM56N2


title: CAF_sc136


title: Postmortem prefrontal cortex, neuron_AM49P2

value: subject 49


title: Postmortem prefrontal cortex, nonneuron_AM49N2


title: CAF_sc134


title: CAF_sc135


title: Postmortem prefrontal cortex, neuron_AM49P1


title: Postmortem prefrontal cortex, neuron_AM48P2

value: subject 48


title: CAF_sc132


title: Postmortem prefrontal cortex, neuron_AM48P1


title: CAF_sc130


title: Postmortem prefrontal cortex, nonneuron_AM48N1


title: CAF_sc141


title: Postmortem prefrontal cortex, nonneuron_AM48N2


title: CAF_sc129


title: CAF_sc128


title: Postmortem prefrontal cortex, neuron_AM45P2

value: subject 45


title: CAF_sc127


title: CAF_sc125


title: CAF_sc126


title: Postmortem prefrontal cortex, neuron_AM44P2

value: subject 44

value: Postmortem prefrontal cortex


title: Postmortem prefrontal cortex, neuron_AM44P1


title: Postmortem prefrontal cortex, nonneuron_AM45N2


title: Postmortem prefrontal cortex, nonneuron_AM49N1


title: CAF_sc124


title: Postmortem prefrontal cortex, neuron_AM45P1


title: Postmortem prefrontal cortex, nonneuron_AM44N2


title: CAF_sc123


title: Postmortem prefrontal cortex, nonneuron_AM44N1


title: CAF_sc122


title: Postmortem prefrontal cortex, neuron_AM43P2

value: subject 43

value: Bipolar


title: Postmortem prefrontal cortex, neuron_AM43P1

value: neuronal nuclei


title: CAF_sc131


title: CAF_sc120


title: CAF_sc121


title: CAF_sc119


title: CAF_sc117


title: Postmortem prefrontal cortex, nonneuron_AM43N2

value: non-neuronal nuclei


title: Postmortem prefrontal cortex, neuron_AM41P2

value: subject 41


title: Postmortem prefrontal cortex, nonneuron_AM43N1


title: CAF_sc116


title: Postmortem prefrontal cortex, nonneuron_AM45N1


title: Postmortem prefrontal cortex, neuron_AM41P1


title: CAF_sc115


title: Postmortem prefrontal cortex, nonneuron_AM41N1


title: CAF_sc113


title: Postmortem prefrontal cortex, neuron_AM38P2

value: subject 38


title: CAF_sc112


title: Postmortem prefrontal cortex, neuron_AM38P1


title: Postmortem prefrontal cortex, nonneuron_AM38N2


title: CAF_sc133


title: CAF_sc111


title: CAF_sc110


title: CAF_sc109


title: CAF_sc108


title: Postmortem prefrontal cortex, nonneuron_AM38N1


title: CAF_sc118


title: Postmortem prefrontal cortex, nonneuron_AM36N2

value: subject 36


title: Postmortem prefrontal cortex, nonneuron_AM36N1

value: healthy control


title: CAF_sc107


title: CAF_sc105


title: CAF_sc104


title: Postmortem prefrontal cortex, neuron_AM35P2

value: subject 35


title: Postmortem prefrontal cortex, nonneuron_AM41N2


title: Postmortem prefrontal cortex, nonneuron_AM35N2


title: Postmortem prefrontal cortex, neuron_AM35P1


title: CAF_sc102

value: lung adenocarcinoma


title: CAF_sc103

value: CAFs


title: CAF_sc114


title: CAF_sc101


title: Postmortem prefrontal cortex, nonneuron_AM35N1


title: Postmortem prefrontal cortex, neuron_AM34P2

value: subject 34


title: CAF_sc100


title: Postmortem prefrontal cortex, neuron_AM34P1


title: Postmortem prefrontal cortex, nonneuron_AM34N1


title: Postmortem prefrontal cortex, neuron_AM36P2


title: CAF_sc99


title: CAF_sc97


title: Postmortem prefrontal cortex, nonneuron_AM34N2


title: Postmortem prefrontal cortex, neuron_AM30P2

value: subject 30


title: Postmortem prefrontal cortex, neuron_AM36P1


title: CAF_sc98


title: CAF_sc96


title: CAF_sc106


title: CAF_sc95


title: Postmortem prefrontal cortex, nonneuron_AM30N2


title: Postmortem prefrontal cortex, neuron_AM30P1


title: Postmortem prefrontal cortex, nonneuron_AM30N1


title: CAF_sc93


title: Postmortem prefrontal cortex, neuron_AM27P2

value: subject 27


title: CAF_sc92


title: CAF_sc91


title: Postmortem prefrontal cortex, nonneuron_AM27N2


title: CAF_sc94


title: Postmortem prefrontal cortex, neuron_AM25P2

value: subject 25


title: CAF_sc90


title: CAF_sc88


title: Postmortem prefrontal cortex, nonneuron_AM27N1


title: Postmortem prefrontal cortex, neuron_AM25P1


title: Postmortem prefrontal cortex, nonneuron_AM25N2


title: Postmortem prefrontal cortex, neuron_AM24P2

value: subject 24


title: Postmortem prefrontal cortex, neuron_AM24P1

value: Postmortem prefrontal cortex


title: CAF_sc84


title: CAF_sc85


title: CAF_sc87


title: Postmortem prefrontal cortex, nonneuron_AM25N1


title: CAF_sc82


title: Postmortem prefrontal cortex, nonneuron_AM24N1


title: Postmortem prefrontal cortex, neuron_AM22P2

value: subject 22


title: CAF_sc83


title: Postmortem prefrontal cortex, nonneuron_AM24N2


title: Postmortem prefrontal cortex, neuron_AM22P1


title: CAF_sc81


title: Postmortem prefrontal cortex, neuron_AM27P1

value: Bipolar


title: CAF_sc79


title: CAF_sc80


title: CAF_sc89


title: Postmortem prefrontal cortex, neuron_AM19P1

value: subject 19

value: neuronal nuclei


title: CAF_sc77


title: Postmortem prefrontal cortex, neuron_AM19P2


title: CAF_sc76


title: CAF_sc75


title: Postmortem prefrontal cortex, nonneuron_AM19N2

value: non-neuronal nuclei


