title: scRNA_Tcf7fVavCre_2

city: Morgantown

first: Gangqing

last: Hu

address: 64 Medical Center Drive

institute: West Virginia University

data_processing:
Cell Ranger v.3.0.2 were used to process scRNA-seq fastq files which performed alignment filtering barcode counting and unique molecular identifier counting.
Genome_build: mm10
Supplementary_files_format_and_content: UMI versus gene counting matrix for scRNA-Seq

source_name: Bone Marrow

extract_protocol:
cell isolation protocolCells were isolated from bone marrows. Isolated cells were further sorted based on their surface markers.
The scRNA-seq libraries were generated using Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomic) according to manufacturer’s protocol. Briefly, 15,000 live cells were FACS-sorted and used to generate single-cell gel-bead in emulsion (GEM). After reverse transcription, GEMs were disrupted. Barcoded cDNA was isolated and amplified by PCR (12 cycles). Following fragmentation, end repair, and A-tailing, sample indexes were added during index PCR (8 cycles).
Indexed libraries were multiplexed and sequenced on an Illumina NOVO Seq instruments according to the manufacturer's instructions (26 cycles of Read 1, 8 cycles of i7 Index, and 98 cycles of Read2).

tag: mouse strain

value: Bone Marrow

tag: sorting marker


title: Ae.speltoides_pistil_Rep2

status: Public on Aug 22 2023

type: SRA

city: Beijing

first: Zefu

last: Lu

state: Haidian

address: No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China

country: China

institute: Institute of Crop Sciences

library_source: transcriptomic

data_processing:
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters. The remaining reads were aligned to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using HISAT2 v2.0.5. Gene expression values were computed using StringTie v1.3.3b.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: FPKM

molecule: total RNA

organism: Aegilops speltoides

source_name: Ae.speltoides pistil

growth_protocol: 20℃/18℃(day/night) and 16 h/8 h (light/dark).

extract_protocol:
total RNA
For each sample, total RNA was prepared for sequencing with the Illumina NovaSeq 6000 platform following the manufacturer’s instructions.

treatment_protocol: There are 17 tissues of Ae.speltoides, the pistil own 4 treatments and stamen have 5 repeats, the other tissues have 3 treatments. Besides, 7 tissues of wheat, each has 3 treatments.

tag: tissue

value: pistil

tag: cultivar


title: biopsy data from sample 2848225596

city: Philadelphia

first: Yusen

last: Zhou

state: PA

address: 3615 Civic Center Blvd

department: Department of Biomedical and Health Informatics

country: USA

institute: Children's hospital of Philadelphia

data_processing:
Sequenced reads were mapped to GRCh38 human reference genome and quantified using the kallisto pseudoalignment algorithm
Read counts were calculated using TPM
Assembly: GRCh38
Supplementary files format and content: both tab-delimited text (.tsv) and HDF5 files are provided including raw count values calculated for each sample using TPM

organism: Homo sapiens

source_name: Ileum

extract_protocol:
Trizol
Total RNA with RIN values above 6 was normalized to 400ng, converted to cDNA, then used to prepare each library using the Illumina TruSeq Stranded Messenger RNA Library Kit and the IDT for Illumina Unique Dual Index Kit in an automated Sciclone Liquid Handler Instrument. Final libraries were analyzed on a Perkin Elmer Labchip GX for quantification and QC.

value: Ileum

tag: cell type

value: biopsy

tag: disease state

value: IBD

tag: diagnosis

value: IBDU


title: biopsy data from sample 3552931053

source_name: Rectum

value: Rectum

value: NPD

value: CTR


title: scRNA_Tcf7fVavCre_1

state: West Virginia

department: MicroBiology, Immunology, and Cell Biology

molecule: polyA RNA

organism: Mus musculus

tag: genotype


title: Ae.speltoides_pistil_Rep1


title: biopsy data from sample 2646146994

value: UC


title: scRNA_Tcf7flox_3


title: Ae.speltoides_leaf3day_Rep3

source_name: Ae.speltoides leaf 3day

value: leaf 3day


title: biopsy data from sample 2426597717


title: scRNA_Tcf7flox_2


title: biopsy data from sample 2356159714


title: Ae.speltoides_leaf3day_Rep2


title: Ae.speltoides_leaf3day_Rep1


title: biopsy data from sample 2087695933


title: ChIC-seq_Tcf7-KO

library_source: genomic

data_processing:
Library strategy: ChIC-Seq
Reads were aligned to mouse genome (mm10) with bowtie2 version 2.4.2 (PMID: 22388286)
Peak and FDR were calculated  from SICER  version 2.0 (PMID: 24743992) against mm10 genome
Genome_build: mm10
Supplementary_files_format_and_content: First colum: chrom; second column: start; three column: end; four column: peak_read_count; five column: control_read_count; six column: p_value; seven column: fold_change; eight column: FDR;

molecule: genomic DNA

source_name: small intestine lamina propria

extract_protocol:
500 cells for each sample were fixed by 1% w/v formaldehyde solution and incubating at RT  for 10 minutes. The fixed cells were washed with 1 ml PBS, then, 1 ml RIPA buffer was added to each sample, and incubated at RT for 5 minutes with rotation. Cell pellets were rinsed with 500 μl binding buffer twice and resuspended in 50 μl binding buffer. To prepare anti-TCF-1-bound protein A–micrococcal nuclease (pA-MNase; antibody + PA-MNase), anti-TCF-1 and the PA-MNase at a molecular ratio of 1:2 were pre-incubated at 4 °C for 30 minutes in 50 μl binding buffer. TCF-1 + PA-MNase were added to 50 μl binding buffer-resuspended cells and incubated for 1 hour at 4 °C with rotation. Cells were washed using 200 μl wash buffer  three times and pelleted by centrifugation at 600g for 2 minutes. Next, cells were rinsed using 200 μl rinsing buffer. The MNase digestion was initiated by resuspending the rinsed cells in 40 μl reaction solution buffer and incubatingat 37 °C for 3 minutes. The reaction was stopped by adding 80 μl stop buffer and 1 μl proteinase K (Sigma–Aldrich), then incubating at 65 °C overnight. DNA was purified using phenol–chloroformextraction and ethanol precipitation.
the ChIC-seq libraries were prepared through as previously described (PMID: 31358996).

value: small intestine lamina propria

tag: strain


title: scRNA_Tcf7flox_1


title: Ae.speltoides_glume_Rep3

source_name: Ae.speltoides glume

value: glume


title: biopsy data from sample 2071726996

value: CD


title: ChIC-seq_Ctrl

source_name: Peyer's patches

value: Peyer's patches


title: Feces, SPF Stress [Sample 72]

city: Charlottesville

first: Alban

last: Gaultier

state: VA

address: 409 Lane Rd

institute: University of Virginia

description:
Zymo Quick-16STM Primer Set V3-V4
72

data_processing:
Demultiplexed reads were preprocessed using DADA2, and the first 20 base pairs were trimmed from forward and reverse reads prior to merging.
Chimeric reads were filtered out, and taxonomic identification was performed with the standard DADA2 classifier using the silva_nr99_v138.1 16S database.
Supplementary files format and content: Csv file with values absolute counts of ASVs by sample
Library strategy: 16S sequencing

source_name: Feces

growth_protocol: Fecal Pellet

extract_protocol:
ZymoBIOMICS -96 MagBead DNA kit (Zymo Research, Irvine, CA)
Dual-barcoded primers targeting the 16S V4 region

treatment_protocol: Separately Housed Cd4creAhrfl/fl or Ahrfl/fl

value: Feces

tag: treatment

value: Stress Donor

tag: Sex

value: Male


title: CD271-3

city: Modena

first: Elisabetta

last: Palazzo

address: Via del Pozzo

country: Italy

institute: Unimore

description:
Skin Squamous Carcinoma Cell Line
Cancer cells
SCC13 spheroids - CD271 vector
190820_0269_rna-seq_results.gene.rpkm.geo.xlsx

data_processing:
Demultiplex and convert to FastQ (bcl2fastq, Illumina).
Map to hg19 (Tophat 2.1.1).
Calculate RPKM (Partek GS 7.0).
Log2 transform with 0.1 RPKM offset (Partek GS 7.0).
ANOVA comparison (Partek GS 7.0).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 190820_0269_rna-seq_results.gene.rpkm.geo.xlsx: Excel file containing RPKM values.
Supplementary_files_format_and_content: 190820_0269_rna-seq_results.gene.ANOVA.geo.xlsx: Excel file containing ANOVA results.

source_name: SCC13 spheroids

growth_protocol: SCC13 spheroids were obtained by liquid overlay method and maintained in SCC medium (45% DMEM, 45% Ham’s F12, 10% fetal bovine serum, 2% L-Glutamine, 1% penicillin/streptomycin/amphotericin, 1M HEPES, and 400 ng/mL hydrocortisone).

extract_protocol:
Trizol extraction of total RNA from spheroids was performed according to the manufacturer's instructions.
Library was generated by using NEBNext Ultra II kit according to the manufacturer's instructions.

treatment_protocol: SCC13 spheroids were transduced with CD271 or empty (mock) retroviral vector, in the presence of 8 μg/ml polybrene. 48 hours after infection, spheroids were collected for total RNA isolation and sequencing.

value: SCC13 derived spheroids

tag: vector

value: CD271 overexpressing


title: Feces, SPF Naïve [Sample 71]

description:
Zymo Quick-16STM Primer Set V3-V4
71

value: Naive Donor


title: biopsy data from sample 1878769109

value: biopsy


title: Ae.speltoides_glume_Rep1


title: BDL_rep2

type: RNA

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

country: Japan

institute: Kanazawa University

description:
BDL_004
Gene expression in mouse kidney 2 weeks after BDL-operations.

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >25.0 pmol Cy3/ug cRNA) was fragmented at 60˚C for 30 minutes in a reaction volume of 55 ul containing 1x Fragmentation Buffer (Agilent) and 2x Blocking Agent (Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM(Agilent) was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray 8x60K (G4858A #28005, Agilent Technologies) for 17 hours at 65˚C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37˚C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol AgilentG3_GX_1Color and Grid: 028005_D_F_20120201) to obtain background subtracted and spatially detrended Processed Signal intensities.
Data were normalized and filtered with three filters with GeneSpring software 12.1 (Agilent Technologies). In brief, raw data were normalized with their 75 percentile values. In the first filter, when the value of a probe was lower than 20 percentile value in any samples, the probe was excluded. In the second filter, when the flag of a probe was compromised in any samples, the probe was excluded. In the last filter, when the value (log scale) of CV was over 50 percent in both conditions, the probe was excluded. After filtering, control probes were excluded, and log scale values were transformed into normal scale.

source_name: kidney, BDL-operations, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with NucleoSpin RNA (Macherey-Nagel) according to the manufacturer's instructions.

treatment_protocol: Two pair RNAs were isolated from Kidney tissues which were collected from mice 2 weeks after BDL and sham operations.

value: kidney

value: bile duct ligation (BDL) operation


title: biopsy data from sample 1737224884

value: Rectum

value: NPD


title: Feces, SPF Naïve [Sample 70]

description:
Zymo Quick-16STM Primer Set V3-V4
70


title: CD271-2


title: BDL_rep1

description:
BDL_003
Gene expression in mouse kidney 2 weeks after BDL-operations.

source_name: kidney, BDL-operations, replicate 1


title: sham_rep2

description:
BDL_002
Gene expression in mouse kidney 2 weeks after sham-operations.

source_name: kidney, sham-operations, replicate 2

value: sham operation


title: biopsy data from sample 1643751206

value: IBD

value: IBDU


title: sham_rep1

description:
BDL_001
Gene expression in mouse kidney 2 weeks after sham-operations.

