title: TGFbeta-I


title: SC146_YUMMER_Exer_8

status: Public on Jul 01 2023

type: SRA

city: Houston

first: Keri

last: Schadler

state: TX

address: 1515 Holcombe Blvd

country: USA

institute: MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We demultiplexed the single cell transcriptome files into FASTQ and aligned them to the mouse genome (mm10) using 10X Genomics Cell Ranger v.6.1.2.
Supplementary files format and content: mm10

molecule: total RNA

organism: Mus musculus

source_name: Melanoma tumor

growth_protocol: Prior to mouse injection, YUMMER1.7 cells were maintained in: DMEM/F12 media containing 10% FBS, 1X PSA, 1X Non-essential amino acids

extract_protocol:
Melanoma tumors were harvested and place in cold 8%FBS-HBSS until processed within two hours of harvest. Tumors were minced into small pieces and digested for 15 minutes at 37 degrees in 1mg/mL Collagenase H and 200ug/mL DNase in RPMI media. Digests were pushed through 100um strainer and RBCs were lysed. Cell viability was measured (all samples were >70%) and cells were resuspended for scRNA-seq subsequent processing.
Single cell libraries were captured and barcoded using the 10X Genomics Single Cell Chromium 3’ V3 chemistry reagents kit (10x Genomics, 1000121) according to the manufacturer’s protocol.

tag: tissue

value: Melanoma tumor

tag: cell line

tag: cell type

value: whole tumor dissociation

tag: strain

tag: age

value: 6-8 weeks

tag: Sex

value: male

tag: treatment

value: Exercise


title: SC146_YUMMER_Exer_5

description: 10x Genomics


title: JK2-78-16 RNA-Seq for CRC organoids

city: Madison

first: Dustin

last: Deming

state: WI

address: 1111 Highland Ave., WIMR II, Rm. 6507

department: Hematology-Oncology

institute: University of Wisconsin

library_source: transcriptomic

data_processing:
Adapter-trimmed (Skewer v0.1.123; Jiang et al., 2014)
Aligned using Spliced Transcripts Alignment to a Reference (STAR v2.5.3a) software (Dobin, et al., 2013) using ensembl annotation
Expression estimation using RSEM v1.2.31 (RNASeq by Expectation Maximization; Li and Dewey, 2011)
Genome_build: Mus musculusGRCm38.p5 (assembly accession GCA_00001635.7)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Colorectal Cancer Organotypic culture

growth_protocol: PCO suspensions were immediately mixed at a 1:1 ratio with Matrigel matrix (Corning).Droplet suspensions were plated and set for three to five minutes at37°C then least 30 minutes to solidify the matrix andavoid direct interface of PCOs with plastic interface. Plated cultures were overlaid with 450uL of feeding medium of 1:1 advanced DMEM/F12 with 1x Glutamax, 10mM HEPES and 100 U/ml pen/strep combined with WNT3a conditioned media and supplemented with EGF 50ng/ml. Plates were incubated at 37°C in 5% CO2 and medium was replaced every 48-72 hours.

extract_protocol:
Organoids were collected from ~4-6 wells, and washed in 1x sterile PBS, and stored at -80°C as a cell pellet until both DNA and RNA isolation. All RNA samples were collected fromin triplicate biological replicates at baseline and resistance to EGFRi with persistent growth at 100% physiologic Cmax.
An RNA library was constructed using TruSeq Stranded total RNA with rRNA reduction (Illumina). Quality control was performed by Eukaryote Total RNA electrophoresis using NanoDropOne. The library included 2x150bp paired end reads with sequencing was performed by NovaSeq 6000 using MiSeq NanoCell at UW Biotechnology Center.

treatment_protocol: Following maturation, PCOs were treated with stepwise dose escalation.  Cultures were started at 20% physiologic Cmax panitumumab (46ug/ml) and assessed for growth (normalized change in diameter at 96hours). If cultures surpassed ≥20% growth, stepwise dose escalation was repeated with interval increase of 20% Cmax. Time to resistant (TTR) was defined by duration of time from the initiation of dose escalation to persistent growth at 100% Cmax panitumumab (230ug/ml).

value: Panitumumab 230ug/mL

tag: sample type

value: Panitumumab Resistant


title: JK2-78-17 RNA-Seq for CRC organoids


title: SC146_YUMMER_Sed_3

description: 10x Genomics

value: Sedentary


title: CTRL-II

city: Zurich

first: Tomas

last: Valenta

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
The nf-core/rnaseq bioinformatics pipeline version 3.5 [doi: https://doi.org/10.1101/610741] was used for subsequent read processing. Individual steps included removal of sequencing adapters and low-quality reads with Trim Galore! (www.bioinformatics.babraham.ac.uk/projects/trim_galore) and quantification of gene expression with Salmon [doi: https://doi.org/10.1038/nmeth.4197] using GRCm39 reference [doi: https://doi.org/10.1093/nar/gkaa1077]. Estimated expression per gene served as input for differential expression analysis using the DESeq2 R Bioconductor package [doi: https://doi.org/10.1186/s13059-014-0550-8]. Genes exhibiting a minimum absolute log2 fold change of 1 (|log2| FC ≥ 1) and statistical significance (adjusted p-value < 0.05) between the compared sample groups were considered differentially expressed.
Assembly: GRCm39 reference
Supplementary files format and content: BMPs_normcounts.csv: ;-delimited file containing normalized gene expression for each sample
Supplementary files format and content: TGFb_normcounts.csv: ;-delimited file containing normalized gene expression for each sample
Supplementary files format and content: MCs_normcounts.csv: ;-delimited file containing normalized gene expression for each sample

source_name: Small intestinal epithlelium

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen 74004), DNAseI treatment was included
Sequencing libraries were prepared from total RNA using the KAPA mRNA Hyperprep Kit, , followed by size distribution analysis in the Agilent 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent)

value: Small intestinal epithlelium

value: Small intestinal organoids

value: Epithelilal cells

tag: genotype

value: Untreated (control)


title: JK2-78-15 RNA-Seq for CRC organoids

value: Base culture


title: BMP7VI

value: recombinant Bmp7, 500 ng/ml, 24 h


title: JK2-78-25 RNA-Seq for CRC organoids


title: SC146_YUMMER_Sed_2

description: 10x Genomics


title: JK2-78-14 RNA-Seq for CRC organoids


title: CTRL-III


title: BMP7III


title: SC146_YUMMER_Sed_1

description: 10x Genomics


title: JK2-78-13 RNA-Seq for CRC organoids


title: siMCs-HIGH

source_name: Small intestinal mesenchyme

value: Small intestinal mesenchyme

value: Pdgfra positive mesenchymal cells

value: Mesenchymal cells

value: Immortalisation and sort


title: JK2-78-24 RNA-Seq for CRC organoids


title: BMP7II


title: Total, B1, VDJ, rep2

city: New Haven

first: Yexin

last: Yang

state: CT

address: 300 Cedar St., The Anlyan Center

department: Department of Immunobiology

institute: Yale School of Medicine

description: 10x Genomics

data_processing:
Libraries were sequenced on the NovaSeq 6000 Sequencing System (Illumina). Single-cell V(D)J libraries were sequenced with 2 × 150 bp paired-end reads and single-cell gene expression libraries were sequenced with 2 × 100 bp paired-end reads. Details for the sequencing matrix are listed in the supplemental information (Table S1 and S2). FASTQ sequences were generated, demultiplexed and aligned to the reference genome using the Cell Ranger package (10X Genomics).
Reconstructed V(D)J sequences from Cell Ranger output were further analyzed by using the Change-O package. V(D)J germline assignments were performed with IgBLAST using the IMGT reference gene database.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: BCR annotation csv files

source_name: Peritoneal lavage

extract_protocol:
To isolate peritoneal cells, the peritoneal wash was obtained by injecting 3-6 mL of 2% FBS with 2 mM EDTA in PBS into the peritoneal cavity. Following gentle shaking, the whole fluid was withdrawn by syringe and placed into 15 mL conical tubes. Peritoneal cells were then pelleted by centrifugation and washed with PBS. Antigen-baiting-enriched ERV-reactive B-1 cells and total B-1 cells were isolated by fluorescence-activated cell sorting (FACS).
Sorted ERV-reactive B-1 cells and total naïve B-1 cells were counted and loaded into the Chromium Controller (10X Genomics) for single-cell partitioning and barcoding. Single-cell V(D)J libraries were generated using the Chromium Single Cell V(D)J Reagent kit (10X Genomics) while single-cell gene expression libraries were generated using the Chromium Single Cell 5’ Reagent kit (10X Genomics), per the manufacturer’s instruction.