title: CAF_sc86


title: CAF_sc74


title: CAF_sc73


title: Postmortem prefrontal cortex, nonneuron_AM18N2

value: subject 18


title: Postmortem prefrontal cortex, neuron_AM18P2


title: Postmortem prefrontal cortex, neuron_AM18P1


title: CAF_sc72


title: CAF_sc70


title: CAF_sc71


title: Postmortem prefrontal cortex, neuron_AM16P2

value: subject 16


title: Postmortem prefrontal cortex, nonneuron_AM18N1


title: Postmortem prefrontal cortex, nonneuron_AM16N2

value: healthy control


title: CAF_sc68


title: Postmortem prefrontal cortex, nonneuron_AM22N2


title: Postmortem prefrontal cortex, nonneuron_AM22N1


title: Postmortem prefrontal cortex, neuron_AM16P1


title: CAF_sc67


title: CAF_sc65


title: CAF_sc78


title: CAF_sc66


title: Postmortem prefrontal cortex, neuron_AM15P2

value: subject 15


title: CAF_sc64

value: lung adenocarcinoma


title: Postmortem prefrontal cortex, neuron_AM15P1


title: Postmortem prefrontal cortex, nonneuron_AM15N2


title: Postmortem prefrontal cortex, nonneuron_AM15N1


title: Postmortem prefrontal cortex, nonneuron_AM19N1


title: CAF_sc62

value: CAFs


title: CAF_sc61


title: Postmortem prefrontal cortex, neuron_AM14P2

value: subject 14


title: CAF_sc60


title: Postmortem prefrontal cortex, neuron_AM14P1


title: Postmortem prefrontal cortex, nonneuron_AM14N2


title: CAF_sc58


title: CAF_sc59


title: CAF_sc69


title: Postmortem prefrontal cortex, nonneuron_AM16N1


title: Postmortem prefrontal cortex, neuron_AM13P2

value: subject 13


title: Postmortem prefrontal cortex, neuron_AM13P1


title: Postmortem prefrontal cortex, nonneuron_AM13N2


title: CAF_sc57


title: CAF_sc55


title: CAF_sc53


title: CAF_sc54


title: CAF_sc56


title: Postmortem prefrontal cortex, neuron_AM11P1

value: subject 11


title: Postmortem prefrontal cortex, neuron_AM11P2


title: Postmortem prefrontal cortex, nonneuron_AM13N1


title: CAF_sc52


title: CAF_sc63


title: CAF_sc51


title: Postmortem prefrontal cortex, nonneuron_AM11N2


title: CAF_sc49


title: Postmortem prefrontal cortex, neuron_AM9P2

value: subject 9


title: Postmortem prefrontal cortex, nonneuron_AM11N1


title: CAF_sc50


title: CAF_sc48


title: Postmortem prefrontal cortex, neuron_AM9P1


title: Postmortem prefrontal cortex, nonneuron_AM14N1


title: CAF_sc45


title: Postmortem prefrontal cortex, nonneuron_AM9N1


title: Postmortem prefrontal cortex, nonneuron_AM9N2


title: Postmortem prefrontal cortex, neuron_AM8P2

value: subject 8


title: CAF_sc46


title: CAF_sc47


title: Postmortem prefrontal cortex, neuron_AM8P1

value: Postmortem prefrontal cortex


title: CAF_sc43


title: Postmortem prefrontal cortex, nonneuron_AM8N1


title: Postmortem prefrontal cortex, nonneuron_AM8N2


title: Postmortem prefrontal cortex, neuron_AM7P2

value: subject 7


title: CAF_sc44


title: Postmortem prefrontal cortex, nonneuron_AM7N2


title: CAF_sc40


title: CAF_sc41


title: CAF_sc39


title: CAF_sc37


title: CAF_sc38


title: CAF_sc36


title: Postmortem prefrontal cortex, nonneuron_AM7N1


title: Postmortem prefrontal cortex, neuron_AM6P1

value: subject 6

value: Bipolar


title: CAF_sc42


title: Postmortem prefrontal cortex, neuron_AM6P2

value: neuronal nuclei


title: CAF_sc35


title: CAF_sc34


title: Postmortem prefrontal cortex, nonneuron_AM6N1

value: non-neuronal nuclei


title: CAF_sc33


title: Postmortem prefrontal cortex, neuron_AM5P2

value: subject 5


title: Postmortem prefrontal cortex, neuron_AM5P1


title: Postmortem prefrontal cortex, nonneuron_AM5N1


title: Postmortem prefrontal cortex, nonneuron_AM5N2


title: CAF_sc32


title: CAF_sc30


title: Postmortem prefrontal cortex, nonneuron_AM6N2


title: CAF_sc31


title: Postmortem prefrontal cortex, neuron_AM4P2

value: subject 4


title: CAF_sc29


title: Postmortem prefrontal cortex, neuron_AM7P1

value: healthy control


title: CAF_sc28


title: Postmortem prefrontal cortex, neuron_AM4P1


title: Postmortem prefrontal cortex, nonneuron_AM4N1


title: Postmortem prefrontal cortex, neuron_AM3P2

value: subject 3


title: Postmortem prefrontal cortex, neuron_AM3P1


title: Postmortem prefrontal cortex, nonneuron_AM4N2


title: CAF_sc24

value: lung adenocarcinoma


title: CAF_sc22

value: CAFs


title: Postmortem prefrontal cortex, neuron_AM2P2

value: subject 2


title: CAF_sc23


title: Postmortem prefrontal cortex, nonneuron_AM3N1


title: CAF_sc21


title: CAF_sc26


title: Postmortem prefrontal cortex, nonneuron_AM3N2


title: Postmortem prefrontal cortex, neuron_AM2P1


title: CAF_sc20


title: Postmortem prefrontal cortex, nonneuron_AM2N2


title: CAF_sc19


title: Postmortem prefrontal cortex, neuron_48P2

source_name: Postmortem prefrontal cortex, NeuN+, hmC+

treatment_protocol: Genomic DNA extracted from neuronal and nonneuronal nuclei isolated from two control subjects was used for immunoprecipitation using rat 5-hmC monoclonal antibody included in the hMeDIP kit (#AF-104-0016) according to the manufacturer’s protocol (Diagenode, Denville, NJ, USA).