source_name: kidney, sham-operations, replicate 1


title: CD271-1


title: Feces, ex-germ free Stress Feces Recipient [Sample 69]

description:
Zymo Quick-16STM Primer Set V3-V4
69

value: Stress Recipient

value: Female


title: Ae.speltoides_floret_meristem_Rep3

source_name: Ae.speltoides floret meristem

value: floret meristem


title: Ae.speltoides_floret_meristem_Rep2


title: biopsy data from sample 1375752274

value: Ileum

value: CD


title: MOCK-3

description:
Skin Squamous Carcinoma Cell Line
Cancer cells
SCC13 spheroids - Empty vector
190820_0269_rna-seq_results.gene.rpkm.geo.xlsx

value: Empty (mock)


title: Feces, SPF Stress [Sample 73]

description:
Zymo Quick-16STM Primer Set V3-V4
73

value: Feces

value: Stress Donor

value: Male


title: Feces, ex-germ free Stress Feces Recipient [Sample 68]

description:
Zymo Quick-16STM Primer Set V3-V4
68


title: biopsy data from sample 1204719929

value: biopsy

value: CTR


title: Ae.speltoides_flagleaf_20day_Rep3

source_name: Ae.speltoides flag leaf 20day

value: flag leaf 20day


title: Feces, ex-germ free Stress Feces Recipient [Sample 67]

description:
Zymo Quick-16STM Primer Set V3-V4
67


title: Ae.speltoides_floret_meristem_Rep1


title: D16S_CAP

city: Chapel Hill

first: Yu

last: Mikami

state: NC

address: 125 Mason Farm Rd

department: Marsico lung institute

institute: The University of North Carolina at Chapel Hill

library_source: transcriptomic single cell

data_processing:
cellranger v7.0.1
Seurat v4
Minimal gene count>400, Percent mitochondrial genes<20%
Assembly: GRCh38, GENCODE v40
Supplementary files format and content: R data set (rds)

growth_protocol: HBE cells were seeded onto the Transwell cell culture inserts. After confluency on the Transwell, the apical medium was removed and the cells were cultured on ALI condition with UNC-ALI medium at least for 4 weeks.

extract_protocol:
The cell dissociation procedure followed the manufacturer’s protocols for the 10x Genomics Chromium system with modifications. A 5 mM EDTA in Accutase solution (Sigma) was administered to both apical and basolateral HBE surfaces and cultures incubated for 20 min at 37 ˚C. The cells detached from the Transwell membrane were centrifuged (300g x 2 min at 4 C) and washed twice with 10% fetal bovine serum (FBS, Sigma) in Dulbecco's Modified Eagle Medium (DMEM, Sigma). The cells were then resuspended in DMEM with 10% FBS with gentle pipetting using wide-bore pipette tips and passed through a 40 µm cell strainer (Fisher Science #22363547) to remove clumps. Cell counting and viability were determined using an automated cell counter (Countess 3FL, Thermo).
Single-cell suspensions targeting approximately 10,000 cells were loaded onto a 10x Genomics Chromium Next GEM Chip G (10x Genomics) device following the manufacturer’s instructions. After GEM generation, the library preparation was performed following the instructions for the 10x Chromium Next GEM Single Cell 3’ GEM Library kit v3.1 (10x Genomics).

treatment_protocol: normoxia, symmetrical hypoxia (3.5% O2), or asymmetrical hypoxia (3.5% O2 basolateral with apical cap ~ 1% O2) for 5 days.

tag: condition

value: Asymmetrical hypoxic (3.5% O2 basolateral with apical cap)

tag: cell

value: HBE cells (ALI)

tag: batch


title: Ae.speltoides_glume_Rep2

value: glume


title: Feces, ex-germ free Stress Feces Recipient [Sample 66]

description:
Zymo Quick-16STM Primer Set V3-V4
66


title: MOCK-1

value: SCC13 derived spheroids


title: Ae.speltoides_flagleaf_20day_Rep2


title: Feces, ex-germ free Stress Feces Recipient [Sample 65]

description:
Zymo Quick-16STM Primer Set V3-V4
65


title: D16S_HYPOX

value: Symmetrical hypoxia (3.5% O2)


title: D15S_HYPOX


title: Feces, ex-germ free Stress Feces Recipient [Sample 64]

description:
Zymo Quick-16STM Primer Set V3-V4
64

value: Stress Recipient


title: Ae.speltoides_flagleaf_15day_Rep3

source_name: Ae.speltoides flag leaf 15day

value: flag leaf 15 day


title: Feces, ex-germ free Naïve Feces Recipient [Sample 63]

description:
Zymo Quick-16STM Primer Set V3-V4
63

value: Female


title: Ae.speltoides_flagleaf_15day_Rep2


title: Feces, ex-germ free Naïve Feces Recipient [Sample 62]

description:
Zymo Quick-16STM Primer Set V3-V4
62

value: Naive Recipient


title: Ae.speltoides_flagleaf_15day_Rep1


title: MOCK-2


title: D15S_CAP


title: D2R_p0_HYPOX_5d

data_processing:
cellranger v5.0.1
Seurat v4
Minimal gene count>400, Percent mitochondrial genes<20%
Assembly: GRCh38, GENCODE v36
Supplementary files format and content: R data set (rds)

treatment_protocol: Normoxia or Hypoxia (1% O2 and 5% CO2) for 6hr or 5days.

value: Hypoxoxia

tag: time point


title: Ae.speltoides_flagleaf_10day_Rep3

source_name: Ae.speltoides flag leaf 10day

value: flag leaf 10 day


title: Feces, ex-germ free Naïve Feces Recipient [Sample 61]

description:
Zymo Quick-16STM Primer Set V3-V4
61

value: Feces


title: Feces, ex-germ free Naïve Feces Recipient [Sample 60]

description:
Zymo Quick-16STM Primer Set V3-V4
60


title: Ae.speltoides_flagleaf_10day_Rep2


title: D2R_p0_HYPOX_6h

value: Hypoxia


title: Feces, ex-germ free Naïve Feces Recipient [Sample 59]

description:
Zymo Quick-16STM Primer Set V3-V4
59


title: Ae.speltoides_flagleaf_10day_Rep1


title: D2R_p0_NORM_6h

value: Normoxia


title: eTSCC_Normal5

city: Toon

first: Saika

last: Masato

state: Ehime

department: Department of Oral and Maxillofacial Surgery

institute: Ehime University Graduate School of Medicine

hyb_protocol: Hyb protocol was performed according to the manufacturer's instructions.

scan_protocol: The signal was developed and scanning was undertaken using a GeneAtlas Imaging Station(Affymetrix).

data_processing:
Obtained CEL files were log2 transformed by Expression Console without normalization and then quantile normalized by  GeneSpring GX 14.9.1 software
The samples of each clinical condition were independently divided into retrospective study. With this study, an unpaired Student’s t tests for continuous variables were used to compare the characteristics between the 2 clinical groups. We set differences with P values of less than 0.05 were considered statistically significant.

label: biotin

source_name: Left tongue_Normal sample

label_protocol: 500 ng of total RNA was labeled using according to the manufacturer's instructions.

extract_protocol: Total RNA was harvested from the fresh-frozen samples, which were collected at the time of biopsy before surgery, by either taking tissues from tissue part and normal part. When collected the samples in biopsy, put in ISOGEN and stored at -80 degrees. Total RNA used in this study was extracted by tissues after homogenization with TissueLyser (Qiagen) and ISOGEN (Nippon Gene) according to the manufacturer's protocol. The collected total RNA was quantified to 10 ng/μl by Qubit Fluorometer (Thermo Fisher Scientific) and stored at -80 degrees

tag: gender

value: male

tag: age

tag: clinical tumour size

tag: clinical stage

value: II

tag: pathological stage

value: Ⅲ

tag: pathological diagnosis

value: SCC

tag: pathological grade

tag: latent cervical lymph node metastasis

value: Yes


title: eTSCC_Normal1

value: No


title: eTSCC_Normal3

source_name: Right tongue_Normal sample

value: female

value: I


title: eTSCC_Normal2


title: Ae.speltoides_flagleaf_20day_Rep1

tag: tissue

value: flag leaf 20day

tag: cultivar


title: eTSCC_Normal4


title: D16S_NORM

value: HBE cells (ALI)


title: D66Q_p0_HYPOX_5d


title: Ae.speltoides_grain_4day_Rep3

source_name: Ae.speltoides grain 4day

value: grain 4day


title: D66Q_p0_HYPOX_6h


title: D15S_NORM


title: Feces, ex-germ free Naïve Fecese Recipient [Sample 57]

description:
Zymo Quick-16STM Primer Set V3-V4
57

tag: strain

tag: treatment

value: Naive Recipient

value: Female


title: eTSCC_LNM14

source_name: Right tongue_biopsy sample


title: eTSCC_LNM13


title: Ae.speltoides_grain_4day_Rep2


title: H306

data_processing:
STAR aligner v2.7.4a
GENCODE human v37, primary_assembly
StringTie assembler v2.1.5
Assembly: GRCh38
Supplementary files format and content: count, TPM

growth_protocol: HBE cells were expanded on CRCY medium and feeder cells, then the cells were passaged and seeded onto the Transwell cell culture inserts. After confluency on the Transwell, the apical medium was removed and the cells were cultured on ALI condition with UNC-ALI medium at least for 4 weeks.

extract_protocol:
The normoxia or hypoxia treated cells were lysed with buffer RLT (QIAGEN) and mRNA was collected using RNeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Normoxia or Hypoxia (1% O2 and 5% CO2) for 6hr, 24h, and 5days.


title: Ae.speltoides_grain_20day_Rep3

source_name: Ae.speltoides grain 20day

value: grain 20day


title: Ae.speltoides_grain_4day_Rep1


title: H305


title: eTSCC_LNM12


title: eTSCC_LNM15


title: D66Q_p0_NORM_6h


title: D65Q_p0_HYPOX_5d

value: Hypoxoxia


title: eTSCC_LNM11

source_name: Left tongue_biopsy sample


title: H304

value: Hypoxia


title: Feces, ex-germ free Naïve Feces Recipient [Sample 58]

description:
Zymo Quick-16STM Primer Set V3-V4
58

value: Feces

tag: Sex


title: D65Q_p0_HYPOX_6h

tag: condition


title: H303

tag: cell


title: D65Q_p0_NORM_6h

value: Normoxia

tag: batch


title: Ae.speltoides_grain_20day_Rep1


title: Ae.speltoides_grain_15day_Rep3

source_name: Ae.speltoides grain 15day

value: grain 15 day


title: eTSCC_LNM9

value: male


title: eTSCC_LNM10

value: II

value: SCC


title: 161236_Ros_Low_10_S14

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

data_processing:
Short read quality control was performed using FastQC v0.11.5
The sequencing adapters and low-quality end reads were trimmed using Trim Galore v0.6.6
STAR v.2.7.9a was used to align the raw reads to GENCODE human reference genome v38. After removing low quality alignments, (mapq < 15)
featureCounts v2.0.1 was used for gene expression quantification
DESeq2 v1.32.0  was used to identify differentially expressed genes between treatment and control groups
Gene set enrichment analysis (GSEA) was performed using fgsea v1.18.0 and Bader lab gene sets, updated August 2021 (http://baderlab.org/GeneSets)
Limma v3.48.3 was used for gene expression batch correction
Assembly: GENCODE human reference genome v38
Supplementary files format and content: Gene expression – Raw counts
Supplementary files format and content: Gene expression – Corrected counts

source_name: primary AML

growth_protocol: Cells were cultured in X-Vivo media supplemented with cytokines and BIT

extract_protocol:
RNA was extracted using Qiagen’s RNeasy micro kit 3ng of RNA was used for construction of sequencing libraries
Library preparation completed using TakaraStranded Total RNA pico input mammalian V3 kit
RNA sequencing using 100-cycle paired read protocoland multiplexing to obtain ~40 millionreads/sample