value: Peritoneal lavage

value: B-1 cells

value: C57BL/6 wild-type


title: JK2-78-22 RNA-Seq for CRC organoids


title: JK2-78-12 RNA-Seq for CRC organoids


title: JK2-78-18 RNA-Seq for CRC organoids


title: Total, B1, VDJ, rep1

description: 10x Genomics


title: BMP5VI

value: recombinant Bmp5, 500 ng/ml, 24 h


title: SC146_YUMMER_Exer_6

description: 10x Genomics

value: Melanoma tumor

value: whole tumor dissociation

value: 6-8 weeks

value: male

value: Exercise


title: JK2-78-10 RNA-Seq for CRC organoids


title: JK2-78-11 RNA-Seq for CRC organoids


title: ERV, B1, VDJ, rep2

description: 10x Genomics


title: BMP5III

value: Small intestinal epithlelium

value: Small intestinal organoids

value: Epithelilal cells


title: ERV, B1, VDJ, rep1

description: 10x Genomics


title: JK2-78-9 RNA-Seq for CRC organoids

value: Base culture


title: CTRL-I

value: Untreated (control)


title: BMP4VI

value: recombinant Bmp4, 500 ng/ml, 24 h


title: JK2-78-8 RNA-Seq for CRC organoids


title: Total, B1, GEX, rep2

description: 10x Genomics


title: BMP4III


title: Total, B1, GEX, rep1

description: 10x Genomics


title: JK2-78-6 RNA-Seq for CRC organoids


title: JK2-78-7 RNA-Seq for CRC organoids


title: ERV, B1, GEX, rep1

description: 10x Genomics


title: BMP3IV

value: recombinant Bmp3, 500 ng/ml, 24 h


title: JK2-78-5 RNA-Seq for CRC organoids


title: BMP4II


title: 19096X9 Control 5 IFNg + FK866

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

data_processing:
The mouse GRCm38 genome and gene annotation files were downloaded from Ensembl release 102
A reference database was created using STAR version 2.7.6a with splice junctions optimized for 150 base pair reads.
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16.
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.30.1
Assembly: mm10
Supplementary files format and content: FeatureCount output files combined into a tab-delmited raw count matrix

molecule: polyA RNA

source_name: B16F10 cells

growth_protocol: Mouse B16f10 melanoma cell lines were grown in DMEM supplemented with 10% FBS, 1% penicillin-streptomycin and 1% L-glutamine at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA isolated via miRNeasy Qiagen RNA isolation kit

treatment_protocol: For the IFNg stimulation/Nampt inhibition experiments, B16f10 cells were stimulated with either mouse or human IFNg (50ng/mL mouse IFNg Ebioscience Cat # 14-8311-63) and FK866 (50nM R&D Systems Cat # 4808/10) 6 hours for RNA isolation.

tag: agent

value: IFNg + FK866

tag: time point

value: 6 hr treatment


title: BMP3III


title: 19096X8 Control 4 IFNg + FK866


title: JK2-78-4 RNA-Seq for CRC organoids


title: JK2-78-3 RNA-Seq for CRC organoids


title: BMP3II


title: wt_light rep 2

city: Berkeley

first: Nicole

middle: Anne

last: Repina

state: CA

address: Stanley Hall

department: Bioengineering

institute: UC Berkeley

description:
sample name:
Repina_5

data_processing:
Quality of reads was evaluated using the FASTQC tool
Adapter trimming was performed using Fastq-mcf and Cutadapt
Contamination removal using Bowtie2
Paired-end reads were aligned to the reference human genome (GRCh38, Ensemble database) using STAR alignment software
Raw read counts were estimated using HTSeq
Normalization and differential expression analysis were performed in
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file includes normalized counts for each sample (DESeq output)

source_name: hESC

growth_protocol: hESC H9 cells grown in E8 media

extract_protocol:
Cells were lifted with Accutase at 37 ˚C for 5min, centrifuged, and resuspended in TRI reagent (Zymo Research). To achieve higher RNA yields, two to three wells were pooled, constituting a single biological replicate. RNA was purified using an RNA extraction kit (R2051, Zymo Research) as per manufacturer recommendations with an on-column DNase digestion to remove residual genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols for TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Cells were kept in dark or illuminated with 0.8 uW/mm2 light for 48 hrs

value: stem cell

value: optoWnt

value: illuminated


title: BMP2VI

value: recombinant Bmp2, 500 ng/ml, 24 h


title: 19096X7 Control 3 IFNg + FK866


title: wt_light rep 3

description:
sample name:
Repina_6


title: wt_light rep 1

description:
sample name:
Repina_4


title: BMP5II

value: recombinant Bmp5, 500 ng/ml, 24 h


title: Cry2_light rep 3

description:
sample name:
Repina_3

value: WT


title: JK2-78-2 RNA-Seq for CRC organoids


title: BMP2IV


title: JK2-78-1 RNA-Seq for CRC organoids


title: 19096X6 Control 5 IFNg

value: IFNg


title: Cry2_light rep 2

description:
sample name:
Repina_2


title: BMP2III


title: 19096X5 Control 4 IFNg


title: ERV, B1, GEX, rep2

description: 10x Genomics

value: Peritoneal lavage

value: B-1 cells

value: C57BL/6 wild-type


title: WT12

city: West Hollywood

first: AGCT

last: Core

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

description: aggre_wt3_wt12_hfk_normalize_expr_matrix.csv

data_processing:
Raw sequencing data is demultiplexed and converted to fastq format by using bcl2fastq v2.20
Space Ranger software v1.0.0 (10X Genomics) is used for reads alignment, tissue detection, fiducial detection, and barcode/UMI counting with default parameter.
Seurat v3.2 in R v3.3.1 is used for advanced downstream data analysis and then normalized using SCTransform.
Genome_build: hg38
Supplementary_files_format_and_content: expression matrix was created with Seurat v3.2 in R; rows represent gene names, columns represent spot barcodes; values are SCTransformed counts

source_name: Wilms Tumor

extract_protocol: Human fetal kidney (hFK) was obtained from the CHLA Tissue Bank from elective terminations. Wilms’ Tumor (WT) samples were obtained from the CHLA Pathology department. Tumor and hFK samples were collected and transported on ice at 4°C in RPMI-1640 (Gibco, # 11875093) and used within 1-6hrs RPMI. Samples were flash frozen in Tissue-Tek® O.C.T. Compound (Sakura® Finetek, #4583) on dry ice and stored in -80°C. Samples were sectioned at 10µm size using a cryostat (Rotary Microtome-Leica, Rotary Cryostat CM1510), stored in  -80°C until analysis.