value: subject 48

tag: immunoprecipitation antibody

value: rat 5-hmC monoclonal antibody

value: prefrontal cortex


title: CAF_sc18


title: Postmortem prefrontal cortex, bulk_ref

source_name: Postmortem prefrontal cortex, bulk, ratIgG

value: neuronal and non-neuronal nuclei


title: CAF_sc15


title: CAF_sc16


title: Postmortem prefrontal cortex, nonneuron_AM2N1

value: Postmortem prefrontal cortex


title: Postmortem prefrontal cortex, nonneuron_48N2

source_name: Postmortem prefrontal cortex, NeuN-, hmC+


title: Postmortem prefrontal cortex, nonneuron_35N1

value: subject 35


title: Postmortem prefrontal cortex, neuron_35P1


title: CAF_sc14


title: CAF_sc25


title: CAF_sc13


title: CAF_sc27


title: CAF_sc12


title: CAF_sc10


title: CAF_sc11


title: Cultured SK-N-SH cells, control_SH-20

description: Control

source_name: Cultured SK-N-SH cells, control

growth_protocol: Cells from a human neuroblastoma cell line, SK-N-SH (American Type Culture Collection), were cultured for 8 d in Eagle's minimal essential medium containing 10% fetal bovine serum and supplemented with one of the four drugs or DMSO. The medium was changed on days 2, 5 and 8.

treatment_protocol: Valproate and lithium were directly dissolved into the medium. Carbamazepine was dissolved in dimethylsulfoxide (DMSO) before it was added to the medium.

tag: cell line

value: neuroblastoma cell line SK-N-SH

value: control

tag: dose


title: Cultured SK-N-SH cells, control_SH-14

description: Control


title: Cultured SK-N-SH cells, control_SH-8

description: Control


title: CAF_sc9


title: CAF_sc8


title: CAF_sc7


title: Cultured SK-N-SH cells, Carbamazepine (0.1 mM)_SH-6

value: Carbamazepine


title: Cultured SK-N-SH cells, Carbamazepine (0.05 mM)_SH-5


title: CAF_sc17


title: CAF_sc5


title: Cultured SK-N-SH cells, Lithium (1.2 mM)_SH-4

value: Lithium


title: Cultured SK-N-SH cells, DMSO (0.5ul/ ml)_SH-18

description: Treated with DMSO (0.5ul/ ml)

value: DMSO

value: 0.5ul/ ml


title: CAF_sc4


title: Cultured SK-N-SH cells, Lithium (0.6 mM)_SH-3


title: CAF_sc2


title: CAF_sc3


title: CAF_sc1


title: Cultured SK-N-SH cells, Valproate (0.3 mM)_SH-1

value: Valproate


title: MB_P5_3

description: Boyden_chamber_co_culture_gene_read_count.txt

data_processing:
The reads were mapped to the transcriptome using STAR
A Python program using HT-seq package was written to count the reads for each gene in each sample
Genome_build: mm10
Supplementary_files_format_and_content: raw read count of each gene

source_name: tCAFs co-culture with 393P cell line (boyden chamber)

extract_protocol:
CAFs are enriched by FACS and cells are then lysed for RNA-seq
Sonication and ligation

tag: culture

value: tCAFs co-culture with 393P cell line

tag: sample type

value: boyden chamber

tag: replicate


title: Cultured SK-N-SH cells, DMSO (1ul/ ml)_SH-17

description: Treated with DMSO (1ul/ ml)

source_name: Cultured SK-N-SH cells, DMSO (1ul/ ml)

value: 1ul/ ml


title: MB_P5_2


title: MB_P5_1


title: MB_P4_2


title: MB_P4_3


title: MB_P4_1


title: Vehicle input DNA ChIP - GH1991_pulsatile_140

city: Bristol

first: Benjamin

middle: P

last: Flynn

state: County (optional)

address: Dorothy Hodgkin Building, Whitson street

country: United Kingdom

institute: University of Bristol

description: ChIP-Seq

data_processing:
Basecalling RTA 1.18.61 Illumina instrument run time analysis software
Adapters removed by Trimmomatic-0.36, -phredd33 SE
Aligned using bowite2 (default parameters)
Duplicate tags removed by samtools (default parameters) and normalised to a total of 10 million by makeTagDirectory -single -genome rn6 -checkGC (HOMER v4.9.1)
Approximate ChIP-fragment densities compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate by makeUCSCfile (HOMER v4.9.1)
Enrichment of GR tags to 1 % input control, were identified by findPeaks (HOMER v4.9.1) using relaxed settings -F1 -L1 -P.1 -LP.01 -poisson .1 -style factor. Replicate concordance was assessed using an irreproducible discovery rate (IDR v2.0.3) set to 0.01. Overlapping enrichments between replicates were merged using mergePeaks (HOMER v4.9.1) and filtered according to the IDR estimated confidence threshold. Overlapping confident enrichment regions were merged again (mergePeaks) to create a single list of enriched GR locations across conditions.
pSer2 Pol2 enrichment regions were manually restricted to transcript coding regions larger than twice the fragment length (> 320b) and limited to 10 Kb from the transcriptional start site (TSS) based upon Ensemble release Rnor_6.0.92 co-ordinates.
Raw tags counted within GR and pSer2 Pol2 regions by annotatePeaks.pl -raw  (HOMER v4.9.1)
Input tags subtracted and differential enrichment identified by DESeq2 analysis by getDifferentialExpression.pl -AvsA -log2fold 0  (HOMER v4.9.1) (n=2)
Input tags subtracted and differential enrichment identified by DESeq2 analysis by getDifferentialExpression.pl -AvsA -log2fold 0 -norm2total  (HOMER v4.9.1) (n=2)
List of IDR filtered enriched regions after 140 min (PLS_GR_140_peaks.txt) and 180 min (PLS_GR_180_peaks.txt) pulsatile CORT infusion, 140 min (CNS_GR_140_peaks.txt) and 180 min (CNS_GR_180_peaks.txt) constant CORT infusion, 140 min and 180 min VEH infusion (VEH_GR_peaks.txt) and resultant merged regions from all treatments (GR_peaks.txt). Approximate ChIP-fragment densities are compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate (all bedGraph.gz files). Final matrix includes peak ID (column 1), GR enrichment locations (columns 2-5), whether a region was enriched to input control by each infusion condition (column 6-10),normalised tag counts (columns 27-36) and DESeq2 results, formatted by log2 fold change, Wald test p-value, Benjamin-Hochberg adjusted p-value and wether an enriched peak was detected for either compared treatment (columns 37-75) (GRChIP_allresults.txt).
Enrichment regions were manually restricted to transcript coding regions larger than twice the fragment length (> 320b) and limited to 10 Kb from the transcriptional start site (TSS) based upon Ensemble release Rnor_6.0.92 co-ordinates (pSer2Pol2_intragenic_regions.txt). Approximate ChIP-fragment densities are compiled for visualisation purposes (i.e. UCSC genome browser) for each replicate (all bedGraph.gz files). Final matrix includes gene ID (column 1), chr pSer2 Pol2 enrichment locations and strand (columns 3-6), normalised tag counts (columns 22-31) and DESeq2 results, formatted by log2 fold change, Wald test p-value and Benjamin-Hochberg adjusted p-value (columns 32-61) (pSer2Pol2ChIP_allresults.txt).
Genome_build: rn6