treatment_protocol: Cells were enriched for LSCs and AML blasts by cell sorting and ROS levels, prior to treatment with YC8-02 inhibitor

tag: disease state

value: AML

value: Peripheral Blood

tag: cell type

value: ROS low Leukemic stem cells


title: H301

tag: time point


title: 161236_Ros_Low_25_S15


title: Ae.speltoides_grain_15day_Rep2


title: H302


title: eTSCC_LNM7

tag: gender

value: female

tag: age

tag: clinical tumour size

value: Yes


title: Ae.speltoides_grain_15day_Rep1


title: eTSCC_LNM6

tag: clinical stage

value: I

tag: pathological stage

tag: pathological diagnosis


title: eTSCC_LNM8

tag: pathological grade

tag: latent cervical lymph node metastasis


title: H206

value: HBE cells (ALI)


title: H205


title: Ae.speltoides_grain_20day_Rep2

tag: tissue

tag: cultivar


title: 161236_Ros_High_25_S18

value: ROS High AML blasts

tag: treatment


title: H204

tag: condition


title: Ae.speltoides_grain_10day_Rep3

source_name: Ae.speltoides grain 10day

value: grain 10 day


title: eTSCC_LNM5


title: 161236_Ros_High_10_S17


title: H203

tag: cell


title: 161236_Ros_High_0_S16


title: 161236_Ros_Low_0_S13


title: Ae.speltoides_grain_10day_Rep1


title: eTSCC_LNM3


title: Ae.speltoides_grain_10day_Rep2


title: 140337_Ros_Low_25_S3


title: eTSCC_LNM4


title: whole exome sequencing of Y771_Y2181

data_processing:
Library strategy: exome-seq
Raw reads were trimmed with FastQC and Trimmomatic v0.334 with default parameters, and got the clean reads. Then the bwa software was used to map the reads to the IWGSC RefSeq V1.0.
The gatk software was used to call variation, and the variation information was saved as gVCF file.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: gVCF files were generated using gatk software, represents the variation information.

organism: Aegilops bicornis

extract_protocol: genomic DNA

value: leaf


title: whole exome sequencing of Y770_Y2180


title: H202

value: Hypoxia


title: 140337_Ros_Low_10_S2


title: H201


title: H106


title: eTSCC_LNM2


title: whole exome sequencing of Y615

source_name: Y615 leaf


title: 140337_Ros_Low_0_S1


title: H105


title: eTSCC_LNM1


title: whole exome sequencing of Y614

source_name: Y614 leaf


title: eTSCC_14

value: No


title: H104


title: eTSCC_13


title: 140337_Ros_High_10_S5


title: whole exome sequencing of Y441

source_name: Y441 leaf


title: H103


title: 140337_Ros_High_0_S4


title: eTSCC_12


title: eTSCC_11


title: H102


title: 090765_Ros_Low_25_S9


title: H101


title: eTSCC_15


title: N06

value: Normoxia


title: 090765_Ros_Low_0_S7


title: 140337_Ros_High_25_S6


title: BW25113 nudC KO, replicate 2

city: Vilnius

first: Kotryna

last: Kvederaviciute

address: Sauletekio av. 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

data_processing:
The quality of raw sequencing reads was evaluated using FASTQC program v0.11.9. Reads were quality (PHRED threshold 20) and length (minimum length 20) filtered using Trim Galore! v0.6.5
Processed reads were mapped to the reference Escherichia coli BW25113 strain K-12 (NZ_CP009273.1) genome using hisat2 v2.2.0 (options —no-unal --no-spliced-alignment -X 500 --no-mixed —no-discordant) and deduplicated using UMI-tools.
Gene expression was evaluated using StringTie using NCBI gene annotation (sRNAs were added manually). Differentially expressed genes were identified using DESeq2 package.
Assembly: NZ_CP009273.1
Supplementary files format and content: tab-delimited text files include transcripts coordinates, coverage and FPKM values for each Sample

organism: Escherichia coli

source_name: nudC KO in the E. coli K-12 background strain BW25113

growth_protocol: Bacteria cultures were grown in LB medium at 24°C till exponential growth phase and collected after premixing with 1/8 volume of ice-cold STOP solution (5% acid phenol, 95% ethanol).

extract_protocol:
Total RNA was extracted using RNazol RT (RN 190) (Molecular Research Center, Inc.) according to the manufacturer’s recommendations.
rRNAs were depleted using RiboMinus Bacteria 2.0 Transcriptome Isolation Kit (Invitrogen). The remaining RNA was fragmented into approximately 100-400 nt long pieces in ZnCl2 buffer and dephosphorylated using T4 PNK (Thermo Fisher Scientific). 140 ng of fragmented and dephosphorylated RNA was then used for RNA library preparation according to the NEXTflex Small RNA-seq Kit v3 (PerkinElmer) with minor modifications: at Steps E and G incubation at 42°C and 72°C was extended to 60 min, at Step G 9 PCR cycles were performed and Steps F and H1 were carried out as described in an alternative protocol for Preparing Libraries without Size Selection. RNA libraries up to 500 nt in length were purified from PAA gel as outlined in Step H2.

tag: strain

tag: genotype

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, rph-1, {delta}(rhaD-rhaB)568, {delta}nudC767::kan, hsdR514


title: BW25113 nudC KO, replicate 3

value: nudC KO in the E. coli K-12 background strain BW25113


title: BW25113 nudC KO, replicate 1


title: N05


title: eTSCC_10


title: 090765_Ros_High_25_S12

tag: disease state

tag: cell type


title: 090765_Ros_High_10_S11


title: N04


title: N03


title: eTSCC_09

tag: gender

value: male


title: BW25113 wt, replicate 2

source_name: E. coli K-12 background strain BW25113

value: E. coli K-12 background strain BW25113

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, rph-1, {delta}(rhaD-rhaB)568, hsdR514


title: BW25113 wt, replicate 3


title: 090765_Ros_High_0_S10

value: AML

value: Peripheral Blood


title: whole exome sequencing of CIae70

source_name: CIae70 leaf


title: BW25113 wt, replicate 1


title: 090765_Ros_Low_10_S8

value: ROS low Leukemic stem cells


title: eTSCC_05

tag: age

value: SCC


title: eTSCC_07

value: female

tag: clinical tumour size

value: I

value: II


title: N02

value: HBE cells (ALI)


title: eTSCC_08

tag: clinical stage


title: 697 MZ1, rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al.. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: counts

source_name: B-ALL cells

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: B-ALL cells


title: 697 MZ1, rep1


title: N01


title: BW25113 csdA KO, ADRPC-, rep1

data_processing:
The quality of raw sequencing reads was evaluated using FASTQC program v0.11.9. Reads were trimmed with SeqPurge and cutadapt.
Processed reads were mapped to the reference Escherichia coli BW25113 strain K-12 (NZ_CP009273.1) genome using hisat2 v2.2.0 (options --score-min L,0,-0.3 --no-unal --no-mixed —no-spliced-alignment).
5’-NAD-RNA were identified using DESeq2 package (quantification performed with stringtie)
Assembly: NZ_CP009273.1
Supplementary files format and content: tab-delimited text files include transcripts coordinates, coverage and FPKM values for each Sample

source_name: csdA KO in the E. coli K-12 background strain BW25113

extract_protocol:
Total RNA was extracted using RNazol RT (RN 190) (Molecular Research Center, Inc.) according to the manufacturer’s recommendations.
NAD captureSeq libraries were prepared according to the modified protocol provided by (Winz et al. 2017).

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, {delta}csdA738::kan, rph-1, {delta}(rhaD-rhaB)568, hsdR514


title: eTSCC_03

tag: pathological stage

tag: pathological diagnosis

value: No


title: S-66N5d

treatment_protocol: Normoxia or Hypoxia (1% O2 and 5% CO2) for 5days.

value: Normoxia

tag: time point


title: eTSCC_04

tag: pathological grade

tag: latent cervical lymph node metastasis


title: 697 DMSO, rep2

tag: treatment

value: DMSO


title: BW25113 csdA KO, ADRPC+, rep3

value: csdA KO in the E. coli K-12 background strain BW25113


title: BW25113 csdA KO, ADRPC+, rep2


title: S-65N5d

tag: condition


title: eTSCC_06


title: G-51N5d

tag: cell


title: 697 DMSO, rep1


title: whole exome sequencing of Y432

organism: Aegilops longissima

source_name: Y432 leaf

tag: tissue

value: leaf

tag: cultivar


title: G-44N5d


title: Clovi_3

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

country: Germany

institute: Institute for Bioinformatics and Medical Informatics

description: Q12ST024A0_20220125112857__No_12_S12_R1_001

data_processing:
All read mappings were performed against Escherichia coli K12 BW25113 (NZ_CP009273.1)
The mappings of all samples were conducted with HISAT2 v2.1.0. Spliced alignment of reads was disabled (HISAT2 parameter --no-spliced-alignment). Library type was set to reverse (--rna-strandness)
resulting mapping files in SAM format were converted to BAM format using SAMtools v1.9
Gene counts for all samples were computed with featureCounts v1.6.443 based on the annotation of the respective reference genome, where the selected feature type was set to transcript records (featureCounts parameter -t transcript)
Batch correction on a slightly larger data set using ComBat-Seq with batch and group parameters set
Assembly: Escherichia coli K12 BW25113 (NZ_CP009273.1)
Supplementary files format and content: counts_for_publication.txt

source_name: bacterial cells

extract_protocol:
1/10 volume EtOH/Phenol was added to 500 µl of sample and mixed for 1 min. After incubation on ice for 5 min, the samples were centrifuged for 1 min at 20 000 xg at 4°C. The supernatant was discarded, and the pellet was resuspended in 1 ml TRIzol. Each sample was transferred to one screw-cap tube with glass beads and cells were lysed via bead-beating for 2x 6.5 ms/s for 30 s. In between the two runs the cells were kept on ice for 2 min.  200 µl chloroform was added to the samples, mixed and incubated 2-3 min before centrifugation of the samples for 15 min, 12 000 xg, 4°C. The aqueous supernatant was taken, mixed with 500 µl isopropanol and samples were centrifuged for 10 min, 21 000 xg, 4°C. The supernatant was discarded, and the pellet was resuspended in 500 µl 75% EtOH. After centrifugation for 5 min, 20 000 xg, 4°C, the supernatant was discarded, and the pellet was dried at RT. The pellet was resuspended in 100 µl RNA-grade water and RNA was concentrated via the MN RNA clean up kit (Machery-Nagel).
RNA samples were DNase I digested(DNase I recombinant, Rnase-free, Millipore Sigma), cleaned up (RNA Clean & Concentrator-5, Zymo Research), quantified (Qubit RNA BR Assay Kit, ThermoFisher) and normalized to 100 ng in 11 µl nuclease-free water. Library preparation was performed according to the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus Reference Guide. Library concentration was measured with Qubit DNA HS Assay Kit, (ThermoFisher) on a Qubit Fluorometer (invitrogen) and fragment length was assessed with an Agilent 2100 Bioanalyzer (Agilent High sensitivity DNA Kit, Agilent). Samples were equimolarly pooled and sequenced on NextSeq™ 500 High Output Kit v2.5 (75 cycles) flow cell (Illumina) with 1 x 75 bp read length.