value: Female

value: 5 years old

tag: tumor type

value: No evidence of Anaplasia COG Stage III


title: Cry2_light rep 1

description:
sample name:
Repina_1


title: WT3

value: Male

value: 6 years old

value: Diffuse Anaplasia COG Stage I


title: BMP2II

value: Small intestinal epithlelium

value: Small intestinal organoids

value: Epithelilal cells


title: 19096X4 Control 3 IFNg

value: 6 hr treatment


title: wt_dark rep 3

description:
sample name:
Repina_18

value: stem cell

value: optoWnt

value: kept in dark


title: hFK

source_name: Fetal Kidney


title: noBMPVI

value: Untreated (control)


title: 19096X3 Control 5 Media

value: Media


title: 19096X2 Control 4 Media


title: noBMPIV


title: 19096X1 Control 3 Media


title: noBMPIII


title: wt_dark rep 2

description:
sample name:
Repina_17


title: RNA_Huh7_shCon_1

city: seoul

first: Jueng Soo

last: You

address: 120 Neungdong-ro

country: South Korea

institute: Konkuk University

data_processing:
Data were filtered and trimmed using Trimmomatic
The sequenced reads aligned to the human reference genome (hg38 assembly) using STAR
Read count and Transcripts Per Million (TPM) values were calculated using RSEM
For differentiailly expressed gene analysis, DEseq was used
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited format expression tables include Transcripts Per Million (TPM) values

source_name: Huh7 cell line

extract_protocol:
RNA was harvested using Trizol reagent. 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

value: Huh7 cell line

value: Human hepatocyte-derived carcinoma cell line

value: untreated

value: wild type


title: RNA_Huh7_shCon_2


title: noBMPII


title: Cry2_dark rep 2

description:
sample name:
Repina_14

value: WT


title: wt_dark rep 1

description:
sample name:
Repina_16


title: TolDC + LPS, day 7 02

city: Westmead

first: Jennifer

last: Li

address: 176 Hawkesbury Rd

country: Australia

institute: Westmead Institute for Medical Research

description: Enriched: live, CD11c+ DC

data_processing:
Aligned to mm10 by STAR aligner
Cutadapt to remove adapter sequences
DGE analysing using EdgeR, Limma
Assembly: GRCm38-mm10
Supplementary files format and content: tab

source_name: Bone marrow

extract_protocol:
ISOLATE II RNA Mini Kit (Bioline, London, UK)
Stranded mRNA Prep Ligation Kit (Illumina, San Diego, CA)

value: Bone marrow

value: Dendritic cell


title: RNA_Huh7_shNUP210_2


title: TolDC + LPS, day 7 03

description: Enriched: live, CD11c+ DC


title: TolDC + LPS , day 7 01

description: Enriched: live, CD11c+ DC


title: Cry2_dark rep 3

description:
sample name:
Repina_15


title: Sirt7KO, Aged_Male_Mouse_Liver, 16h_Fasting, biol_rep_3

city: Kumamoto

first: Tomonori

last: Tsuyama

state: Kumamoto

address: 1-1-1, Honjo Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto university

data_processing:
Sequence reads were trimmed for illumina adaptor sequence using Trim Galore (v 0.6.5).
Trimmed sequence reads were mapped to mouse transcriptome (GRCm38) and quantified by Salmon (v 1.2.1) with default setting.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values

source_name: Liver

extract_protocol:
RNA was harvested using ReliaPrep RNA Miniprep System (Promega). 1 ng of total RNA was used for the reverse transcription reaction with a SMART-seq HT (Takara Bio).
RNA libraries were prepared using Nextera XT Library Prep Kit (Illumina).

treatment_protocol: Livers were collected from 24-month-old male WT and Sirt7 KO mice after 16 hours fasting.

value: Liver

value: Liver cells

value: Sirt7 knockout

value: male

value: Fasting (16 hours)


title: Sirt7KO, Aged_Male_Mouse_Liver, 16h_Fasting, biol_rep_2


title: TolDC, day 7 03

description: Enriched: live, CD11c+ DC


title: Cry2_dark rep 1

description:
sample name:
Repina_13

value: stem cell


title: Sirt7KO, Aged_Male_Mouse_Liver, 16h_Fasting, biol_rep_1


title: control3

city: Hong Kong

first: chunhao

last: cao

address: Hong Kong

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

data_processing:
Perform quality analysis on acquired fastq sequence files using fastQC software. Use Trimmomatic software to remove adapters and make appropriate modifications to base pairs, trim base pairs, and filter low-quality sequences.
Use hisat2 software to align fasta sequences to a reference genome. First, build an index file by downloading or copying the reference genome sequence file Ref and genome annotation file and using the hisat2-build command.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include count values for all Samples

organism: Rattus norvegicus

source_name: Fibroblast-like synoviocytes

growth_protocol: Fibroblast-like synoviocytes cells were inoculated in DMEM medium containing high level of glucose medium supplemented with FBS (15%), and antibiotics (100U/ml penicillin, and 100 μg/ml streptomycin). A cell culture incubator (Sanyo, Japan) was used to culture the cells at 5% CO2 and 37°C.

extract_protocol:
The Qiagen RNeasy Kit (Cat#74106, USA) was used to isolate and purify total RNAs. The quality of RNA samples was determined using Nanodrop (Thermo Fisher Scientific). An Agilent 2100 Bioanalyzer was used to evaluate the results.
In Novogene (China), RNA libraries were prepared, and data was processed. Next, 1μg of RNA was utilized for each sample, followed by generating libraries using Illumina NEBNext UltraTM RNALibrary Prep Kit (NEB, USA), as suggested by the manufacturer. The first step was to purify mRNA by binding polyA to mRNA using OligodT-labeled magnetic beads (llumina Inc., San Diego, USA). The mRNA was then mixed with NEBNext First Strand Synthesis Reaction Buffer (5X). A short fragment of 200-300 bp in size was obtained by mixing. MMuLV Reverse Transcriptase without RNase H activity and random hexamer primers were used to generate first-strand cDNA. Conversion of this cDNA to double-stranded cDNA using RnaseH and DNA Polymerase I. Under the function of 3'-5' exonuclease and polymerase, fragmentation overhangs were translated to blunt ends. DNA fragments were adenylated, and the fragments were then ligated to the sequencing adapter by A and T complementary base pairing. Then, sequencing libraries were constructed using the AMPure XP system purification method (Beckman Coulter, Shanghai, China) and PCR methods.Finally, the libraries were evaluated by the Agilent Bioanalyzer 2100 system. Poly(A) selected paired-end sequencing libraries were generated according to the instructions in the TruSeq manual. The sequencer Illumina HiSeq 2000 was emploved to sequence all the libraries.

treatment_protocol: Fresh medium was used to replace the culture medium every 2 days. When the confluence of cells reached 85%, trypsin digestion and passage to the 4th generation at a ratio of 1:3 for follow-up experiments. Two experimental groups were used in the current study, namely the TNF-α group (cells were administered with TNF-α at a concentration of 10 ng/ml), and EMO group (co- administered with 80 μmol/L EMO and 10 ng/ml TNF-α)

tag: disease state

value: rheumatoid arthritis

value: Fibroblast-like synoviocytes

value: TNF-a

tag: time

value: Day 5


title: control2


title: ago10-1 2h BAP biol. Repl. 3

city: Tübingen

first: Sebastian

last: Wolf

state: Baden-Württemberg

address: Auf der Morgenstelle 32, ZMBP, ZMBP

country: Germany

institute: ZMBP, Universität Tübingen

data_processing:
read alignment with RNA STAR using TAIR10_chr_all.fas.gz genome
read counts were extracted oth feautureCounts and TAIR10.42.gtf as gene annotation file
Differential gene expression was assessed by DESeq261.
Assembly: TAIR10
Supplementary files format and content: xlsx file with normalized counts (DeSeq2 output) for each sample

organism: Arabidopsis thaliana

source_name: root tips

growth_protocol: plate grown seedlings, 6 days after germination, 150 µE

extract_protocol:
RNA was extracted from 50 mg of root tips (1mm)  GeneMATRIX Universal RNA/ miRNA Purification Kit (Cat. No. E3599 Distributor Roboklon GmbH) after homgenization in liquid nitrogen.
commercial (MWG Eurofins)

value: root tips

value: 6-Benzyladenine (2hours)


title: WT, Aged_Male_Mouse_Liver, 16h_Fasting, biol_rep_3


title: control1


title: TolDC, day 7 02

description: Enriched: live, CD11c+ DC


title: ago10-1 2h BAP biol. Repl. 1


title: ago10-1 2h BAP biol. Repl. 2


title: WT, Aged_Male_Mouse_Liver, 16h_Fasting, biol_rep_2


title: TolDC, day 7 01

description: Enriched: live, CD11c+ DC


title: Emodin3

value: TNF-a + emodin


title: BMDC + LPS , day 7 03

description: Enriched: live, CD11c+ DC

value: LPS


title: WT, Aged_Male_Mouse_Liver, 16h_Fasting, biol_rep_1

value: WT


title: Col-0 2h BAP biol. Repl. 3

value: wildtype


title: Emodin2


title: Col-0 2h BAP biol. Repl. 2


title: BMDC + LPS , day 7 02

description: Enriched: live, CD11c+ DC

value: Bone marrow

value: Dendritic cell


title: RNA_Huh7_shNUP210_1

value: Huh7 cell line

value: Human hepatocyte-derived carcinoma cell line

value: untreated


title: BMDC + LPS , day 7 01

description: Enriched: live, CD11c+ DC


title: Tex/Tim3+ CD28neg #2

city: New York

first: Dan

last: Filipescu

state: New York

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

description:
Poly-A enriched RNA, unstranded
RNA-seq of P14 CD28flox creERT2+ Tex (CD28neg) sorted from LCMV cl13 chronically infected mice 2 weeks post tamoxifen