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
ChIP-Seq  Dissection and fixing  Liver was dissected and 0.4 g fixed in 1 % (v/v) formaldehyde (Sigma, UK), phosphate buffered saline (1.37 M NaCl, 2.68 mM KCl, 10.14 mM Na2HPO4, pH 7.4) solution for 10 min at room temperature. Formaldehyde cross-linking was quenched with addition of glycine (final conc. 125 mM) for 5 min and washed three times in ice cold phosphate buffered saline supplemented with 2 mM NaF, 0.2 mM sodium orthovanadate and 1X cOmplete protease inhibitor (Roche Diagnostics). Fixed liver was stored at -80 °C in 0.2 g samples in 500 µl of S1 Buffer (10 mM HEPES, pH 7.9, 10 mM KCl, 15 mM MgCl2, 0.1 mM (EDTA), pH 8) supplemented with 0.5 mM Dithiothreitol and 2 mM NaF, 0.2 mM sodium orthovanadate and 1X cOmplete protease inhibitor.   ChIP assay  Samples were thawed slowly on ice and adjusted to a final volume of 1 ml/ sample with supplemented S1 buffer and Dounce homogenised. Lysate was centrifuged at 4000 rpm (4 °C) and lysed in supplemented (2mM NaF and 0.2 mM sodium orthovanadate and 1X cOmplete protease inhibitor) sodium dodecyl sulphate (SDS) lysis buffer (2 % SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8.1)). Chromatin was sonicated using a Branson Sonifier 450 (Branson Ultrasonics, Danbury, CT, USA) to 300-500 bp fragments with multiple 10-sec bursts at 10 % output and centrifuged at 13,000 rpm at 4 °C to remove cellular debris from the chromatin suspension. Sheared chromatin was stored at -80 °C.  ChIP buffers were prepared in house, as described in the EZ ChIP kit protocol (Upstate Biotechnology, Lake Placid, NY, USA) with some modifications for use with animal tissue (as described where relevant). Sheared chromatin was removed from -80 °C storage and thawed slowly on ice, diluted to 50 µg in 100 µl of SDS lysis buffer and 0.9 ml with supplemented (2mM NaF, 0.2 mM NaVan and 1X cOmplete protease inhibitor) ChIP dilution buffer (0.01 % SDS, 1.1 % Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, 167 mM NaCl). Inputs were immunoprecipitated against either a GR antibody cocktail (2 µg of PA1-510A, 4 µl of PA1511A (Thermo Fisher, USA) and 4 µg of M-20X sc-1004X (Santa Cruz, USA)) or the serine 2 phosphorylated RNA polymerase II complex (2 µl ab5095 (Abcam, UK)). Rabbit IgG antibodies were used as negative control (2 µg of sc-2027 (Santa Cruz, USA)). Inputs were incubated overnight at 4 °C and incubated with protein A Dynabeads for 4 hrs (Sigma-Aldrich, UK). To reduce non-specific binding, the DNA-Antibody-Dynabead slurries were sequentially washed with 150 mM salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1), 500 mM salt buffer (0.1 % SDS, 1 % Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1), LiCl buffer (0.25 M LiCl, 1 % IGEPAL-CA630, 1 % deoxycholic acid sodium salt, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and twice in TE buffer (10 mM Tris-HCl, 1 mM EDTA) (pH 8.0). Complexes were eluted from the Dynabeads in 1 % SDS 100 mM and 0.1M NaHCO3. NaCl was added (300 mM final concentration) and crosslinks reversed overnight at 65 °C. RNA was removed using RNase treatment (Roche Diagnostics) at 65 °C and protein was digested using proteinase K (Ambion, Huntington, UK) after adjusting each solution with EDTA (1 mM final) and Tris-HCl (4 mM final) at 45 °C. DNA was extracted using 25:24:1 phenol-chloroform-isoamyl alcohol (Sigma, UK) followed by 24:1 chloroform-isoamyl alcohol (Sigma, UK). DNA in the aqueous phase was precipitated overnight at -20 °C in 2.5 VOL 100 % ethanol and 20 µg glycogen (Sigma-Aldrich, UK). DNA was pelleted by centrifugation at 13,000 rpm, 4 °C and washed in 70 % Ethanol (13,000 rpm, 4 °C), air dried and suspended in 40 µl nuclease free water (Ambion, Huntington, UK).  For each ChIP-seq replicate/condition/timepoint, liver samples from 6 rats were collected (72 rats in total). From each replicate/condition/timepoint, 10 x 100ug chromatin aliquots were prepared and immunoprecipitated with antibodies to either GR or pSer2 Pol2 before pooled, concentrated using a UniVapo Vacuum concentrator (Transcriptomics facility, UOB) to approx. 35 µl and sequenced. Note: Two separate ChIP-seq experiments were performed independently to allow for concordant peak calling analysis as previously described
ChIP-Seq  Library prepared according to TrueSeq SBS v3-HS kit protocol (Illumina)

tag: strain

value: Sprague Dawley

tag: Sex

value: Male

value: Liver

value: Vehicle infusion - pulsatile - 140min

tag: chip antibody


title: Corticosterone input DNA ChIP - GH2010_constant_180_rep2

description: ChIP-Seq

value: Corticosterone infusion - constant - 180min


title: Corticosterone input DNA ChIP - GH2007_constant_180_rep1

description: ChIP-Seq


title: Corticosterone input DNA ChIP - GH2004_constant_140_rep2

description: ChIP-Seq

value: Corticosterone infusion - constant - 140min


title: MB_P3_3


title: Vehicle input DNA ChIP - GH1994_pulsatile_180

description: ChIP-Seq

value: Vehicle infusion - pulsatile - 180min


title: MB_P3_2


title: Corticosterone input DNA ChIP - GH2001_constant_140_rep1

description: ChIP-Seq


title: Corticosterone input DNA ChIP - GH1804_pulsatile_140_rep2

description: ChIP-Seq

value: Corticosterone infusion - pulsatile - 140min


title: Cultured SK-N-SH cells, Valproate (0.6 mM)_SH-2

value: neuroblastoma cell line SK-N-SH


title: Corticosterone input DNA ChIP - GH1798_pulsatile_180_rep1

description: ChIP-Seq

value: Corticosterone infusion - pulsatile - 180min


title: Corticosterone input DNA ChIP - GH1800_pulsatile_180_rep2

description: ChIP-Seq


title: MB_P3_1


title: Corticosterone input DNA ChIP - GH1802_pulsatile_140_rep1

description: ChIP-Seq


title: MB_P2_2


title: MB_P2_3


title: Vehicle RNA Pol2 (pSer2) ChIP - GH1996_pulsatile_180

description: ChIP-Seq

value: 2 ug ab5095 (Abcam, UK)