value: bacterial cells

value: Clovibactin


title: BW25113 csdA KO, ADRPC+, rep1

tag: strain

tag: genotype


title: eTSCC_02

tag: gender

value: male


title: Clovi_2

description: Q12ST023AQ_20220125112957__No_11_S11_R1_001

tag: cell type


title: BW25113 csdA KO, ADRPC-, rep2


title: whole exome sequencing of Y431


title: BW25113 nudC KO, ADRPC-, rep2

value: nudC KO in the E. coli K-12 background strain BW25113

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3), {lambda}-, rph-1, {delta}(rhaD-rhaB)568, {delta}nudC767::kan, hsdR514


title: Clovi_1

description: Q12ST022AI_20220125112857__No_10__S10_R1_001


title: Teixo_3

value: Teixobactin


title: eTSCC_01

value: female

tag: age

tag: clinical tumour size

value: SCC


title: whole exome sequencing of Y2138

source_name: Y2138 leaf


title: B-62N5d


title: whole exome sequencing of Y154

source_name: Y154 leaf


title: B-52N5d


title: BW25113 nudC KO, ADRPC+, rep3


title: S-66H5d

value: Hypoxia


title: Teixo_1


title: BW25113 nudC KO, ADRPC+, rep2


title: BW25113 nudC KO, ADRPC+, rep1


title: S-65H5d

value: HBE cells (ALI)


title: whole exome sequencing of PI604141

source_name: PI604141 leaf


title: WT_2.3

description: Q12ST015A1_20220125112857__NC_3_S3_R1_001


title: B-44N5d


title: WT_2.2

description: Q12ST014AR_20220125112857__NC_2_S2_R1_001


title: whole exome sequencing of Y151

source_name: Y151 leaf


title: BW25113 wt, ADRPC-, rep2

value: E. coli K-12 background strain BW25113

value: F-, {delta}(araD-araB)567, {delta}lacZ4787(::rrnB-3),{lambda}-, rph-1, {delta}(rhaD-rhaB)568, hsdR514


title: WT_2.1

description: Q12ST013AJ_20220125112857__NC_1_S1_R1_001


title: BW25113 wt, ADRPC-, rep3


title: BW25113 nudC KO, ADRPC-, rep1


title: G-44H5d


title: G-51H5d


title: Streptococcusoralis_Mono_Saliva_Rep1

city: Columbus

first: Justin

middle: Ray

last: Kaspar

state: OH

address: 305 W 12th Ave

department: Biosciences

institute: The Ohio State University

data_processing:
Step 1: FASTQ Groomer
Step 2: FASTQ Quality Trimmer
Step 3: Cutadapt removing GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Step 4: Map with Bowtie for Illumina
Step 5: sort
Step 6: htseq-count (see our publication for details)
Assembly: NC_004350.2 for S. mutans UA159; CP079724.1 for S. oralis
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Streptococcus oralis

source_name: whole cell lysate

growth_protocol: Bacterial cells used for extraction of RNA were grown in TY medium, with or without 50% human saliva, in the presence of 5% CO2 at 37°C without agitation, until they reached mid-exponential phase (OD600 ≈ 0.4)

extract_protocol:
Total RNA was extracted from bacterial cells using the RNeasy Mini kit (Qiagen), with chromosomal DNA removed using a DNase I kit (Qiagen). To remove 16S and 23S rRNAs, 10 µg of total RNA was treated using the MICROBExpressTM Bacterial mRNA Enrichment Kit
cDNA libraries were created from 100 ng enriched mRNA samples using the NEBNext Ultra Directional RNA Library Prep kit for Illumina and NEBNext multiplex Oligos for Illumina (New England Biolabs, Ipswich, MA) following instructions from the supplier.

treatment_protocol: Cells were harvested by centrifugation at 4°C for 5 min, treated with bacterial RNAprotect Bacteria Reagent (Qiagen), and immediately stored at -80°C.

value: whole cell lysate

value: Saliva; growth to OD600 0.4


title: WT_1.3


title: B-62H5d


title: B-52H5d


title: WT_1.2


title: Teixo_2


title: BW25113 wt, ADRPC+, rep2


title: Streptococcusoralis_Mono_TYG_Rep3

value: TYG; growth to OD600 0.4


title: BW25113 wt, ADRPC+, rep3


title: Streptococcusoralis_Mono_TYG_Rep2


title: BW25113 wt, ADRPC+, rep1


title: WT_1.1


title: B-44H5d


title: Streptococcusoralis_Mono_Saliva_Rep3


title: Streptococcusoralis_Mono_TYG_Rep1


title: Streptococcusoralis_Mono_Saliva_Rep2


title: rpb1_met4_aa_snf2_rap_2_ip

status: Public on Aug 21 2023

city: Kansas City

first: Andrew

middle: Joseph

last: Price

state: MO

address: 1000 E. 50th Street

department: Computational Biology

institute: Stowers Institute for Medical Research

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.20
Reads were aligned to UCSC genome sacCer3 with bowtie2 aligner (version 2.4.2 ).
Assembly: sacCer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to log phase (OD600 ~0.4-0.8) in YPD broth at 30C and harvested for study.

extract_protocol:
Whole cell extracts were sonicated, clarified and DNA-protein complexes were isolated using anti-Rpb1 antibody
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following the manufacturer’s instructions

treatment_protocol: Cells were either treated with 1ug/mL rapamycin ("rap") or an equivalent volume of DMSO for 90 minutes prior to harvest

tag: chip antibody

value: Rpb1 (BioLegend 664906)

value: rapamycin


title: rpb1_met4_aa_snf2_rap_1_input


title: rpb1_met4_aa_snf2_rap_1_ip


title: rpb1_met4_aa_snf2_1_input


title: rpb1_met4_aa_rap_1_input

value: wt


title: rpb1_met4_aa_rap_2_ip


title: rpb1_met4_aa_snf2_rap_2_input


title: rpb1_met4_aa_snf2_2_input


title: rpb1_met4_aa_snf2_2_ip


title: rpb1_met4_aa_snf2_1_ip


title: rpb1_met4_aa_1_ip


title: rpb1_met4_aa_2_input


title: rpb1_met4_aa_2_ip


title: rpb1_met4_aa_1_input


title: rpb1_met4_aa_rap_1_ip


title: HHY221_deltasnf2_YPD_NoRap_1

description: RNA-seq

data_processing:
Illumina bcl2fastq2 v2.18 was used to generate fastq files
Reads were aligned to UCSC genome sacCer3 with STAR aligner (version 2.7.3a), using Ensembl 106 gene models.
TPM and RPKM are calculated using RSEM v1.3.0
Raw Read counts are calculted using STAR (version 2.7.3.a)
Assembly: UCSC genome sacCer3

source_name: snf2 YPD 1

extract_protocol:
For RNA-seq, RNA harvested using hot phenol RNA extraction & poly-A enriched
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions


title: S. cerevisiae, wt (no tag), 37°C

city: Paris

first: Benoit

last: Palancade

address: 15 rue Helene Brion

country: France

institute: Institut Jacques Monod, CNRS

description: MATalpha his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 +pRS313

data_processing:
Reads were trimmed using fastx trimmer (FASTX-Toolkit tools).
Reads were mapped to the S. cerevisiae genome (SacCer3) using Bowtie2.
PCR duplicates were filtered using samtools.
Coverage files were created using bamCoverage tool (deepTools v3.3.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization, and formatted in the bigWig file format.
Assembly: SacCer3
Supplementary files format and content: BigWig

source_name: S288C-derivative strain

growth_protocol: Strains were grown overnight at 30°C in SC-His medium, diluted down the next morning and incubated at 25°C until reaching exponential phase.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode) and NPC-bound DNA was immunoprecipitated with anti-Myc antibodies.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit from NEB according to the manufacturer's instructions. The quality of the librairies was controlled by using the BioAnalyzer 2100 system (Agilent)

treatment_protocol: Heat shock was performed by adding an equivalent volume of pre-warmed medium at 49°C and further incubation at 37°C for 15 minutes, upon agitation.

tag: cell line

value: S288C-derivative strain

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 +pRS313

value: heatshock 37degreeC

tag: treatment time

value: c-Myc monoclonal antibody (9E10; sc-40)


title: S. cerevisiae, Nic96-myc, 37°C

description: MATalpha his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 Nic96-13myc-KanMX + pRS313

data_processing:
Reads were trimmed using fastx trimmer (FASTX-Toolkit tools).
Reads were mapped to the S. cerevisiae genome (SacCer3) using Bowtie2.
PCR duplicates were filtered using samtools.
Coverage files were created using bamCoverage tool (deepTools v3.3.2) with bin size 10 bases and reads per kilobase per million (RPKM) normalization, and formatted in the bigWig file format.
Assembly: SacCer3
Supplementary files format and content: BigWig, bed file containing called peaks using MACS2

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 Nic96-13myc-KanMX + pRS313


title: HHY221_YPD_NoRap_3

description: RNA-seq

source_name: wt YPD 3


title: HHY221_deltasnf2_YPD_NoRap_3

description: RNA-seq

source_name: snf2 YPD 3


title: S. cerevisiae, wt (no tag), 25°C


title: HHY221_deltasnf2_YPD_NoRap_2

description: RNA-seq

source_name: snf2 YPD 2


title: S. cerevisiae, mft1∆ (no tag), 37°C

description: MATalpha his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 mft1::KanMX + pRS313

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 mft1::KanMX + pRS313


title: HHY221_YPD_NoRap_2

description: RNA-seq

source_name: wt YPD 2


title: HHY221_YPD_NoRap_1

description: RNA-seq

source_name: wt YPD 1


title: rpb1_met4_aa_rap_2_input


title: s_snf5_cys_2

description: RNA-seq

data_processing:
Illumina bcl2fastq2 v2.18 was used to generate fastq files
Reads were aligned to UCSC genome sacCer3 with STAR aligner (version 2.7.3a), using Ensembl 98 gene models.
TPM and RPKM are calculated using RSEM v1.3.0
Raw Read counts are calculted using STAR (version 2.7.3.a)
Supplementary_files_format_and_content: abundance measurements

source_name: snf5 cys 2

extract_protocol:
For RNA-seq, RNA harvested using Qiaquick RNA extraction kit & Ribo-depleted.
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions

treatment_protocol: cys samples grown in YPD + 3mM cysteine for 30 mins at 30C prior to harvesting


title: s_snf5_cys_3

description: RNA-seq

source_name: snf5 cys 3


title: S. cerevisiae, Nic96-myc mft1∆, 37°C

description: MATalpha his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 Nic96-13myc-KanMX mft1::NatMX + pRS313

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 Nic96-13myc-KanMX mft1::NatMX + pRS313


title: s_snf5_cys_1

description: RNA-seq

source_name: snf5 cys 1


title: S. cerevisiae, Nic96-myc, 25°C

description: MATalpha his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 Nic96-13myc-KanMX +pRS313

value: MATalpha his3delta1 leu2delta0 lys2delta0 ura3delta0 Nic96-13myc-KanMX +pRS313


title: s_snf5_ypd_3

description: RNA-seq

source_name: snf5 YPD 3


title: s_snf5_ypd_2

description: RNA-seq

source_name: snf5 YPD 2


title: s_snf2_ypd_2

description: RNA-seq


title: s_snf2_cys_2

description: RNA-seq

source_name: snf2 cys 2


title: s_snf2_ypd_1

description: RNA-seq


title: s_snf2_cys_1

description: RNA-seq

source_name: snf2 cys 1


title: s_snf2_cys_3

description: RNA-seq

source_name: snf2 cys 3


title: s_snf2_ypd_3

description: RNA-seq


title: s_wt_cys_3

description: RNA-seq

source_name: wt cys 3


title: s_wt_cys_1

description: RNA-seq

source_name: wt cys 1


title: s_wt_ypd_3

description: RNA-seq


title: s_wt_input_2

description: ChIP-seq

data_processing:
bcl2fastq2-v2.20.0.422 was used to generate fastq files.
Reads were aligned to scaCer3 genome using bowtie2-2.3.4.1 with options --local --very-sensitive-local  --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Genome_build: scaCer3
Supplementary_files_format_and_content: bigwig

source_name: untagged Input 2

extract_protocol:
For ChIP-seq, whole cell extracts were sonicated, clarified and DNA-protein complexes were isolated using anti-myc antibody
Sequencing libraries were prepared using High Throughput Library Prep Kit (KAPA Biosystems) following the manufacturer’s instructions