data_processing:
Raw reads were quasi-mapped to the Gencode M25 (GRCm38.p6) gene set using salmon v.1.2.1 (Patro et al., 2017).
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: sf - table of gene expression counts and TPM generated by salmon

source_name: Sorted P14 PD1+ Tim3+ CD28neg T cells

extract_protocol:
Cells were sorted in lysis reagent (QIAGEN). After addition of chloroform (Sigma) and centrifugation, RNA was isolated from the aqueous phase using an RNEasy Micro kit (QIAGEN).
1 ng RNA from 10,000 sorted cells was used as input for the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB).

value: T cells

value: CD28flox creERT2+_CD28neg

tag: batch

value: F


title: Col-0 2h BAP biol. Repl. 1


title: Emodin1

value: rheumatoid arthritis

value: Fibroblast-like synoviocytes


title: Tex/Tim3+ CD28neg #3


title: ago10-1 mock biol. Repl. 3

value: mock


title: SCI, 3

city: xi'an

first: Erliang

address: xin si street

country: China

institute: tangdu hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and Ballgown were used to perform expression level for genes by calculating FPKM.
Assembly: rattus_norvegicus ensembl release101
Supplementary files format and content: Excel files include FPKM values for each isoform

source_name: spinal cord

growth_protocol: Wistar female rats of 8 weeks of age (From SPF (Beijing) Biotechnology Co., Ltd, China) weighing between 200 and 230 g were group housed in cages (n = 3/group) and maintained in an environmentally controlled room (22 – 24 ° C) with a 12-h light/dark cycle and were provided with adequate food and water.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Agilent 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA(1ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the poly(A) RNA was fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded mRNA Library Prep Kit(Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).

value: spinal cord

tag: condition

value: model of spinal cord injury

value: No ES


title: SCI, 2


title: BMDC, day 7 02

description: Enriched: live, CD11c+ DC


title: Tex/Tim3+ CD28+ #3

description:
Poly-A enriched RNA, unstranded
RNA-seq of P14 CD28flox creERT2neg Tex (CD28+) sorted from LCMV cl13 chronically infected mice 2 weeks post tamoxifen

source_name: Sorted P14 PD1+ Tim3+ CD28+ T cells

value: CD28flox creERT2neg_CD28+


title: SCI, 1


title: BMDC, day 7 01

description: Enriched: live, CD11c+ DC

value: WT


title: ago10-1 mock biol. Repl. 1

value: root tips


title: NC skin

city: Guangzhou

first: Yang

last: Sun

address: Nanfang Hospital

institute: Nanfang Hospital, Southern Medical University

data_processing:
The raw reads were further processed with a bioinformatic pipeline tool, BMKCloud online platform.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: skin

extract_protocol:
RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations

value: skin

value: NC


title: Tex/Tim3+ CD28+ #2


title: ES, 3

value: ES


title: Col-0 mock biol. Rep. 3

value: wildtype


title: Tex/Tim3+ CD28+ #1


title: Col-0 mock biol. Rep. 2


title: ago10-1 mock biol. Repl. 2


title: ES, 1


title: ES, 2


title: MNs skin

value: MNs


title: Col-0 mock biol. Rep. 1


title: PRP skin

value: PRP


title: Tpex/CD73+ CD28neg #4

description:
Poly-A enriched RNA, unstranded
RNA-seq of P14 CD28flox creERT2+ Tpex (CD28neg) sorted from LCMV cl13 chronically infected mice 2 weeks post tamoxifen

source_name: Sorted P14 PD1+ CD73+ CD28neg T cells

value: T cells

value: CD28flox creERT2+_CD28neg


title: PRP-MNs skin

value: PRP-MNs


title: BMDC, day 7 03

description: Enriched: live, CD11c+ DC

value: Bone marrow

value: Dendritic cell


title: Tpex/CD73+ CD28neg #5

value: F


title: CT26 STK24 KO+PD-1 Ab replicate3

city: Shinanomachi,Shinjukuku

first: Shigeki

last: Ohta

state: Tokyo

institute: Keio University

data_processing:
Samples were sequenced using Illumina Novaseq 6000 with paired-end 2 x 150-bp cycle
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.38 with "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36" as command option
Mapping of sequence reads using HISAT2 version 2.1.0
Raw read counts were determined using featureCounts version 1.6.3
Assembly: mm10
Supplementary files format and content: BigWig files were generated using deepTools bamCoverage version 3.2.1

source_name: colorectal carcinoma cell

growth_protocol: CT26  cells (5 × 10^5 cells/mouse) were transplanted into mouse and 3 weeks later each tumor was isolated.

extract_protocol:
Total RNA was extracted with the NucleoSpin  RNA(Takarabio, Kusatsu, Japan).
Libraries were prepared for sequencing using library creation kits (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)

treatment_protocol: IgG, PD-1 antibody(200 ug/mouse) were treated at day4,8,12,16.

value: colon

value: Balb/C


title: Tpex/CD73+ CD28neg #2


title: Tex/Tim3+ CD28neg #1


title: VDof1_N_input

city: Wuhan

first: Wei

last: Hua

address: Xudong 2nd

institute: CAAS

library_source: genomic

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of Arabidopsis_thaliana from https://www.Arabidopsis.org/ using STAR software (version 2.5.3a) with default parameters.
The RSeQC（version 2.6）was used for reads distribution analysis.
The MACS2 software（Version 2.1.1）was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: leaf

extract_protocol:
The tissue/cell was fixed in 1% formaldehyde for 10 min at room temperature by a vacuum pump, after which 0.125 M glycine was added and the mixture was sat for 5 min to terminate the crosslinking reaction. The tissue was then collected and frozen in liquid nitrogen, and grinded by tissue lyser. The grinded powder was treated with lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The 10% lysis sonicated chromatin was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-GFP antibody（Abcam,ab290）and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “Input”，respectively. The DNA of input and IP was extracted by phenol-chloroform method. The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

value: leaf

tag: chip antibody

value: rabbit IgG (Cell Signaling Technology)


title: Tpex/CD73+ CD28neg #1


title: CT26 STK24 KO+PD-1 Ab replicate2


title: CT26 STK24 KO+PD-1 Ab replicate1


title: VDof1_N_IP

tag: tissue

value: anti-GFP antibody(Abcam,ab290)


title: Tpex/CD73+ CD28+ #5

description:
Poly-A enriched RNA, unstranded
RNA-seq of P14 CD28flox creERT2neg Tpex (CD28+) sorted from LCMV cl13 chronically infected mice 2 weeks post tamoxifen

source_name: Sorted P14 PD1+ CD73+ CD28+ T cells

value: CD28flox creERT2neg_CD28+


title: HO mass, vehicle, Day5

city: Philadelphia

first: Maurizio

last: Pacifici

state: PA

address: 3615 Civic Center Blvd

department: Surgery

institute: The Children's Hospital of Philadelphia

description: 10X Genomics

data_processing:
Cell Ranger (version 3.0.2) was used to demultiplex reads, followed by extraction of cell barcode and UMIs. The cDNA insert was aligned to the reference mouse genome (mm10)
Seurat package V3 was used for filtering, variable gene selection, dimensionality reduction analysis and clustering. Doublets or cells with poor quality (genes>6000, genes<200, or >5% genes mapping to mitochondrial genome) were excluded.
Expression was naturally log transformed and normalized for scaling the sequencing depth to a total of 1 x 10^4 molecules per cell.
Assembly: mm10
Supplementary files format and content: tab-separated files and matrix files

source_name: matrigel implant

extract_protocol:
Ectopic tissue masses were harvested on day 5 from implantation site, minced and dissociated into single cell suspension by treatment with dispase (50 U/ml in Hanks' balanced salt solution) for 2 hours at 30 degrees Celsius. Cells were then suspended in 5% FBS/DMEM at a concentration of 700 to 1200 cells per microliter.
cDNA libraries of cells from each group were generated by Chromium Controller, barcoded, and purified as described by the manufacturer and sequenced using a 2 x 150 paired-end configuration on an Illumina HiSeq platform at a sequencing depth of ~ 400 million reads.