title: Vehicle RNA Pol2 (pSer2) ChIP - GH1993_pulsatile_140

description: ChIP-Seq


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH2009_constant_180_rep1

description: ChIP-Seq


title: MB_P1_2


title: MB_P1_1


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH2006_constant_140_rep2

description: ChIP-Seq


title: MB_SQ5_3

source_name: tCAFs co-culture with 344SQ cell line (boyden chamber)

value: tCAFs co-culture with 344SQ cell line


title: MB_SQ5_1


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH1838_pulsatile_180_rep1

description: ChIP-Seq


title: MB_SQ4_3


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH1990_pulsatile_140_rep2

description: ChIP-Seq


title: MB_SQ4_2


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH1840_pulsatile_140_rep1

description: ChIP-Seq


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH1839_pulsatile_180_rep2

description: ChIP-Seq


title: MB_SQ4_1


title: MB_SQ3_1


title: MB_P2_1


title: Vehicle GR ChIP - GH1995_pulsatile_180

description: ChIP-Seq

value: 2ug PA1-510A, 4ul PA1511A (Thermo Fisher, USA) and 4ug M-20X sc-1004X (Santa Cruz, USA)


title: MB_SQ3_2


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH2003_constant_140_rep1

description: ChIP-Seq


title: Corticosterone RNA Pol2 (pSer2) ChIP - GH2012_constant_180_rep2

description: ChIP-Seq


title: MB_SQ5_2


title: Corticosterone GR ChIP - GH2011_constant_180_rep2

description: ChIP-Seq


title: MB_P1_3


title: MB_SQ3_3


title: Vehicle GR ChIP - GH1992_pulsatile_140

description: ChIP-Seq


title: MB_SQ2_3


title: MB_SQ2_1


title: Corticosterone GR ChIP - GH2002_constant_140_rep1

description: ChIP-Seq


title: Corticosterone GR ChIP - GH2005_constant_140_rep25

description: ChIP-Seq


title: Corticosterone GR ChIP - GH1801_pulsatile_180_rep2

description: ChIP-Seq


title: Corticosterone GR ChIP - GH1799_pulsatile_180_rep1

description: ChIP-Seq


title: MB_SQ1_3


title: MB_SQ1_2


title: MB_SQ1_1


title: Corticosterone GR ChIP - GH1805_pulsatile_140_rep2

description: ChIP-Seq


title: Corticosterone GR ChIP - GH1803_pulsatile_140_rep1

description: ChIP-Seq


title: MB_A5_3

source_name: tCAFs in vitro culture (boyden chamber)

value: tCAFs in vitro culture


title: MB_A5_2


title: PDL1 OE 3 Sample 3, PC9 erlotinib resistant cells

city: Rehovot

first: Yosef

last: Yarden

address: Herzl St 234

department: Biological Regulation

country: Israel

institute: Weizmann Institute of Science

description:
PC9ER cells- PD-L1 expression in wt vs ox lung cancer cells_DEoutput_All.xlsx
ox3

data_processing:
RNA-seq reads were mapped to the human genome (hg19 assembly) with STAR (Dobin et al., 2013) and gene expression levels were quantified using RSEM (Li and Dewey, 2011) and Bowtie2.
GENCODE v26 annotations were used for further analysis. Differential expression in WCE samples was computed using DESeq2 (Love et al., 2014) with default parameters. Subcellular localization was quantified similarly using DESeq2, using gene-level RSEM output.
Single end RNA-Seq
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 output file

source_name: PC9 erlotinib resistant cells

growth_protocol: Human PC9ER cells  were grown in RPMI-1640 (Gibco BRL) supplemented with 10% heat inactivated fetal calf serum (Gibco), 1mM sodium pyruvate, and a penicillin streptomycin mixture (100 U/ml; 0.1 mg/ml).

extract_protocol:
Qiagen RNA purification Kit
SENSE mRNA-Seq Library prep kit (Lexogen)

treatment_protocol: Cells were seeded in 10-well plates at 50% confluence, and 24 h later, they were transfected with siRNA control and siRNA PD-L1 SMART pool using the Lipofectamine 2000 transfection reagent. For Overexpression: cells were seeded in 10-well plates at 50% confluence, and 24 h later, they were transfected with PDL1 plasmid and vector control using Lipofectamine 2000 transfection reagent and harvested after 48h.

value: PC9 ER

tag: drug resistance

value: Erlotinib

value: PDL1 OE 3 Sample 3


title: PDL1 OE 3 Sample 4, PC9 erlotinib resistant cells

value: PDL1 OE 3 Sample 4


title: MB_SQ2_2

value: boyden chamber


title: MB_A5_1


title: PDL1 OE 3 Sample 2, PC9 erlotinib resistant cells

value: PDL1 OE 3 Sample 2


title: MB_A4_3


title: PDL1 OE 2 Sample 4, PC9 erlotinib resistant cells

description:
PC9ER cells- PD-L1 expression in wt vs ox lung cancer cells_DEoutput_All.xlsx
ox2

value: PDL1 OE 2 Sample 4


title: PDL1 OE 3 Sample 1, PC9 erlotinib resistant cells

value: PDL1 OE 3 Sample 1


title: MB_A2_2


title: MB_A4_2


title: MB_A3_1


title: MB_A3_3


title: PDL1 OE 1 Sample 3, PC9 erlotinib resistant cells

description:
PC9ER cells- PD-L1 expression in wt vs ox lung cancer cells_DEoutput_All.xlsx
ox1