value: Myc (Millipore 05-724)


title: s_wt_input_1

description: ChIP-seq

source_name: untagged Input 1


title: s_wt_ip_2

description: ChIP-seq

source_name: untagged IP 2


title: s_wt_ypd_2

description: RNA-seq


title: s_met4_myc_snf5_ypd_input_1

description: ChIP-seq

source_name: Met4-13Myc snf5 YPD Input 1


title: s_wt_cys_2

description: RNA-seq

source_name: wt cys 2


title: s_wt_ypd_1

description: RNA-seq


title: s_met4_myc_snf5_ypd_input_2

description: ChIP-seq

source_name: Met4-13Myc snf5 YPD Input 2


title: s_wt_ip_1

description: ChIP-seq

source_name: untagged IP 1


title: s_met4_myc_snf5_ypd_ip_2

description: ChIP-seq

source_name: Met4-13Myc snf5 YPD IP 2


title: s_met4_myc_snf5_ypd_ip_1

description: ChIP-seq

source_name: Met4-13Myc snf5 YPD IP 1


title: s_met4_myc_snf2_ypd_input_2

description: ChIP-seq

source_name: Met4-13Myc snf2 YPD Input 2


title: s_met4_myc_snf2_ypd_input_1

description: ChIP-seq

source_name: Met4-13Myc snf2 YPD Input 1


title: s_snf5_ypd_1

description: RNA-seq

source_name: snf5 YPD 1


title: s_met4_myc_snf2_ypd_ip_1

description: ChIP-seq

source_name: Met4-13Myc snf2 YPD IP 1


title: s_met4_myc_snf2_ypd_ip_2

description: ChIP-seq

source_name: Met4-13Myc snf2 YPD IP 2


title: s_met4_myc_ypd_input_2

description: ChIP-seq

source_name: Met4-13Myc YPD Input 2


title: s_met4_myc_ypd_input_1

description: ChIP-seq

source_name: Met4-13Myc YPD Input 1


title: s_met4_myc_ypd_ip_1

description: ChIP-seq

source_name: Met4-13Myc YPD IP 1


title: s_met4_myc_ypd_ip_2

description: ChIP-seq

source_name: Met4-13Myc YPD IP 2


title: 144H-R3 (biological replicate 1)

city: New York

last: Koff

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: D6; released from DOXY-palbo 144 hours

data_processing:
Libraries were pooled and run on an Illumina HiSeq 2500, high output, to 40 million single, 125 nucleotide-long reads
reads aligned to human ref seq hg19 with  RNASeq aligner STAR (version_2.4.0c)
raw counts were imputed into R studio version 3.2.0 (cran.r-project.org) and differential gene expression determined with Bioconductor package DEseq2 comparing expression in growth arrested quiescent cells to each time point
Genes annotated in Gencode version 18 were quantified with featureCounts (subhead package version 1.4.3-p1).
Assembly: human reference sequence hg19 with the RNASeq aligner STAR (version_2.4.0c).   between the groups of samples. Enrichment of differential expression in sets of genes was determined using Gene Set Enrichment Analysis (GSEA) on gene groupings from MSigDB, as well as custom sets (Subramanian et al, 2005).

growth_protocol: LS8817 Tet-On-FMDM2 cells are cultured in DME containing 10% fetal bovine serum and 2mM glutamine in 5% CO2 at 37 degree celsius

extract_protocol:
RNA was isolated using Rneasy as described by the manufacturer (QIAGEN).  RNA quality was checked on a BioAnalyzer to ensue a minimume RNA integrity value of 7.  All experiments were performed with three biologic replicates
Libraries were generated using 500 ng of input RNA per sample according to the manufacturer’s instructions for TruSeq mRNA Library Prep Kit V2 (Illumina) with 8 cycles of PCR.

treatment_protocol: cells are pretrated with doxycycline to induce MDM2 and then treated with doxycycline and palbociclib to induce growth arrest.  After all cells have arrested, doxycycline is removed and geroconversion to senescecence is followed over time

value: dedifferentiated liposarcoma


title: 120H-R4 (biological replicate 2)

description: D5; released from DOXY-palbo 120 hours


title: 4-weeks-R4 (biological replicate 2)

description: D28; released from DOXY-palb0 28 days


title: 96H-R3 (biological replicate 1)

description: D4; released from DOXY-palbo 96 hours


title: DOXY-PD-R4 (biological replicate 2)

description: D0, quiescence; pre-treated doxy, followed by 72 hours with DOXY and palbociclib


title: 144H-R4 (biological replicate 2)

description: D6; released from DOXY-palbo 144 hours


title: 3-weeks-R4 (biological replicate 2)

description: D21; released from DOXY-palbo 21 days


title: 3-weeks-R5 (biological replicate 3)

description: D21; released from DOXY-palbo 21 days


title: 96H-R5 (biological replicate 3)

description: D4; released from DOXY-palbo 96 hours


title: DOXY-PD-R3 (biological replicate 1)


title: 72H-R5 (biological replicate 3)

description: D3: released from DOXY-palbo 72 hours


title: 2-weeks-R4 (biological replicate 2)

description: D14; released from DOXY-palbo 14 days


title: 96H-R4 (biological replicate 2)

description: D4; released from DOXY-palbo 96 hours


title: 72H-R3 (biological replicate 1)

description: D3: released from DOXY-palbo 72 hours


title: 144H-R5 (biological replicate 3)

description: D6; released from DOXY-palbo 144 hours


title: DOXY-R4 (biological replicate 2)

description: doxycycline treated cells


title: CONTROL-R5 (biological replicate 3)

description: untreated cells


title: DOXY-R3 (biological replicate 1)

description: doxycycline treated cells


title: DOXY-R5 (biological replicate 3)

description: doxycycline treated cells


title: CONTROL-R4 (biological replicate 2)

description: untreated cells


title: CONTROL-R3 (biological replicate 1)

description: untreated cells


title: 4-weeks-R5 (biological replicate 3)

description: D28; released from DOXY-palb0 28 days


title: 120H-R3 (biological replicate 1)

description: D5; released from DOXY-palbo 120 hours


title: 120H-R5 (biological replicate 3)

description: D5; released from DOXY-palbo 120 hours


title: 72H-R4 (biological replicate 2)

description: D3: released from DOXY-palbo 72 hours


title: DOXY-PD-R5 (biological replicate 3)


title: Healthy control1

city: Suita, Osaka

first: Wang

last: Renjie

address: 1-1 Yamadaoka

institute: Osaka University

data_processing:
An Illumina HiSeq 2500 platform in 75-base single-end mode was used for sequencing.
Illumina CASAVA 1.8.2 software was used for base calling.
Sequenced reads were mapped to the human reference genome sequence (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
Fragments per kilobase of exon per million mapped fragments were calculated using Cuffnorm version 2.2.1.
Ingenuity Pathway Analysis was used to identify canonical pathways of differentially expressed genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: iPSC

growth_protocol: iPSC-derived CMs were maintained in chemical defined medium (500mL of RPMI1640, 213 μg/mL of L-Ascorbic acid, and 75 μg/mL of albumin) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using NucleoSpin (Takara Bio) following the manufacturer’s procedure.
Library preparation was performed using the TruSeq stranded mRNA sample prep kit (Illumina).

treatment_protocol: Each iPSC line was differentiated to cardiomyocyte by adding 6μM CHIR-99021（Cayman Chemical） with Stemfit（Ajinomoto） for 48h（day0-day2）.Then change the medium to chemical defined medium and add 2μM Wnt-C59(Selleck Chemicals) for the next 48h.

value: iPSC

tag: group

value: Healthy control 1

value: cardiomyocyte differentiation


title: Healthy control2

value: Healthy control 2


title: Healthy control3

value: Healthy control 3


title: Isogenic

value: Isogenic corrected TNNI3-WT


title: Homozygous

value: Homozygous TNNI3-R170W


title: RCM

value: Heterozygous TNNI3-R170W


title: NMR, Heart, Uox, NMR35, vl0461

city: London

first: Diego

last: Villar

address: 4 Newark Street, Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
ChIP-seq peak files were generated my MACS2 callPeak function (default parameters).
4C data was processed with pipe4C (Krijger et al. 2020)
Supplementary files format and content: MACS2 peak files for each ChIP and input combination (.narrowPeak extension)
Supplementary files format and content: 4C wig files for each 4C experiment

organism: Heterocephalus glaber

source_name: Heart

extract_protocol:
Tissues were prepared by direct perfusion of the liver with PBS, followed by dicing the whole organs (liver and heart) in small pieces around 1cm3. Blood clots within the heart ventricles were removed. Cross-linking of the diced tissue was performed in 1% formaldehyde solution for 20 min, addition of 250 mM glycine and incubation for a further 10 min to neutralize the formaldehyde. After homogenization of cross-linked tissues in a dounce tissue grinder, samples were washed twice with PBS and lysed according to published protocols (SCHMIDT et al. 2009 for ChIP and Krijger et al. 2020 for 4C) to solubilize DNA-protein complexes. For ChIP, chromatin was fragmented to 300 bp average size by sonication on a Misonix sonicator 3000 with a 418 tip (1/16 inch diameter). Chromatin from 50-200 mg of dounced tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729), H3K4me1 (abcam ab8895), TBX5 (Insight bio sc-515536), RXRA (sc-553), FOXA1 (ab70382), HNF4A (ARP31946), CEBPA (sc-9314) and HNF6 (sc-13050). For 4C, locus-specific 4C templates were made using two rounds of enzyme digestion (primary and secondary) and ligation. Purified 4C templates were amplified by inverse PCR with bait-specific primers.
Illumina sequencing libraries were prepared from ChIP-enriched or 4C-enriched DNA using ThruPLEX DNA-seq library preparation kit (Takara Bio) or NEBNext Ultra II DNA Library Prep Kit for Illumina with up to 10ng of input DNA and 8-15 PCR cycles. After PCR, libraries were pooled in equimolar concentrations and sequenced on Illumina HiSeq 4000, NextSeq 500 or NovaSeq 6000 instruments.
ChIP-Seq, 4C-Seq

treatment_protocol: We performed chromatin immunoprecipitation experiments followed by high throughput sequencing (ChIP-seq) or 4C-seq using liver and heart tissue samples isolated from naked mole-rat, Damaraland mole-rat, guinea pig and mouse. At least two independent biological replicates from different animals were performed for each species and antibody. Wherever possible, tissues from young adult males were used. Tissues were prepared immediately post-mortem (typically within an hour) to maximize experimental quality. Post-mortem tissues were kept on ice until processed to minimize potential loss of protein-DNA interactions during post-mortem time. Sample allocations to experimental batches were randomised to ensure unbiased distributions of species, tissue, individual and sex, using the R/Bioconductor package OSAT (YAN et al. 2012).