treatment_protocol: Mice were orally administered nothing (Matrigel only), vehicle (corn oil/DMSO) or Palovarotene (4 mg/kg) for 5 days.

value: matrigel implant

value: vehicle (corn oil/DMSO)

value: female

value: 6-8 weeks


title: HO mass, Palovarotene, Day5

description: 10X Genomics

value: Palovarotene


title: HO mass, matrigel only, Day5

description: 10X Genomics

value: nothing (Matrigel only)


title: Tpex/CD73+ CD28+ #4

value: T cells


title: Planktonic_0285_BR3

city: Singapore

first: Xianghui

last: Liu

address: 60 Nanyang Drive, SBS-01N-27

country: Singapore

institute: Nanyang Technological Univ. of Singapore

data_processing:
Quality of reads was access using FasQC v0.11.7
Ribosomal RNA reads were discarded using SortMeRNA v4.2.0 and remaining non-RNA reads were trimmed using Trimmomatic v0.38 and mapped against P. aeruginosa PAO1 reference genome
Aligned data were sorted with SAMTools v1.13 and used as input for feature counts function from the Rsubread v2.4.3 to generate a matrix of annotated genes with their corresponding raw counts
The count data were subjected to DESeq2 v1.30.1 for differential gene expression levels and statistical signficance
Supplementary files format and content: Tab-delimited text count table for all samples
Supplementary files format and content: rpkm normalized table for all samples

organism: Pseudomonas aeruginosa

growth_protocol: For planktonic growth condition, the cells were cultivated in flask with ABTG medium for 4 hours at 37oC (200 rpm, shaking condition). For biofilm growth condition, the cells were cultivated in flow chamber system with continous ABTG medium supplied for 72 hours at  37oC

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Mini Kit (catalogue number: 74104, Qiagen®, Germany). Then, samples were treated with DNase using Turbo DNA-free™ kit (catalogue number: AM1907, Thermo Fisher Scientific, USA) and purified DNA-free RNA samples were subjected to ribosomal depletion using the Ribo-Zero™ Magnetic Kits (Illumina, USA).  Complementary DNAs (cDNAs) were reverse transcribed using a NEBNext RNA first and second strand synthesis module (NEB®, USA). cDNAs were subjected to Illumina’s TruSeq Stranded mRNA protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: deltaPA0285 mutant

tag: mode of_growth

value: Planktonic

tag: growth condition

value: 4 hours in shaking condition


title: HSC45 with siTM4SF1-AS1 rep2

type: RNA

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: HSC45 cells transfected with a siRNA targeting TM4SF1-AS1 (replicate 2)

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: HSC45 cells were cultured in RPMI-1640 supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated at 37ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: HSC45 cells were transfected with a siRNA targeting TM4SF1-AS1 or a control siRNA using a Lipofectamine RNAiMAX according to manufacturer's instruction. Ninety-six hours after transfection, total RNA was extracted.

tag: sirna

value: siRNA targeting TM4SF1-AS1


title: Planktonic_0285_BR2

tag: strain


title: CT26 STK24KO+IgG replicate3

tag: cell type

value: colon


title: PHx_DKO_2d

city: La Jolla

first: Yan

last: Liang

address: 9500 Gilman Drive, BRFII Room 1220 Bay B

institute: UC San Diego

data_processing:
Sequenced reads were processed using CellRanger package (v3.0.2) with default parameters.
genome build: GRCm38
Supplementary_files_format_and_content: h5 files with raw counts for every gene and every cell; raw counts

extract_protocol:
Mouse liver was perfused with collagenase H (Roche). Hepatocytes were isolated by centrifugation and purified using 45% Percoll (sigma-aldrich).
Chromium Single Cell 3’ Reagent Kits (V3 chemistry, 10x Genomics)

treatment_protocol: PHx was performed on mice at age of 8-10 weeks with the use of Buprenorphine hydrochloride (Par Pharmaceutical) as a pain relief for the surgery.

value: DKO

tag: cell/sample type

value: Hepatocytes

tag: phx


title: Planktonic_0285_BR1

tag: genotype


title: HSC45 with siControl rep2

description: HSC45 cells transfected with a control siRNA (replicate 2)

value: control siRNA


title: PHx_WT_2d

data_processing:
Sequenced reads were processed using CellRanger package (v3.0.2) with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: h5 files with raw counts for every gene and every cell

value: WT


title: Tpex/CD73+ CD28neg #3

value: CD28flox creERT2+_CD28neg

tag: Sex

value: F


title: Tpex/CD73+ CD28+ #3

value: CD28flox creERT2neg_CD28+


title: Tpex/CD73+ CD28+ #2


title: CT26 STK24KO+IgG replicate1

value: Balb/C


title: HSC45 with siControl rep1

description: HSC45 cells transfected with a control siRNA (replicate 1)


title: CT26 STK24KO+IgG replicate2


title: PHx_WT_4h


title: Biofilm_0285_BR3

value: Biofilm

value: 72 hours in flow chamber


title: Tpex/CD73+ CD28+ #1


title: Biofilm_0285_BR2


title: CT26+PD-1 Ab replicate3


title: PHx_SKO_2d

value: SKO


title: Biofilm_0285_BR1


title: CT26+PD-1 Ab replicate2


title: PHx_SKO_4h


title: Planktonic_WT_BR3

value: wild-type


title: CT26+PD-1 Ab replicate1


title: CT26+IgG replicate3


title: HSC45 with siTM4SF1-AS1 rep1

description: HSC45 cells transfected with a siRNA targeting TM4SF1-AS1 (replicate 1)


title: Planktonic_WT_BR2


title: Biofilm_WT_BR3


title: IF172 M6

first: Ruteja

middle: A

last: Barve

state: MO

address: 4515 McKinley Ave

department: Genetics

institute: Washington University

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: colon mucosa biopsy

extract_protocol: oligo-dT

tag: sample group

value: IF

value: sigmoid colon

tag: time point

value: 6 Month


title: Biofilm_WT_BR2


title: CT26+IgG replicate1


title: Biofilm_WT_BR1


title: IF169 M12

value: Control

value: 12 Month


title: IF172 BL

value: Baseline


title: B/C TSC Wildtype biol rep 3 HiC library #2

city: Chapel Hill

first: Joseph

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Rd

department: Pharmacology

institute: UNC Chapel Hill

description:
bc-tsc_wt_merged_mm9-B6.hic.gz
bc-tsc_wt_merged_mm9-CAST.hic.gz

data_processing:
Hi-C reads were aligned using BWA as a part of the Juicer pipeline (Durand et al. 2016a).
For all Hi-C analyses in this study, read pairs that had a mapping quality greater than or equal to 10 were used. For allele-specific retention of Hi-C contacts, read pairs in which at least one read end overlaps a B6/CAST SNP were extracted from the Juicer output merged_nodups.txt file using a modified Juicer diploid script.
Assembly: All mouse reference NCBI build 37/mm9 genome annotations were obtained from the UCSC genome browser (Lee et al. 2022). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/; (Keane et al. 2011). The CAST/EiJ (CAST) pseudogenome creation was performed as in (Calabrese et al. 2012; Calabrese et al. 2015; Schertzer et al. 2019a).
Supplementary files format and content: HIC files of allele-specific Hi-C contacts; files are generated from merged biological replicate/clone data.