value: PDL1 OE 1 Sample 3


title: PDL1 OE 2 Sample 2, PC9 erlotinib resistant cells

value: PDL1 OE 2 Sample 2


title: PDL1 OE 2 Sample 3, PC9 erlotinib resistant cells

value: PDL1 OE 2 Sample 3


title: MB_A4_1


title: MB_A2_1


title: OE 3 Control 4, PC9 erlotinib resistant cells

description:
PC9ER cells- PD-L1 expression in wt vs ox lung cancer cells_DEoutput_All.xlsx
c3

value: OE 3 Control 4


title: MB_A3_2


title: PDL1 OE 1 Sample 4, PC9 erlotinib resistant cells

value: PDL1 OE 1 Sample 4


title: PDL1 OE 2 Sample 1, PC9 erlotinib resistant cells

value: PDL1 OE 2 Sample 1


title: PDL1 OE 1 Sample 1, PC9 erlotinib resistant cells

value: PDL1 OE 1 Sample 1


title: OE 3 Control 3, PC9 erlotinib resistant cells

value: OE 3 Control 3


title: MB_A1_2

value: tCAFs in vitro culture


title: MB_A1_3


title: MB_A1_1


title: OE 3 Control 1, PC9 erlotinib resistant cells

value: PC9 ER

value: OE 3 Control 1


title: OE 2 Control 4, PC9 erlotinib resistant cells

description:
PC9ER cells- PD-L1 expression in wt vs ox lung cancer cells_DEoutput_All.xlsx
c2

value: Erlotinib

value: OE 2 Control 4


title: OE 3 Control 2, PC9 erlotinib resistant cells

value: OE 3 Control 2


title: 344SQ_shZEB1_agg_3 (0827_SQZ3)

source_name: tCAFs co-culture with 344SQ_shZEB1 cell line (multicellular aggregates)

value: multicellular aggregates


title: 344SQ_shZEB1_agg_1 (0827_SQZ1)

value: tCAFs co-culture with 344SQ_shZEB1 cell line


title: OE 2 Control 3, PC9 erlotinib resistant cells

value: OE 2 Control 3


title: OE 2 Control 2, PC9 erlotinib resistant cells

value: OE 2 Control 2


title: PDL1 OE 1 Sample 2, PC9 erlotinib resistant cells

value: PDL1 OE 1 Sample 2


title: 344SQ_shCTL_agg_1 (0827_SQ1)

source_name: tCAFs co-culture with 344SQ_shCTL cell line (multicellular aggregates)


title: MB_A2_3

value: boyden chamber


title: 344SQ_agg_3 (SQ3)

description: multicellular_aggregate_gene_read_count.txt

source_name: tCAFs co-culture with 344SQ cell line (multicellular aggregates)

value: tCAFs co-culture with 344SQ cell line


title: 344SQ_shCTL_agg_2 (0827_SQ2)

value: tCAFs co-culture with 344SQ_shCTL cell line


title: OE 2 Control 1, PC9 erlotinib resistant cells

value: OE 2 Control 1


title: 344SQ_shCTL_agg_3 (0827_SQ3)


title: siRNA PDL1 3, PC9 erlotinib resistant cells

description:
PC9ER cells -Scramble vs si-PD-L1_ DEoutput_all_04032019_PDL1_KD.xlsx
s3

value: siRNA PDL3


title: OE 1 Control 4, PC9 erlotinib resistant cells

description:
PC9ER cells- PD-L1 expression in wt vs ox lung cancer cells_DEoutput_All.xlsx
c1

value: OE 1 Control 4


title: OE 1 Control 2, PC9 erlotinib resistant cells

value: OE 1 Control 2


title: CAF-GFP_agg_1 (CAF1)

source_name: tCAFs in vitro culture (multicellular aggregates)

value: tCAFs in vitro culture


title: siRNA control 3, PC9 erlotinib resistant cells

description:
PC9ER cells -Scramble vs si-PD-L1_ DEoutput_all_04032019_PDL1_KD.xlsx
c3

value: PC9 ER

value: siRNA control


title: siRNA PDL1 2, PC9 erlotinib resistant cells

description:
PC9ER cells -Scramble vs si-PD-L1_ DEoutput_all_04032019_PDL1_KD.xlsx
s2

value: Erlotinib

value: siRNA PDL2


title: CAF-GFP_agg_3 (CAF3)

value: multicellular aggregates


title: 393P_agg_3 (3P3)

source_name: tCAFs co-culture with 393P cell line (multicellular aggregates)

value: tCAF co-culture with 393P cell line


title: siRNA control 2, PC9 erlotinib resistant cells

description:
PC9ER cells -Scramble vs si-PD-L1_ DEoutput_all_04032019_PDL1_KD.xlsx
c2


title: CAF-GFP_agg_2 (CAF2)


title: 393P_agg_2 (3P2)


title: 344SQ_shZEB1_agg_2 (0827_SQZ2)

value: tCAFs co-culture with 344SQ_shZEB1 cell line


title: siRNA control 1, PC9 erlotinib resistant cells

description:
PC9ER cells -Scramble vs si-PD-L1_ DEoutput_all_04032019_PDL1_KD.xlsx
c1


title: 393P_agg_1 (3P1)


title: OE 1 Control 3, PC9 erlotinib resistant cells

value: OE 1 Control 3


title: 344SQ_agg_2 (SQ2)


title: OE 1 Control 1, PC9 erlotinib resistant cells

value: OE 1 Control 1


title: CAF_sc6

source_name: tCAFs from KrasLA1 mice

value: lung adenocarcinoma

value: CAFs


title: 344SQ_agg_1 (SQ1)

value: tCAFs co-culture with 344SQ cell line


title: MEOX1-HA_TGFb_Rep3

city: San Francisco

first: Pawel

last: Przytycki

address: 1650 Owens Street

department: GIDB

institute: Gladstone Institutes

data_processing:
Cluster generation, sequencing, and base calling was performed on Illumina NextSeq 500.
Trimming of known adapters and low-quality regions of reads was performed using Fastq-mcf. Sequence quality control was assessed using FastQC.
Alignment to the mm10 reference genome was performed using Bowtie 2.2.4. Peaks were called using GEM.
Genome_build: Mm10
Supplementary_files_format_and_content: We provide BigWig files for PROseq We provide bed files and bigWig files for ChIPseq.