value: Heart

value: wild-type

tag: developmental stage

value: adult

tag: age (months)

tag: Sex

value: male

tag: individual

tag: bait

value: Uox


title: DMR, Heart, Nebl, DMR2, vl0467

organism: Fukomys damarensis

tag: tissue

value: 36 (estimated)

value: Nebl

tag: treatment


title: DMR, Heart, Ppargc1a, DMR2, vl0465


title: NMR, Heart, Ppargc1a, NMR35, vl0455


title: NMR, Heart, Nebl, NMR35, vl0459


title: NMR, Liver, Ppargc1a, NMR34, vl0454

source_name: Liver

value: Liver


title: U251 FB-3

city: Hangzhou

first: Chen

last: Zhichao

address: Shenyuan 11-407, NO.2318, Yuhangtang Rd, Yuhang District, 311121, Hangzhou, Zhejiang, P.R.China

institute: Hangzhou Normal University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38.107
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: 200 uM FB for 48h


title: U251 FB-4


title: U251 CTL-4

value: Without special treatment


title: U251 CTL-1


title: U251 CTL-2


title: U251 FB-2


title: U251 CTL-3


title: NMR, Liver, Uox, NMR34, vl0460


title: NMR, Heart, Igf1r, NMR35, vl0451


title: DMR, Liver, CEBPA, DMR4, vl0428

description: ChIP-seq

value: 48 (estimated)

tag: antibody

value: CEBPA


title: DMR, Liver, FOXA1, DMR4, vl0422

description: ChIP-seq

tag: genotype


title: DMR, Heart, input, DMR6, vl0416

description: ChIP-seq

value: female

value: input


title: DMR, Liver, RXRA, DMR4, vl0419

description: ChIP-seq

value: RXRA


title: DMR, Liver, HNF6, DMR1, vl0414

description: ChIP-seq


title: DMR, Liver, HNF4A, DMR4, vl0425

description: ChIP-seq


title: DMR, Liver, CEBPA, DMR1, vl0415

description: ChIP-seq


title: DMR, Liver, FOXA1, DMR1, vl0413

description: ChIP-seq


title: DMR, Liver, RXRA, DMR1, vl0412

description: ChIP-seq


title: DMR, Heart, TBX5, DMR6, vl0411

description: ChIP-seq


title: U251 FB-1


title: Seeds, 30 DAA, rep 2

city: Piotrków Trybunalski

first: Waldemar

last: Wojciechowski

address: ul. Gliniana 14

country: Poland

institute: Generiks Sp. z o.o. Sp. k.

data_processing:
Quality filtering and adapter trimming with BBDUK 2 v. 37.02, default parameters
Expression values were calculated with RSEM v1.2.28 (strand-specific data)
Supplementary files format and content: Provided are files with tab-separated values exactly as output by RSEM; it contains particular gene names and their expression values (raw and normalized)

organism: Lupinus luteus

source_name: seeds

growth_protocol: Yellow lupine, Taper variety, was cultivated under field conditions in the Nicolaus Copernicus University's experimental field, in Piwnice near Torun (Poland, 53°05′42.0″N 18°33′24.6″E).

extract_protocol:
Quick-RNA™ Plant Miniprep
TruSeq Stranded Total RNA Seq with Plant Ribo-Zero depletion

tag: cultivar

value: Taper

value: seeds

tag: time

value: 30 DAA


title: Seeds, 30 DAA, rep 1


title: Leaf 5, 37 days, rep 1

source_name: leaf

value: leaf

value: 37 days


title: Leaf 3, 10 days, rep 3

value: 10 days


title: Leaf 5, 37 days, rep 2


title: Seeds, 20 DAA, rep 1

value: 20 DAA


title: Apical meristem, 37 days, rep 2

source_name: apical meristem

value: apical meristem


title: Apical meristem, 37 days, rep 3


title: Leaf 3, 10 days, rep 1


title: NMR, Heart, H3K4me1, NMR30,  do17606

value: Heart

value: wild-type

value: adult

value: male


title: NMR, Heart, input, NMR30,  do17612


title: Seeds, 20 DAA, rep 2


title: 2-weeks-R5 (biological replicate 3)

description: D14; released from DOXY-palbo 14 days

tag: cell type

value: dedifferentiated liposarcoma


title: Leaf 3, 10 days, rep 2


title: Apical meristem, 37 days, rep 1


title: Apical meristem, 30 days, rep 3

value: 30 days


title: NMR, Heart, H3K27ac, NMR35,  do17590


title: NMR, Heart, H3K4me3, NMR35,  do17589


title: Apical meristem, 30 days, rep 2


title: NMR, Liver, H3K27ac, NMR34,  do17587

value: Liver


title: Seeds, 20 DAA, rep 3


title: NMR, Liver, input, NMR34,  do17596

value: input


title: NMR, Liver, H3K4me1, NMR34,  do17588


title: Seeds, 10 DAA, rep 3

value: 10 DAA


title: NMR, Liver, H3K4me3, NMR34,  do17586


title: Apical meristem, 20 days, rep 2

value: Taper

value: 20 days


title: Apical meristem, 20 days, rep 1


title: Apical meristem, 20 days, rep 3


title: NMR, Heart, input, NMR35,  do17597


title: Seeds, 10 DAA, rep 2

value: seeds


title: NMR, Liver, input, NMR35,  do16811


title: NMR, Liver, input, NMR32,  do16810


title: Seeds, 30 DAA, rep 3

value: 30 DAA


title: NMR, Liver, H3K27ac, NMR35,  do16802


title: NMR, Liver, H3K4me3, NMR35,  do16801


title: Vector-WGS-75d-2

city: Beijing

first: Yongjie

last: Liu

address: No. 1 West Beichen Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology

description: Vector.cnv.75d.xls, Vector.indel.75d.vcf.gz, Vector.snp.75d.vcf.gz, Vector.sv.75d.xls

data_processing:
(1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 50%; (3) Removing reads whose unknown base ('N' base) ratio is more than 10%.
All clean reads were aligned to the human reference genome (GRCh38/hg38) using Burrows-Wheeler Aligner (BWA V0.7.12).
PCR duplicates reads were removed using Picard
Local realignment around InDels and Base Quality Score Recalibration
SNP and InDel calling, Variant filtering,Copy number variant calling and Structural variant calling.
Assembly: hg38/Grhc38
Library strategy: DNA-seq

source_name: MCF-10A cell line

growth_protocol: MCF-10A cells were maintained in F-12 supplemented with 10% horse serum, insulin, cholera toxin, EGF and hydrocortisone in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
Harvest MCF-10A cells were grown with indicated treatments and count the cells. Cells should be intact and in a homogenous, single-cell suspension. Genomic DNAs were extracted and subjected to whole genome sequencing.
WGS libraries were prepared using WGS protocol. The qualified genomic DNA sample was randomly fragmented by Covaris technology and the fragment of 350bp was obtained after fragment selection. The end repair of DNA fragments was performed and an "A" base was added at the 3'-end of each strand. Adapters were then ligated to both ends of the end repaired/dA tailed DNA fragments, then amplification by ligation-mediated PCR (LM- PCR ), then single strand separation and cyclization. The rolling circle amplification (RCA) was performed to produce DNA Nanoballs (DNBs). The qualified DNBs were loaded into the patterned nanoarrays and pair-end read were read through on the BGISEQ-500 platform and high-throughput sequencing are performed for each library to ensure that each sample meet the average sequencing coverage requirement. Sequencing-derived raw image files were processed by BGISEQ-500 basecalling Software for base-calling with default parameters and the sequence data of each individual is generated as paired-end reads, which is defined as "raw data" and stored in FASTQ format.

treatment_protocol: MCF-10A clones stably overexpressing NFIB via lentivirally delivered NFIB expression vector. These clones were further cultured 30 or 75 days and NFIB overexpression MCF-10A cells under the treatment of oxaliplatin or 5-fluoracil at 75 days. Cells were collected for next library construction.


title: NMR, Liver, H3K4me1, NMR32,  do16800


title: NMR, Liver, H3K4me1, NMR35,  do16803


title: NMR, Liver, H3K27ac, NMR32,  do16799


title: NMR, Liver, H3K4me3, NMR32,  do16798


title: Apical meristem, 30 days, rep 1


title: Vector-WGS-30d-5

description: Vector.cnv.30d.xls, Vector.indel.30d.vcf.gz, Vector.snp.30d.vcf.gz, Vector.sv.30d.xls


title: Vector-WGS-30d-6


title: Vector-WGS-30d-4


title: Vector-WGS-30d-2


title: MEF, DMSO, Pidd-KO, rep3

city: San Juan de Alicante

first: Sergio

last: Niñerola

state: Alicante

address: Avenida Santiago Ramon y Cajal, s/n

department: Molecular Neurobiology and Neuropathology

country: Spain

institute: CSIC-Instituto de Neurociencias de Alicante

data_processing:
Adapters were trimmed using trim_galore (v 0.6.4_dev). Alignment was done with STAR (v 2.6.1) to mouse genome (mm10). Aligned files were processed using samtools (v 1.9) and bedtools  (v 2.25.0) and only reads with mapq > 30 were considered for further analysis. Counts were quantified to exons using Rsubread (v 2.0.1) and Mus_musculus.GRCm38.99.gtf from Ensembl.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files contains raw data for each samples

source_name: Primary mouse embryonic fibroblast

growth_protocol: Primary MEF were obtained from 13.5 embryos by tryptic digestion. Cells were cultured in DMEM  containing  10%  FCS,  1%  L-glutamine  and  100  U/mL  penicillin and 100 μg/mL streptomycin (P/S).

extract_protocol: Total RNA from cultured primary MEF was extracted using RNAeasy Mini Kit (Quiagen) as per the manufacturer ́s instructions. DNA was removed by on-column digestion using the RNAse-Free DNAse Set (Quiagen, 79254) and RNA concentration was determined with a NanoDrop. High quality RNA was used for downstream application. mRNA-sequencing libraries were prepared using 200 ng of total RNA using NEBNext Ultra II Directional RNA library prep kit with UMI Adaptors. The libraries were pooled equimolarly and sequenced on 2 lanes of Hiseq 3000/4000 with the following configuration: 51+19+8 (single read).

treatment_protocol: ZM447439 (2 μM; Selleck Chemicals, S1103) or DMSO for 72 h

value: Primary mouse embryonic fibroblast

value: DMSO


title: Vector-WGS-30d-3


title: MEF, ZM, Pidd-KO, rep2

value: ZM


title: Oxaliplatin-WGS-2

description: Oxaliplatin.cnv.75d.xls, Oxaliplatin.indel.75d.vcf.gz, Oxaliplatin.snp.75d.vcf.gz, Oxaliplatin.sv.75d.xls


title: Vector-WGS-30d-1


title: MEF, DMSO, Pidd-KO, rep2


title: MEF, ZM, Pidd-KO, rep1


title: MEF, ZM, Pidd-KO, rep3


title: MEF, DMSO, Pidd-KO, rep1


title: Oxaliplatin-WGS-1


title: MEF, ZM, WT, rep3

value: WT


title: NFIB-WGS-75d-2

description: NFIB.cnv.75d.xls, NFIB.indel.75d.vcf.gz, NFIB.snp.75d.vcf.gz, NFIB.sv.75d.xls


title: MEF, ZM, WT, rep2


title: Vector-WGS-75d-1


title: Seeds, 10 DAA, rep 1


title: NFIB-WGS-75d-1


title: MEF, DMSO, WT, rep2


title: NFIB-WGS-30d-3

description: NFIB.cnv.30d.xls, NFIB.indel.30d.vcf.gz, NFIB.snp.30d.vcf.gz, NFIB.sv.30d.xls


title: NFIB-WGS-30d-1


title: MEF, DMSO, WT, rep3


title: NFIB-WGS-30d-2


title: 5-fluoracil-WGS-2

description: Fluorouracil.cnv.75d.xls, Fluorouracil.indel.75d.vcf.gz, Fluorouracil.snp.75d.vcf.gz, Fluorouracil.sv.75d.xls