source_name: F1-hybrid B/C trophoblast stem cells

growth_protocol: TSCs were cultured as in (Quinn et al. 2006). Briefly, TSCs were cultured on gelatin-coated, pre-plated irradiated mouse embryonic fibroblast (irMEF) feeder cells in TSC media (RPMI [Gibco, cat #: 11875093], 20% qualified FBS [Gibco, cat #: 26140079], 0.1mM penicillin-streptomycin [Gibco, cat #: 15140122], 1mM sodium pyruvate [Gibco, cat #: 11360070], 2mM L-glutamine [Gibco, cat #: 25030081], 100uM beta-mercaptoethanol [Sigma-Aldrich, cat #: 63689]) supplemented with 25ng/mL FGF4 (Gibco, cat #: PHG0154) and 1ug/mL Heparin (Sigma-Aldrich, cat #: H3149) just before use, at 37°C in a humidified incubator at 5% CO2. At passage, TSCs were trypsinized with 0.125% Trypsin-EDTA in PBS solution (Gibco, cat #: 25200-072) for ~4 minutes at room temperature and gently dislodged from the plate with a sterile, cotton-plugged Pasteur pipette. To deplete irMEFs from TSCs prior to all harvests, TSCs were pre-plated for 45 minutes at 37°C, transferred to a fresh culture plate, and then cultured for three days in 70% irMEF-conditioned TSC media supplemented with growth factors as above.

extract_protocol: Arima-HiC+, performed according to manufacturer instruction.

treatment_protocol: Prior to crosslinking for Hi-C, TSCs were passaged once off of irMEFs as described above. TSCs were then trypsinized and washed once with PBS. 5-10 million cells were crosslinked in resuspension with 10mL of 1% formaldehyde (Thermo Scientific, cat #: 28906) in PBS solution for 10 minutes at room temperature, quenched with 200mM glycine for 5 minutes at room temperature, and then washed twice with ice-cold PBS. Cells were then divided into 5 aliquots (1-2 million cells/aliquot), where one aliquot was used for each Hi-C experiment. Importantly, for the removal of all PBS washes and crosslinking solution, cells were spun at 160 x g for 5 minutes.

tag: cell line

value: F1-hybrid B/C trophoblast stem cells

tag: parent of_origin

value: C57BL/6J mother X CAST/EiJ father

tag: passage number

value: Wildtype


title: CT26+IgG replicate2

value: colon


title: brain_14d_BYHWD_rep3

city: Changsha

first: Teng

address: Xiangya Road

institute: central south university xiangya hospital

description: lncRNA+mRNA

hyb_protocol: The cyanine 3-labeled cRNA was hybridized to the lncRNA microarray slide by Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242).

scan_protocol: The microarray was scanned using Agilent DNA Microarray Scanner (Agilent p/n G2565BA) after washing.

data_processing: The lncRNA+mRNA raw data was extracted through Agilent Feature Extraction Software and summarized, and normalized using the GeneSpring GX v12.1 software.

source_name: brain, 14d, BYHWD, rep3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442). The labeled cRNAs were purified by RNeasy Mini Kit. The quantity and quality of RNA were valued by a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). The OD 260/280 ratio between 1.8 and 2.1 are acceptable.

growth_protocol: Mice were housed in a well-ventilated room (four rats in one cage) at a constant room temperature (25 ± 1℃) and controlled humidity (50 ± 10%), with a 12 h light/dark cycle. All procedures involving the use and care of animals were performed in accordance with the guidelines of Central South University for the care and use of animals and were approved by the Medical Ethics Committee of Central South University (Animal ethical number: 2020sydw0929).

extract_protocol: RNA samples isolated using the TRIZOL method. The protocol includes cryopulverization of tissue using the biopulverizer, Homogenization using the Mini-Bead-Beater-16, lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent, phase separation, RNA Precipitation, RNA wash and redissolving the RNA.

treatment_protocol: Mice were randomly assigned to three groups: sham, ICH, and BYHWD. In the BYHWD group, BYHWD powder was dissolved in distilled water and administered to mice (6.19 g/kg) by oral gavage once per day for 14 days. The sham and ICH groups were gavaged with an equal dose of distilled water. The mice were sacrificed under 0.3% pentobarbital sodium (60 mg/kg, intraperitoneally) on the 14th day, and transcardially perfused with saline. Brains were harvested and the ipsilateral basal ganglia were isolated immediately.

value: ipsilateral striatum of brain

tag: gender

value: male

tag: treatment

value: after 14d in the brain of BYHWD mice


title: B/C TSC Wildtype biol rep 3 HiC library #1


title: brain_14d_BYHWD_rep4

description: lncRNA+mRNA

source_name: brain, 14d, BYHWD, rep4

tag: tissue


title: Planktonic_WT_BR1

tag: mode of_growth

value: Planktonic

value: 4 hours in shaking condition


title: IF169 BL


title: brain_14d_BYHWD_rep5

description: lncRNA+mRNA

source_name: brain, 14d, BYHWD, rep5


title: brain_14d_BYHWD_rep2

description: lncRNA+mRNA

source_name: brain, 14d, BYHWD, rep2


title: HeLa-S3 siGLN3_2

type: genomic

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the START-R software.

source_name: nascent DNA from early S-phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification (WGA) was conducted (Seq-plex, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Each cells grown in culture condition defined by ATCC

extract_protocol: cells were incubated with BrdU (50µM) for two hours, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) . To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

tag: knockdown

tag: molecule subtype

value: nascent DNA

source_name: nascent DNA from late S-phase


title: brain_14d_ICH_rep4

description: lncRNA+mRNA

source_name: brain, 14d, ICH, rep4

value: after 14d in the brain of ICH mice


title: B/C TSC Wildtype biol rep 2 HiC library


title: brain_14d_ICH_rep3

description: lncRNA+mRNA

source_name: brain, 14d, ICH, rep3


title: IF168 M12


title: brain_14d_ICH_rep1

description: lncRNA+mRNA

source_name: brain, 14d, ICH, rep1


title: brain_14d_BYHWD_rep1

description: lncRNA+mRNA

source_name: brain, 14d, BYHWD, rep1


title: HeLa-S3 siGLN3_1


title: HeLa-S3 siRif1_2


title: B/C TSC Wildtype biol rep 1 HiC library #2


title: brain_14d_ICH_rep5

description: lncRNA+mRNA

source_name: brain, 14d, ICH, rep5


title: HeLa-S3 siRif1_1


title: MDA-MB-438 treated with Palbociclib replicate 2


title: IF169 M6


title: MDA-MB-438 treated with Palbociclib replicate 1


title: IF168 BL


title: brain_14d_ICH_rep2

description: lncRNA+mRNA

source_name: brain, 14d, ICH, rep2


title: HeLa-S3 siControl_1

value: siControl


title: C/B TSC Airn truncation biol rep 3 HiC library #2

description:
cb-tsc_airn-trunc_merged_mm9-B6.hic.gz
cb-tsc_airn-trunc_merged_mm9-CAST.hic.gz

source_name: F1-hybrid C/B trophoblast stem cells

value: F1-hybrid C/B trophoblast stem cells

value: CAST/EiJ mother X C57BL/6J father

value: Airn truncation


title: C/B TSC Airn truncation biol rep 3 HiC library #1


title: IF167 M12

value: IF

value: sigmoid colon

value: 12 Month


title: B/C TSC Wildtype biol rep 1 HiC library #1

value: F1-hybrid B/C trophoblast stem cells

value: C57BL/6J mother X CAST/EiJ father


title: IF167 M6

value: 6 Month


title: HeLa-S3 siControl_2


title: C/B TSC Airn truncation biol rep 2 HiC library #2


title: MDA-MB-438 treated with DMSO replicate 2


title: IF167 BL

value: Baseline


title: C/B TSC Airn truncation biol rep 2 HiC library #1


title: IF164 M12


title: brain_14d_sham_rep5

description: lncRNA+mRNA

source_name: brain, 14d, sham, rep5

value: ipsilateral striatum of brain

value: male

value: after 14d in the brain of sham mice


title: brain_14d_sham_rep4

description: lncRNA+mRNA

source_name: brain, 14d, sham, rep4


title: C/B TSC Airn truncation biol rep 1 HiC library


title: IF168 M6

source_name: colon mucosa biopsy

value: Control


title: IF164 M6


title: C/B TSC Wildtype biol rep 2 HiC library #2

description:
cb-tsc_wt_merged_mm9-B6.hic.gz
cb-tsc_wt_merged_mm9-CAST.hic.gz

value: Wildtype


title: brain_14d_sham_rep3

description: lncRNA+mRNA

source_name: brain, 14d, sham, rep3


title: random_end_hek293t_N50 biol rep 1-10

city: Seattle

middle: Martin

last: Castillo Hair

state: Washington

address: West Stevens Way NE

department: Electrical and Computer Engineering

institute: University of Washington

description: Polysome profiling of the random-end N50 5'UTR library in HEK293T

data_processing:
bcl2fastq
Custom scripts were used to filter reads where the 3' end matched the expected constant sequence right after the variable 5'UTR region
Starcode was used to collapse UMIs
A custom script was used to calcualte MRLs for each sequence in the library.
Supplementary files format and content: Columns "UTR" or "utr" contain the variable 5'UTR sequence. Columns 0-13 contain the number of UMIs in each polysome fraction, and column "total" contains their sum for each sequence. Columns r0-r13 contain the normalized read count in each polysome fraction, and r_total" contains their sum. Column "rl" contains the calculated MRL.