source_name: Cardiac fibroblasts

growth_protocol: A Tcf21MCM mouse was crossed with a Rosa26-Ai6 mouse (Jackson Laboratory stock# 007906). At 10 weeks of age, intraperitoneal injection of Tamoxifen (75 mg tamoxifen/kg) was done for 5 days (once a day). Tamoxifen was prepared following Jackson Laboratory guidelines https://www.jax.org/research-and-faculty/resources/cre-repository/tamoxifen#). After 5 days of injection, the mouse was sacrificed and the non-CM cells isolated as described in a previous section of this method. 100k ZsGreen positive cells were sorted with BD AriaII sorter and cultured for 3 days at 37C in a humidified incubator with 5% CO2 and maintained in FB medium: high glucose DMEM (Life Technologies) supplemented with 10% fetal bovine serum (FBS) (Hyclone, GE Healthcare), 1x Non-Essential Amino Acid (NEAA), 10U/ml penicillin/streptomycin and 1mM sodium pyruvate (all from Life Technologies). For immortalization, FB were seeded at 105 per 100 mm plate in the afternoon. Next morning, 2 hours before infection, fresh media was added on plates. The SV40 T Antigen Cell Immortalization Kit (Alstem, #CILV01) was used. 5 µl/well lentivirus supernatant (vials have 20ul) in the presence of Polybrene (added to a final concentration of 5 µg/ml). The next day, remove viral supernatant and switch again to FM medium. After 72 hours incubation, subculture the cells into 2 × 100 mm dishes and add the appropriate amount of puromycin for stable cell-line generation (1ug/ml for mouse cardiac FBs).   After 10 days after puromycin selection, multiple clones were picked for expansion. For daily cell culture, FBs were split every 3-4 days and the media was changed every other day. For the FB TGF-β stimulation, FBs were seeded at 1x105/well of 6 well plate at day 1. On day 2, the media was changed to same basal media with 0.5% FBS. On the day 3, TGF-1(Peprotech) was added into the media at concentration of 10ng/ml. Cells were collected on day 5 for RNA extraction and subsequent gene expression analysis with real time PCR.

extract_protocol:
The pHR-HAtag-mMeox1 vector was constructed by PCR amplifying the HA tag-mMeox1 fragment from the vector HA-tag-MEOX1 mouse (Twist Biosciences). For generating the pHR-HAtag-mMEOX1, we replaced the KRAB and dCas9 cassettes from the pHR-SFFV-KRAB-dCas9-mCherry vector with the HA-tag-MEOX1 cassette using Cold-fusion cloning kit (SBI System BioSciences, Palo Alto, CA, USA) following the instruction provided by the manufacturer. The construct was sequencing verified. For generating the lentiviral particles, the same procedure described in the section “CRISPR interference (CRISPRi) for sequence-specific repression” was used. The obtained supernatant was then used for performing transduction on cardiac FBs with the lentiviral vector that express HA-tag-MEOX1 and mCherry. Pure polyclonal population of HA-tag-MEOX1 FBs were sorted by flow cytometry (BD Arial II) for stable mCherry expression. For ChIPseq experiment, cells were treated as follows: 10x106 HA-tag-MEOX1 FBs (either in Unstimulated or TGFb-treated conditions) were pelleted and suspended in 10ml DMEM and cross-linked in 1% formalin solution (Thermo Fisher Scientific) by rocking in room temperature for 10 minutes. Then glycine (final concentration 0.125M) was added to quench the cross-link for 5minutes. Samples were centrifuged at 1000 rcf for 5minutes at 4C. Cells were washed with 10ml of cold 1x PBS supplemented with proteinase inhibitors and phosphatase inhibitors (Roche # 4693132001) and the pellets were snap frozen in liquid nitrogen. All samples were stored at -80C until use. When ready, cell pellets were incubated in cell lysis buffer (20 mM Tris-HCl, pH 8, 85 mM KCl, 0.5% NP-40, protease inhibitors for 10 min on a rotator at 4C. Nuclei were isolated by centrifugation (2,500 x g, 5 min, 4C), resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, pH 8, 1% SDS, protease inhibitors) and incubated on a rotator for 30 min at 4C. Chromatin was sheared using a Covaris S2 sonicator (Covaris Inc) for 20 min (60 s cycles, 20% duty cycle, 200 cycles/burst, intensity = 5) until DNA was in the 200–700 base-pair range. Chromatin was diluted 3-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mMEDTA, 16.7mMTris-HCl, pH 8, 167 mM NaCl, protease inhibitors) and incubated with 3ul of anti-HA antibody (Abcam #9110) at 4C overnight under rotation. Antibody-protein complexes were immunoprecipitated using Pierce Protein A/G magnetic beads at 4C for 2 h under rotation. Beads were washed five times (2-min/wash under rotation) with cold RIPA buffer (50 mM HEPES- KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate), followed by one wash in cold final wash buffer (1xTE, 50 mM NaCl). Immunoprecipitated chromatin was eluted at 65C with agitation for 30 min in elution buffer (50mMTris-HCl pH 8.0, 10mMEDTA, 1% SDS). High-salt buffer (250mM Tris-HCl, pH 7.5, 32.5 mM EDTA, pH 8, 1.25M NaCl) and Proteinase K (New England Biolabs Inc (NEB)) were added and crosslinks were reversed overnight at 65C. Samples were treated with RNase A, and DNA was purified with AMPure XP beads (Beckman Coulter cat #A63881).
Fragmented ChIP and input DNA were end-repaired, 5’-phosphorylated and dA-tailed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Samples were ligated to adaptor oligos for multiplex sequencing (NEB, E7335), PCR amplified, and sequenced on an Illumina NextSeq 500 at the Gladstone Institutes.