title: MEF, DMSO, WT, rep1


title: GuineaPig, Heart, H3K4me3, GuineaPig9,  vl0066

organism: Cavia porcellus

value: Heart


title: 5-fluoracil-WGS-1


title: GuineaPig, Heart, input, GuineaPig9,  vl0009

value: wild-type


title: GuineaPig, Heart, H3K27ac, GuineaPig9,  vl0007

value: adult


title: NMR, Heart, input, NMR31,  vl0068

value: male


title: NMR, Liver, input, NMR30,  vl0070


title: GuineaPig, Heart, H3K4me1, GuineaPig9,  vl0008


title: MEF, ZM, WT, rep1


title: NMR, Liver, H3K4me1, NMR30,  vl0064


title: NFIB-WGS-30d-4


title: NMR, Heart, H3K4me3, NMR34,  vl0065


title: NMR, Liver, H3K27ac, NMR30,  vl0063


title: NMR, Liver, H3K4me3, NMR30,  vl0062


title: NMR, Liver, input, NMR31,  vl0057


title: Xag24h-1

city: Jinju

first: Seon-In

last: Yeom

address: 501, Jinjou-daero

country: South Korea

institute: Gyeongsang National University

data_processing:
A quality control application for high throughput sequence data using FastQC Version 0.11.8
Removes adapter sequences from DNA high-throughput sequencing data using Cutadapt  Version 1.15
A toolkit for the quality control (QC) of next generation sequencing (NGS) data using Trimmomatic Version 0.38
Alignment program for mapping next-generation sequencing reads to Capsicum annuum genome using Hisat2 Version 2-2.1.0
Assembly: Capsicum annuum v1.6
Supplementary files format and content: tab-delimited text files include the values of read count for each sample

organism: Capsicum annuum

source_name: Leaves

extract_protocol:
Three biological replicates at each time point per condition were collected. The leaf samples were flash-frozen in liquid nitrogen and stored at ˗80°C until RNA isolation. Total RNA was extracted from pepper leaf samples (100 mg) using the Trizol reagent. Five micrograms of each RNA sample were used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using strand-specfic RNA-seq Illumina protocols

value: Leaves

tag: timepoint


title: Xag12h-3


title: Xag12h-1


title: Xag12h-2


title: Xag24h-2


title: genomic DNA from brain 6 [205982890108_R02C01]

type: genomic

city: Erlangen

first: Katja

last: Kobow

state: Bavaria

address: Schwabachanlage 6

department: Neuropathology

institute: Universitätsklinikum Erlangen

hyb_protocol: Arrays were imaged using iscan Reader using standard recommended Illumina scanner setting

scan_protocol: Differential DNA methylation analysis was performed with a self-customized Python wrapped cross R package pipeline, utilizing 'Champ,' 'watermelon,' 'DNAMarray,' and 'minfi' as R packages. 'MethQC' and 'Pymethylarray' were used as Python-based array analysis packages. Additional own implementations of lacking functionality were used where needed. All these packages were wrapped by using 'rpy2', an interface to R running embedded in a Python process.

data_processing:
Data was stratified quantile normalized using the ‘minfi‘ ‘preprocessQuantile‘ function
The M-value is calculated as the log2 ratio of the intensities of methylated probe versus unmethylated probe (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-587)
We have utilized our inhouse python pipeline (https://github.com/FAU-DLM/Methylr2py ) including adaptations from 'DNAmArray' pipeline for the probe filtering and imputation. Further most significantly differentially methylated CpGs between each entities/sample group were identified by fitting a regression model using the 'limma'.   The unique most significantly differentially methylated CpGs (adj. p value   <   0.01) within the subgroups are included (total 55374 ID_REFs out of a possible 868564).

label: Cy5 and Cy3

source_name: Cortex

label_protocol: Following FFPE restoration bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation 850K Beadchip using standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from fresh frozen tissue using Qiagen Blood and Tissue DNA Kit according to standard instructions

value: Control - NCx

value: autoptic normal brain and no epilepsy


title: NMR, Heart, input, NMR32,  vl0051

value: input


title: genomic DNA from brain 1 [205982890094_R05C01]


title: genomic DNA from brain 3 [205982890094_R07C01]


title: genomic DNA from brain 7 [205982890108_R03C01]


title: Xag6h-3


title: MCF7 Vector

city: Guangzhou

first: Yu

last: Zhou

state: Guangdong

address: No 58, Zhongshan 2nd street

department: Division of Vascular Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

description: Gene expression in MCF7 stablly transfected with vector plasmid

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression   Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in   Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US),   according to the manufacturer’s instructions. After 17 hours hybridization, slides   were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent   technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan  resolution=3μm, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

source_name: MCF7, Vector

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit,   One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit  (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Control or IL-8 overexpressed MCF7 cells were cultured in DMEM culture medium (Gibco, USA) containing 10% fetal bovine serum (Gibco, USA). All cells were captured in the atmosphere containing 5% CO2 and 37°C.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)


title: genomic DNA from brain 2 [205982890094_R06C01]


title: genomic DNA from brain 5 [205982890108_R01C01]


title: Xag6h-2


title: NMR, Heart, H3K27ac, NMR32,  vl0046


title: genomic DNA from brain 4 [205982890094_R08C01]


title: Xag6h-1


title: NMR, Heart, H3K4me3, NMR32,  vl0045


title: MCF7 IL-8

description: Gene expression in MCF7 stablly transfected with IL-8 plasmid

source_name: MCF7,  IL-8


title: Xag3h-3


title: NMR, Liver, H3K4me1, NMR31,  vl0044

value: Liver


title: Xag3h-1


title: NMR, Heart, H3K4me1, NMR31,  vl0006


title: Xag3h-2


title: NMR, Heart, H3K4me1, NMR32,  vl0054


title: NMR, Liver, H3K27ac, NMR31,  vl0043


title: NMR, Liver, H3K4me3, NMR31,  vl0042


title: Xag1h-3


title: Xag1h-2


title: Xag8ra_Mock_24h-3


title: Xag1h-1


title: Xag8ra_Mock_24h-2


title: chm_3_Starved

city: Berlin

first: Anuroop

middle: Venkateswaran

last: Venkatasubramani

state: Berlin

address: Robert-Rössle-Straße 10

institute: MDC-Berlin

data_processing:
A total of 50 bp paired-end reads were aligned to the D. melanogaster reference genome (release 6) using STAR aligner (version 2.5.3a) with providing GTF annotation (dmel-all-r6.17.gtf). Reads with multiple alignments were filtered by setting outFilterMultimapNmax parameter to 1. Reads were counted per gene with parameter –quantMode GeneCounts. BAM files were converted to normalized bedgraph coverages using genomeCoverageBed command (bedtools version 2.27.1) with -scale parameter set to divide by the total number of reads and multiplied by a million. Bedgraph files were converted to tdf files (igvtools version 2.3.98) to visualize in the IGV browser.
Count tables (read counts per gene) were read into R environment and low count genes were filtered out (at least 3 read per gene in 10% of the samples analyzed together). Differential expression analysis was performed by DESeq2 package (version 1.24) by adding replicate information as batch variable. Samples that were directly compared to each other were fitted in the same DESeq2 model.
Assembly: dmel-all-r6.17.gtf
Supplementary files format and content: Tab-separated text file: read counts per gene

organism: Drosophila melanogaster

source_name: head

growth_protocol: Fly lines were maintained in a incubator (Panasonic, MLR-235H-PE) at 25°C with a 12 hr/12 hr light-dark cycle at 60% relative humidity.

extract_protocol:
30 heads were homogenized with an electrical stirrer with 500 μl of Trizol (Thermo Fisher; cat. no. 15596026). Chloroform was added at the ratio of 1:5 with Trizol and the solutions were mixed for 15 s by inverting the eppendorfs. After 5 min incubation at room temperature, samples were centrifuged at 12,000 x g for 15 min. Aqueous phase was transferred to a new eppendorf from the centrifuged sample, to which isopropanol was added at 1:1 ratio of the obtained aqueous phase, vortexed briefly and incubated for 10 min at room temperature. They were then centrifuged for 10 min at 12,000 x g. Supernatant was discarded and obtained pellet was washed with 750 μl of 80% ethanol. After brief vortexing, samples were centrifuged at 8,000 x g for 5 min. Obtained supernatant was discarded and pellet was air dried for 5 min inside the hood and resuspended in RNase-free water
1 ug of RNA, obtained from fly heads was used for library preparation. Both total and mRNA quality was assessed on a 2100 Bioanalyzer (Agilent Technologies, Cat. No G2939BA) using RNA pico assay kit (Agilent RNA 6000 Pico Kit, cat. No: 5067-1513) using manufacturer’s protocol. rRNA depletion was performed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB #E6310) and library preparation for RNA-sequencing was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) following manufacturer’s protocol.

treatment_protocol: As age, sex, temperature, light-dark cycle and humidity could affect starvation response and resistance, we kept all these constant by using only male flies of age 8-9 days old at 23°C with 60% relative humidity and 12 hr light/12 hr dark cycle (unless stated otherwise). Approx. 50-60 flies were transferred to an empty fly bottle containing a tissue with 4 ml of tap water. Total number of flies for each experiment ranged from 150-250 flies for each genotype/condition tested

value: head

value: chm MYST mutant

value: Starved

value: 24 hr


title: Xag8ra_Mock_24h-1


title: wt_3_Starved

value: control


title: wt_4_Starved


title: NMR, Heart, H3K4me3, NMR31,  vl0004


title: NMR, Heart, H3K27ac, NMR31,  vl0005


title: Xag8ra_Mock_12h-3


title: chm_5_Starved


title: Xag8ra_Mock_12h-2


title: chm_4_Starved


title: Xag8ra_Mock_6h-1


title: wt_1_Starved


title: chm_1_Starved


title: chm_2_Starved


title: Xag8ra_Mock_3h-3


title: Xag8ra_Mock_12h-1


title: wt_5_Fed

value: Fed

value: 0 hr


title: Xag8ra_Mock_6h-2

value: WT


title: wt_5_Starved


title: preop_P69

city: Minneapolis

first: Charles

middle: Scott

last: Cameron

state: Minnesota

address: 420 Delaware St SE

department: Pediatrics

institute: University of Minnesota-Twin Cities,

description:
Extracellular vesicle  total RNA
hiseq_counts

data_processing:
Reads from the 128 samples that underwent total RNA sequencing were processed using the CHURP pipeline. Briefly, read quality was assessed with fastqc, and reads were trimmed using trimmomatic (v.33) to remove the first 3 base pairs of R2 (as these are from the SMART-seq Stranded adapter), adapters and low quality bases. Reads were aligned to hg38 using hisat2 and assigned to genes in Ensembl GrCh38 release 100 using Rsubread.
Assembly: HG38
Supplementary files format and content: text file containing count table

source_name: Serum Sample

extract_protocol:
RNA was harvested using ExoRNeasy Serum/Plasma Midi Kit (QIAGEN, Cat. No. 77144). 2.5 ng of total RNA was used for the construction of sequencing libraries.
SMART-Seq Stranded Kit (Cat. No. 634444) was used to generate cDNA libraries.