growth_protocol: HEK293T cells were cultured on ECM-coated plates in Dubelco's DMEM media supplemented with FBS (5%), penicillin (.05%), and streptomycin (.05%). HepG2 cells were cultured in EMEM + 10% FBS in a T-75 flask. T cells were grown in T cell growth medium (TCGM) at 37C, 5% CO2.

extract_protocol:
Cells were lysed in the presence of cycloheximide to halt translating ribosomes so that polysome profiling could be run with the lysate. Lysis and RNA isolation for HEK293T and HepG2 were performed as described in Sample, Wang et al. 2019. For T cells, cycloheximide was first added dropwise to the media to a final concentration of 100 ug/mL and incubated for 5 additional minutes. Cells were then spined down at 1500 rpm for 5 min and the supernatant was discarded. 300 uL of cold lysis buffer (Sample, Wang et al. 2019) was used to resuspend the cells, and the mixture was incubated on ice for 10 minutes. Cells were then triturated by passing the mixture through a 25-gauge needle ten times. The mixture was spined down at 16,000 rpm for 5 min at 4C and the supernatant was transferred to another tube. 1.5 uL of 1U/uL DNAse was added, the mixture was set on ice for 30 minutes, and stored at -80C. Polysome profiling was performed as in Sample, Wang et al. 2019.
Sequencing libraries for the defined-end reporters were constructed for each extracted polysome fraction as in Sample, Wang, et al. 2019. For the random-end reporter libraries, sequencing library preparation comprised reverse transcription, template switching, and qPCR amplification, all of which were performed separately for each polysome fraction. For reverse transcription, we first mixed 10.5 uL of purified RNA with 2 uL of 2 uM RT primer (AGGGACATCGTAGAGAGTCGTACTTANNNNNNNNNNAGATGAACTTCAGGGTCAGC, where Ns comprise the UMI) and 2uL of 10mM dNTP mixture (NEB), incubated the mixture at 65C for 5 minutes, and placed on ice for at least one minute. Then, we added 4 uL Maxima RT buffer, 0.5 uL Superase-In RNAse inhibitor (Thermo Fisher), and 1 uL Maxima RT RNaseH minus Enzyme (Thermo Fisher), incubated at 50C for 15 min, then 85C for 10 min, and transferred back to ice. Next, we added 1 uL RNase (from bovine pancreas, DNase free, Roche) and 1 uL RNase H (NEB) and incubated at 37C for 15 minutes. Finally, the product was cleaned with KAPA beads (Roche) with a 3x ratio of beads to DNA volume, and resuspended in 25 uL dH2O. For template switching, we added 8 uL Maxima RT buffer, 6 uL 50% PEG-8000, 0.5 uL Superase-In, 1 uL Maxima RT RNaseH minus enzyme, and 0.5 uL of 10 uM template switching oligo (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG). This mixture was incubated at 42C for 30 minutes, then 85C for 10 minutes. Next, 1uL RNase (Roche) and 1uL RNase H (NEB) were added and the mixture was incubated at 37C for 15 minutes. Finally, the product was cleaned with 3x KAPA beads and resuspended in 20 uL dH2O.  qPCR amplification was performed using the KAPA HiFi master mix (Roche) with forward primers AATGATACGGCGACCACCGAGATCTACAC[8nt-long index barcode]AGCGTGACAGGGACATCGTAGAGAGTCGTACTTA and reverse primers CAAGCAGAAGACGGCATACGAGAT[8nt-long index barcode]AAGCAGTGGTATCAACGCAGA, where the barcodes were specific to each polysome fraction. qPCR reactions were stopped before reaching saturation and purified via gel extractions.

treatment_protocol: HEK293T growth and transfection was performed as described in Sample, Wang et al. 2019. HepG2 cells were seeded at 200,000 cells/mL into a T-75 flask and allowed to expand for 3 days. 1ug library mRNA was transfected into one million cells using the Lonza 4D nucleofector. Cell lysis was performed 8 hours later. T cells were enriched from peripheral blood mononuclear cells (PBMCs) isolated via Ficoll-Paque gradient centrifugation from healthy donors. Activation was performed with anti CD3/CD28 antibodies in the presence of IL-2. 1 ug library mRNA was transfected into one million cells with the Lonza 4D Nucleofector, following the manufacturer’s protocol. Transfected cells were plated in T cell growth medium (TCGM) at 1 million cells/mL and incubated at 37C, 5% CO2. Cell lysis was performed 12 hours later.


title: NCI treated with Palbociclib replicate 2


title: brain_14d_sham_rep1

description: lncRNA+mRNA

source_name: brain, 14d, sham, rep1


title: NCI treated with Palbociclib replicate 1


title: random_end_hek293t_N50 biol rep 1-9


title: random_end_hek293t_N50 biol rep 1-12


title: brain_14d_sham_rep2

description: lncRNA+mRNA

source_name: brain, 14d, sham, rep2


title: C/B TSC Wildtype biol rep 2 HiC library #1


title: NCI treated with DMSO replicate 2


title: MDA-MB-438 treated with DMSO replicate 1


title: C/B TSC Wildtype biol rep 1 HiC library #2


title: random_end_hek293t_N50 biol rep 1-11


title: IF161 M6


title: IF161 BL


title: random_end_hek293t_N50 biol rep 1-8


title: C/B TSC Wildtype biol rep 1 HiC library #1


title: NCI treated with Ribociclib replicate 2


title: random_end_hek293t_N50 biol rep 1-7


title: NCI treated with Ribociclib replicate 1


title: InVitro_U266_LEN-R_LEN10

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression in LEN-R U266 cells after 24 h of LEN treatment

hyb_protocol: 1.75 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60℃ for 30 min according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a Human Gene Expression 4x44K v2 Microarray (G4845A-026652) for 17 h at 65 ℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37℃ GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, 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 GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LEN-R U266, 24 h, LEN

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 RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The MM cell lines were incubated in a RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. Following 24h incubation, the cells were then incubated with either 0.1% DMSO or 10 μM of LEN of for 24 hours at 37 ºC

value: LEN-R U266

value: multiple myeloma (MM) cell line

value: Male

tag: age

value: after 24 h of LEN treatment


title: IF160 M12


title: random_end_hek293t_N50 biol rep 1-6


title: Bone marrow cells in treated with deoxycholic acid at 35uM for 1 week [BAT37Da]

city: Charlottesville

first: Anwaruddin

last: Mohammad

state: VA

address: Pinn Hall

department: Bioinformatics Core

institute: University of Virginia

data_processing:
The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6.0
Assembly: NOT PROVIDED
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole bone marrow cells

extract_protocol:
Cells were isolated from our liquid co-culture system, as described above, and lineage-negative cells were FACS sorted to enrich for HSPCs prior to scRNA-seq. Cells were sorted into 1% FACS buffer into low-protein binding microcentrifuge tubes (Thermo Scientific). The cells were then spun down at 800g and resuspended in 50uL of PBS+0.04% BSA and pushed through a pipette tip-mounted flowmi filter (Millipore Sigma) to achieve a single cell suspension.
The Genome Analysis and Technology core generated the single-cell indexed libraries and performed quality control checks to ensure high-quality RNA for downstream analysis.  Briefly, 8000 cells per sample were targeted for use with the 10X genomics chromium controller platform and Chromium single cell 3’ library, and Gel Bead Kit v3.1 reagent. Generated cDNA was subject to quality control using the 4200 TapeStation instrument, using the D5000 Kit (Agilent).