value: Cardiac fibroblasts

value: TGFb

tag: type of experiment

value: ChIP seq


title: MEOX1-HA_TGFb_Rep2

tag: treatment


title: MEOX1-HA_TGFb_Rep3_input


title: siRNA PDL1 1, PC9 erlotinib resistant cells

description:
PC9ER cells -Scramble vs si-PD-L1_ DEoutput_all_04032019_PDL1_KD.xlsx
s1

value: siRNA PDL1


title: MEOX1-HA_TGFb_Rep1


title: NMCD_CRPH_10

city: Shanghai

first: Sibo

last: Zhu

state: China

address: songhulu 2005

institute: Fudan University

data_processing:
HiSeq 2500 instrument (Illumina) and single-end 75-bp read flow cells were used in this study
Sequenced reads were trimmed for adaptor sequence by trimmomatic(v0.36), then mapped to human genome(hg19) by Hisat2(V2.0.5), and counted by featureCounts(v1.5.2)
data was filterd under the standization that a gene expressed at least in 3 samples and a sample must express at leat 200 features
Genome_build: hg19
Supplementary_files_format_and_content: csv file include raw count values for each sample

source_name: ileum

extract_protocol:
Biopsies were obtained during endoscopies, and they were stored in RNA-later at 4 °C overnight and at -80 °C for long-term storage. Total RNA was extracted from cell lysates by grinding the tissues with an abrasive rod to augment cell disruption. RNA was prepared as instructed, and the integrity of RNA was assessed using agarose gel electrophoresis
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Between January 2019 and December 2019, new-onset CD patients from the Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University were recruited in the study. Approximately 5 mg (four mucosal biopsies) of tissue samples were extracted from the inflamed and proximal non-inflamed ileum of CD patients (n=10). IMCD and NMCD were extracted from the biopsy samples, and they were confirmed by light microcopy (Olympus, Tokyo, Japan). Three months prior to recruitment, all patients were instructed to avoid antibiotics, steroids, immunosuppressants, and biologics.

value: Crohn's disease

tag: tissue

value: Non-inflamed mucosa

tag: biomarker

value: CRP high


title: NMCD_CRPH_13


title: NMCD_CRPL_8

value: CRP low


title: NMCD_CRPH_7


title: NMCD_CRPL_6


title: NMCD_CRPL_9


title: MEOX1-HA_Unstim_Rep3

tag: cell type

value: Vehicle


title: MEOX1-HA_Unstim_Rep3_input


title: MEOX1-HA_TGFb_Rep1+2_input


title: NMCD_CRPL_3


title: NMCD_CRPH_1


title: MEOX1-HA_Unstim_Rep2_input


title: NMCD_CRPH_2


title: MEOX1-HA_Unstim_Rep1


title: IMCD_CRPH_13

value: Inflamed mucosa


title: MEOX1-HA_Unstim_Rep1_input


title: MEOX1-HA_Unstim_Rep2


title: IMCD_CRPH_10


title: H3K27ac_TGFb_Rep2

extract_protocol:
For ChIPseq experiment, cells were treated as follows: 10x106 FBs were pelleted (either in the Unstimulated or TGFb-treated conditions) and suspended in 10ml DMEM and cross-linked in 1% formalin solution (Thermo Fisher Scientific) by rocking in room temperature for 10 minutes. Then glycine (final concentration 0.125M) was added to quench the cross-link for 5minutes. Samples were centrifuged at 1000 rcf for 5minutes at 4C. Cells were washed with 10ml of cold 1x PBS supplemented with proteinase inhibitors and phosphatase inhibitors (Roche # 4693132001) and the pellets were snap frozen in liquid nitrogen. All samples were stored at -80C until use. When ready, cell pellets were incubated in cell lysis buffer (20 mM Tris-HCl, pH 8, 85 mM KCl, 0.5% NP-40, protease inhibitors for 10 min on a rotator at 4C. Nuclei were isolated by centrifugation (2,500 x g, 5 min, 4C), resuspended in nuclear lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, pH 8, 1% SDS, protease inhibitors) and incubated on a rotator for 30 min at 4C. Chromatin was sheared using a Covaris S2 sonicator (Covaris Inc) for 20 min (60 s cycles, 20% duty cycle, 200 cycles/burst, intensity = 5) until DNA was in the 200–700 base-pair range. Chromatin was diluted 3-fold in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mMEDTA, 16.7mMTris-HCl, pH 8, 167 mM NaCl, protease inhibitors) and incubated with 2ul of anti-H3K27ac antibody (Abcam #ab4729) at 4C overnight under rotation. Antibody-protein complexes were immunoprecipitated using Pierce Protein A/G magnetic beads at 4C for 2 h under rotation. Beads were washed five times (2-min/wash under rotation) with cold RIPA buffer (50 mM HEPES- KOH, pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-deoxycholate), followed by one wash in cold final wash buffer (1xTE, 50 mM NaCl). Immunoprecipitated chromatin was eluted at 65C with agitation for 30 min in elution buffer (50mMTris-HCl pH 8.0, 10mMEDTA, 1% SDS). High-salt buffer (250mM Tris-HCl, pH 7.5, 32.5 mM EDTA, pH 8, 1.25M NaCl) and Proteinase K (New England Biolabs Inc (NEB)) were added and crosslinks were reversed overnight at 65C. Samples were treated with RNase A, and DNA was purified with AMPure XP beads (Beckman Coulter cat #A63881).
Fragmented ChIP and input DNA were end-repaired, 5’-phosphorylated and dA-tailed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Samples were ligated to adaptor oligos for multiplex sequencing (NEB, E7335), PCR amplified, and sequenced on an Illumina NextSeq 500 at the Gladstone Institutes.


title: IMCD_CRPL_9


title: IMCD_CRPL_8


title: IMCD_CRPL_6


title: IMCD_CRPH_7


title: H3K27ac_TGFb_Rep2_input


title: H3K27ac_TGFb_Rep1


title: H3K27ac_TGFb_Rep1_input


title: NMCD_CRPH_4


title: H3K27ac_Unstim_Rep2_input


title: IMCD_CRPH_4


title: IMCD_CRPL_3


title: H3K27ac_Unstim_Rep1


title: IMCD_CRPH_1


title: H3K27ac_Unstim_Rep2


title: IMCD_CRPH_2


title: H3K27ac_Unstim_Rep1_input


title: SU-DHL-8 cells_siCtrl m6A (m6A-Seq)

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads.
MACS2 (version 2.1.0.20151222) was employed to perform m6A peak calling.Then using Hommer (version:4.7.2) to annotate the m6A Peaks.The nucleotides in m6A Peaks region were used for detection of the consensus m6A motif by DREME (version:4.11.1) and MEME (version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1).Differential methylation was determined by Pyicoenrich (version:2.0.7).
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: SU-DHL-8 cells

extract_protocol:
m6A antibody immunoprecipitation RNA was quality control with QubitTM (Thermo Fisher Scientifc, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Then, 100ng RNA was used for library building following NEBNext® Ultra™ RNA Library Prep Kit protocol for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation andQubit®2.0 (Life Technologies, USA) and then sequenced on Illumina platformat sing-end /pair end reads for 50bp/150bp.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sirna

value: siCtrl

tag: genotype

value: control

tag: ip antibody

value: m6A antibody (Synaptic Systems, 202003)