value: Serum Sample

tag: disease

value: Glioblastoma


title: Xag8ra_Mock_3h-1


title: preop_P70


title: preop_P68


title: preop_P66


title: preop_P65


title: Xag8ra_Mock_1h-3


title: preop_P67


title: preop_P64


title: preop_P63


title: preop_P62


title: preop_P61


title: wt_2_Starved


title: Xag8ra_Mock_3h-2


title: preop_P58


title: preop_P52


title: preop_P59


title: Xag8ra_Mock_1h-2


title: preop_P55


title: Xag8ra_Mock_1h-1


title: preop_P54


title: Bukang0-3


title: Bukang0-1


title: preop_P49


title: preop_P50


title: preop_P48


title: preop_P47


title: preop_P60


title: preop_P46


title: wt_2_Fed


title: chm_2_Fed


title: preop_P45


title: wt_3_Fed


title: wt_4_Fed


title: chm_3_Fed


title: chm_5_Fed


title: chm_4_Fed


title: F_Rep4 RNA-seq

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

state: CA

address: Campus Dr

department: CS

institute: UC Irvine

data_processing:
Alignment to reference assembly mm10 using Tophat from Tuxedo pipeline
Transcript assembly and abundance estimates using Cufflings from the Tuexdo pipeline
Periodicity determined using BIOCYCLE
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: occipital cortex

extract_protocol:
The occupital cortex was harvested immediately after the sacrifice, and flash in liquid nitrogen.  RNA was extracted using Phenol/guanidine-based QIAzol Lysis Reagent (Qiagen #79306)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: mice were subjected to 48 hours fasting or fed ad libitum

value: Cortex homogenate

tag: strain

value: 48 hours fasting

tag: age


title: preop_P51


title: F_Rep3 RNA-seq


title: F_Rep1 RNA-seq


title: wt_1_Fed


title: F_Rep2 RNA-seq


title: Al_Rep4 RNA-seq

value: Ad libitum feeding


title: chm_1_Fed


title: preop_P35


title: preop_P41


title: Al_Rep1 RNA-seq


title: preop_P44


title: preop_P37


title: preop_P39


title: Al_Rep3 RNA-seq


title: preop_P38


title: Al_Rep2 RNA-seq


title: preop_P43


title: preop_P36


title: preop_P34


title: Fasting4 K9BOHB ChIP

data_processing:
Alignment to reference assembly mm10 using Bowtie2 from Tuxedo pipeline
Differential peak calling using MACS2 for F VS AL experiment comparison
Peak annotation for enriched peak signals using in-house software
Genome_build: mm10
Supplementary_files_format_and_content: csv, enriched peak signals

extract_protocol:
The occipital cortex was harvested and snap frozen in liquid nitrogen. Cortical lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with a specific antibody against H3K9-bhb
Libraries were prepared for sequencing using standard Illumina protocols


title: preop_P32


title: Fasting3 K9BOHB ChIP


title: preop_P33


title: preop_P31


title: OSKM-shDdx10-D7-rep2

city: guangzhou

first: gongcheng

last: Hu

state: guangdong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

data_processing:
Raw reads were firstly trimmed adaptors and low quality reads using Trim Galore (v0.4.4), and then mapped to mouse mm10 genome using STAR (v2.5.2a).
Gene expression levels were quantified as read counts generated by RSEM (v1.2.22) with default settings. Raw tag counts were normalized using DESeq2 (v1.22.0).
Genome_build: mm10
Supplementary_files_format_and_content: .tsv file generated from normalized RNAseq data.

source_name: Reprogramming cells,knock down Ddx10

growth_protocol: The reprogramming cells were cultured with iCD1 medium.

extract_protocol:
Total RNA was extracted from cells by lysing with TRIzol.
The RNA samples were subject to library preparation using Vazyme mRNA-seq V3 Library Prep Kit for Illumina. The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

treatment_protocol: 10,000 MEFs at passage 2 were plated in a 12-well plate and then infected twice with retroviral stocks generated with Plat-E cells. 3 volumes of the supernatants of the transfected Plat-E cells were mixed with 1 volume of fresh MEF medium containing polybrene at a final concentration of 8 μg/mL. For infecting OG2 MEFs, the medium of OG2 MEFs was replaced with 2 mL of infection mixture per well in a 12-well plate. Infected cells were cultured with iCD1 medium post infection and renewed daily.

value: Reprogramming cells

value: knock down Ddx10

value: day of reprogramming D7


title: Fasting2 K9BOHB ChIP


title: OSKM-shDdx10-D7-rep1


title: preop_P30


title: preop_P29


title: preop_P28


title: Fasting1 K9BOHB ChIP


title: preop_P27


title: OSKM-shDdx10-D5-rep2

value: day of reprogramming D5


title: preop_P26


title: AL4 K9BOHB ChIP


title: preop_P25


title: preop_P24


title: OSKM-shDdx10-D5-rep1


title: preop_P22


title: AL3 K9BOHB ChIP


title: OSKM-shDdx10-D3-rep2

value: day of reprogramming D3


title: OSKM-shDdx10-D3-rep1


title: AL2 K9BOHB ChIP


title: preop_P20


title: Small RNA of Isoetes sinensis

first: Yunke

last: Zhu

address: Zhongguancun South Street

institute: Chinese Academy of Agricultural Sciences

description: Pooling sample by root,shoot and sporophyte

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Assembly: De nove assemblied in this study
Supplementary files format and content: tab-delimited text files include readcount values for each sample.

organism: Isoetes sinensis

source_name: Isoetes sinensis root,shoot and sporophyte pooling sample

growth_protocol: I. sinensis plant materials were harvested from Yangdongcun, Beilun district, Ningbo, Zhejiang provience, China.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies).
After qualified samples were detected, Small RNA Sample Pre Kit was used to construct the library.  Added adapter to both ends of Small RNA, and then synthesized cDNA  by reverse transcription.

treatment_protocol: Samples were collected from different tissues

value: pool (root, shoot, sporophyte)


title: AL1 K9BOHB ChIP


title: Sporophyte RNA-seq

description: Isoetes sinensis sporophyte sample

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Clean reads were mapped to I.sinensis genome using Hisat2 v2.1.051. Gene expression levels (FPKM) were calculated using Cufflinks with default parameters.
Assembly: De nove assemblied in this study
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: Isoetes sinensis sporophyte sample

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies).
rRNA was removed from total RNA samples using the RiBO-Zero ™ Kit. Fragmentation buffer was added to the enriched RNA to break the RNA into small fragments. Then, the fragment RNA was used as template, and 6bp random hexamers were added to reverse transcription to synthesize the first cDNA strand. The second strand of cDNA is synthesized by adding buffer, dNTPs , DNA polymerase I and RNase H. After purification, terminal repair, addition of A, and sequencing joint treatment, the synthesized double-strand cDNA was degraded with USER enzyme and enriched by PCR. Finally, PCR products were purified with AMPure XP Beads to obtain the final chain specific libraries. After the library construction was completed, Qubit 2.0 was used for preliminary quantification and dilution of the library, and Agilent 2100 was used to detect the size of inserted fragments of the library. After the inserted fragments met the expectations, qPCR was used to accurately quantify the effective concentration of the library to ensure the quality of the library.

treatment_protocol: Samples were collected from root,shoot and sporophyte of I. sinensis, respectively

value: sporophyte


title: preop_P19


title: OSKM-shDdx10-D1-rep2

value: day of reprogramming D1


title: OSKM-shDdx10-D1-rep1


title: Shoot RNA-seq

description: Isoetes sinensis shoot sample

source_name: Isoetes sinensis shoot sample

value: shoot


title: Fasting4 INPUT DNA


title: preop_P18


title: Fasting3 INPUT DNA


title: OSKM-shDdx10-D0-rep2

value: day of reprogramming D0


title: Fasting2 INPUT DNA


title: preop_P15


title: Root RNA-seq

description: Isoetes sinensis root sample

source_name: Isoetes sinensis root sample

value: root


title: Fasting1 INPUT DNA


title: preop_P13


title: lncRNA of Isoetes sinensis

description: Pooling sample of root,shoot and sporophyte

data_processing:
After removing the adapter and primer sequences, low quality reads with more than 20% low quality bases (quality < 20) were filtered out using FastQC packages (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Clean reads were mapped to I.sinensis genome using Hisat2 v2.1.051. Gene expression levels (FPKM) were calculated using Cufflinks with default parameters.
Assembly: De novo assemblied in this study
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies).
rRNA was removed from total RNA samples using the RiBO-Zero ™ Kit. Fragmentation buffer was added to the enriched RNA to break the RNA into small fragments. Then, the fragment RNA was used as template, and 6bp random hexamers were added to reverse transcription to synthesize the first cDNA strand. The second strand of cDNA is synthesized by adding buffer, dNTPs (dTTP in dNTP is replaced by dUTP), DNA polymerase I and RNase H. After purification, terminal repair, addition of A, and sequencing joint treatment, the synthesized double-strand cDNA was degraded with USER enzyme and enriched by PCR. Finally, PCR products were purified with AMPure XP Beads to obtain the final chain specific libraries.

treatment_protocol: Samples were collected from root,shoot and sporophyte of I. sinensis


title: Full length transcriptome of Isoetes sinensis [Iso-seq]

data_processing:
Raw SMRT sequencing reads were processed by removing polymerase reads that were <50 bp and had quality of <0.75, obtaining the clean reads. The non-chimeric sequences in the full-length sequence are called full-length non-chimeric (FLNC) sequences,which is used to assist genome annotation.
Assembly: De novo assemblied in this study

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Life Technologies).
For the PacBio Sequel analysis, the libraries for SMRT genome sequencing were prepared according to the manufacturer’s protocol for the sequencing platform, then sequenced on PacBio Sequel II with single-molecule real-time sequencing.


title: OSKM-shDdx10-D0-rep1


title: preop_P21


title: OSKM-shLuci-D7-rep2

source_name: Reprogramming cells,knock down Ctrl

value: knock down Ctrl


title: GuineaPig, Liver, H3K27ac, GuineaPig9,  do3046

data_processing:
ChIP-seq peak files were generated my MACS2 callPeak function (default parameters).
4C data was processed with pipe4C (Krijger et al. 2020)
Supplementary files format and content: MACS2 peak files for each ChIP and input combination (.narrowPeak extension)
Supplementary files format and content: 4C wig files for each 4C experiment

source_name: Liver

extract_protocol:
Tissues were prepared by direct perfusion of the liver with PBS, followed by dicing the whole organs (liver and heart) in small pieces around 1cm3. Blood clots within the heart ventricles were removed. Cross-linking of the diced tissue was performed in 1% formaldehyde solution for 20 min, addition of 250 mM glycine and incubation for a further 10 min to neutralize the formaldehyde. After homogenization of cross-linked tissues in a dounce tissue grinder, samples were washed twice with PBS and lysed according to published protocols (SCHMIDT et al. 2009 for ChIP and Krijger et al. 2020 for 4C) to solubilize DNA-protein complexes. For ChIP, chromatin was fragmented to 300 bp average size by sonication on a Misonix sonicator 3000 with a 418 tip (1/16 inch diameter). Chromatin from 50-200 mg of dounced tissue was used for each ChIP experiment using antibodies against H3K4me3 (millipore 05-1339), H3K27ac (abcam ab4729), H3K4me1 (abcam ab8895), TBX5 (Insight bio sc-515536), RXRA (sc-553), FOXA1 (ab70382), HNF4A (ARP31946), CEBPA (sc-9314) and HNF6 (sc-13050). For 4C, locus-specific 4C templates were made using two rounds of enzyme digestion (primary and secondary) and ligation. Purified 4C templates were amplified by inverse PCR with bait-specific primers.
Illumina sequencing libraries were prepared from ChIP-enriched or 4C-enriched DNA using ThruPLEX DNA-seq library preparation kit (Takara Bio) or NEBNext Ultra II DNA Library Prep Kit for Illumina with up to 10ng of input DNA and 8-15 PCR cycles. After PCR, libraries were pooled in equimolar concentrations and sequenced on Illumina HiSeq 4000, NextSeq 500 or NovaSeq 6000 instruments.
ChIP-Seq, 4C-Seq

value: Liver

value: wild-type

value: adult

value: male


title: AL4 INPUT DNA

value: Cortex homogenate

value: Ad libitum feeding


title: OSKM-shLuci-D7-rep1

value: Reprogramming cells


title: preop_P11

value: Serum Sample

value: Glioblastoma


title: AL3 INPUT DNA


title: preop_P12


title: GuineaPig, Liver, H3K27ac, GuineaPig8,  do3045


title: preop_P9


title: AL2 INPUT DNA


title: preop_P10


title: AL1 INPUT DNA


title: OSKM-shLuci-D3-rep2

value: day of reprogramming D3


title: OSKM-shLuci-D5-rep2

value: day of reprogramming D5


title: preop_P8


title: OSKM-shLuci-D1-rep2


title: preop_P6


title: GuineaPig, Liver, H3K4me1, GuineaPig7,  do3023


title: OSKM-shLuci-D3-rep1


title: preop_P5


title: GuineaPig, Liver, input, GuineaPig8,  do2432

value: input


title: OSKM-shLuci-D1-rep1

value: day of reprogramming D1