value: whole bone marrow cells

value: deoxycholic acid at 35uM for 1 week


title: IF164 BL

value: IF

value: sigmoid colon


title: IF160 M6


title: Bone marrow cells in treated with deoxycholic acid at 35uM for 1 week [BAT37Db]


title: InVitro_U266_Control_DMSO

description: Gene expression in control U266 cells after 24 h of DMSO treatment

source_name: Control U266, 24 h, DMSO

tag: cell type

value: after 24 h of DMSO treatment


title: Bone marrow cells in treated with deoxycholic acid at 35uM for 1 week [BAT37Dc]


title: IF157 M12

value: 12 Month


title: random_end_hek293t_N50 biol rep 1-4


title: random_end_hek293t_N50 biol rep 1-3


title: Bone marrow cells in treated with deoxycholic acid at 35uM for 1 week [BAT37Dd]


title: InVitro_NCU-MM1_LEN-R_LEN10

description: Gene expression in LEN-R NCU-MM1 cells after 24 h of LEN treatment

source_name: LEN-R NCU-MM1, 24 h, LEN

value: LEN-R NCU-MM1

value: Female


title: InVitro_U266_Control_LEN10

description: Gene expression in control U266 cells after 24 h of LEN treatment

source_name: Control U266, 24 h, LEN


title: IF157 M6

value: 6 Month


title: Bone marrow cells in long term culture media [BAT37Ma]

value: long term culture media


title: random_end_hek293t_N50 biol rep 1-2


title: Bone marrow cells in long term culture media [BAT37Mb]


title: NCI treated with DMSO replicate 1

source_name: nascent DNA from early S-phase

source_name: nascent DNA from late S-phase


title: InVitro_U266_LEN-R_DMSO

description: Gene expression in LEN-R U266 cells after 24 h of DMSO treatment

source_name: LEN-R U266, 24 h, DMSO


title: IF153 M12


title: IF157 BL

value: Baseline


title: random_end_hek293t_N50 biol rep 1-5


title: Bone marrow cells in long term culture media [BAT37Mc]


title: random_end_hek293t_N50 biol rep 1-0


title: random_end_hek293t_N25 biol rep 2-12

description: Polysome profiling of the random-end N25 5'UTR library in HEK293T, replicate 2


title: RNA-seq of WT cells after 30 h growth in ONA solid medium at 28°C - replicate 2

city: Gif-sur-Yvette

first: Stéphanie

middle: Germaine

last: Bury-Moné

address: 1 Avenue de la Terrasse

institute: Institute for Integrative Biology of the Cell

data_processing:
STAR software (Dobin, Davis et al. 2013) was used for mapping RNA-seq to the reference genome (genome-build-accession NCBI_Assembly: GCF_001267885.1) containing only one terminal inverted repeat (TIR), to avoid any biases associated to multiple mapping within the duplicated extremities of the genome (since the two TIR sequences are indiscernable). We used featureCounts program (Liao, Smyth et al. 2014) to quantify reads generated from RNA-sequencing technology according to S. ambofaciens ATCC23877 most recent annotation.
Demultiplexing has been done (bcl2fastq2 V2.2.18.12) and adapters were trimmed with Cutadapt1.15, only reads longer than 10pb were kept.
Assembly: GCF_001267885.1_ASM126788v1

organism: Streptomyces ambofaciens ATCC 23877

growth_protocol: Culture: Around 2.10^6 spores (in 5 µl) of Streptomyces ambofaciens ATCC23877 were spotted on a sterile cellophane covering the plate and grown at 28°C. Thirty hours later, cells were harvested using a sterile cone and deposited into a tube containing 5 ml of cold ethanol. Medium compositions: MMM (0.5 g/l L-asparagine, 0.5 g/l K2HPO4, 0.2 g/l MgSO4, 0.001 g/l FeSO4, 0.5 % mannitol, 10 g/l agar – pH 7.0/7.2) (Kieser T. 2000); HT (1 g/l yeast extract, 1 g/l meat/beef extract, 2 g/l bactotryptone, 10 g/l white dextrin, 0.02 g/l CoCl2, 20 g/l agar – pH 7.3 ; adapted from (Kieser T. 2000); SAF (0.5 g/l yeast extract, 0.5 g/l meat/beef extract, 21 g/l MOPS, 5g/l glucose, 1 g/l enzymatic hydrolysate of casein, 20 g/l agar – pH 7.0) (Sanchez and Brana 1996); ONA (28 g/l Oxoid nutrient agar (CM003) composed of 1 g/l ‘Lab-Lemco’ powder, 2 g/l yeast extract, 5 g/l peptone, 5 g/l NaCl, 15 g/l agar). N-acetylglucosamine (NAG) was added at 25 mM to MMM demium to obtain MMM+NAG condition.

extract_protocol:
Remark : Librairy prepared with Total RNA Stranded (reversely stranded) kit => The R1 file corresponds to antisense orientation, and R2 to the sense orientation.
Cells were then harvested through centrifugation for 15 min at 4,000 g at 4°C, and stored at -20°C. Pellets were washed with 1 ml of DEPC water, centrifuged for 5 min at 16,000 g at 4°C, and homogenized with glass beads (≤ 106 µm; G4649, SIGMA) in 350 µl of lysis buffer (RNeasy Plus Mini Kit, QIAGEN) supplemented with 10 µl/ml β-mercaptoethanol. Samples were processed 3 times for 45 sec each in FastPrep-24TM 5G instrument (MP Biomedicals) at setting 6 with 1 min cooling between the stages. After centrifugation for 10 min at 16,000 g at 4°C, total RNAs were isolated from the supernatants using RNeasy Plus Mini Kit (QIAGEN) and gDNA Eliminator columns, following manufacturer’s recommendations. To remove genomic DNA, RNA samples were incubated from 30 min at 37°C with 20 U of RNase-free DNase I (Roche) in a final reaction volume of 30 µl. RNA were then cleaned up using the RNeasy Mini Kit (QIAGEN), following manufacturer’s recommendations. The absence of DNA in the preparations was checked by PCR on an aliquot. RNA samples were quantified using QubitTM RNA HS Assay kit (ThermoFischer Scientific), following manufacturer’s recommendations.
Total RNA quality was assessed on an Agilent Bioanalyzer 2100, using RNA 6000 pico kit (Agilent Technologies). 500 ng of total RNA were treated with DNAse (Baseline Zero DNAse, Epicentre) prior to ribosomal RNA depletion using the RiboZero bacteria magnetic Kit from Illumina according to the manufacturer recommendations. After the Ribo-Zero step, the samples were checked on the Agilent Bioanalyzer for proper rRNA depletion. Directional RNA-seq libraries were constructed using the Illumina Stranded library preparation kit, according to the manufacturer recommendations.  Libraries were pooled in equimolar proportions and sequenced (Paired-end 2x43 bp) on an Illumina NextSeq500 instrument, using a NextSeq 500 High Output 75 cycles kit.

treatment_protocol:
No treatment
No treatment

value: treptomyces ambofaciens ATCC23888

value: WT

value: ONA solid medium at 28 degree C

tag: time


title: RNA-seq of WT cells after 30 h growth in ONA solid medium at 28°C - replicate 1

value: treptomyces ambofaciens ATCC23887


title: IF153 M6

value: Control


title: IF160 BL


title: RNA-seq of WT cells after 30 h growth in SAF solid medium at 28°C - replicate 3

value: treptomyces ambofaciens ATCC23886

value: SAF solid medium at 28 degree C


title: IF153 BL


title: random_end_hek293t_N25 biol rep 2-11

first: Sebastian


title: ZnT3 conditional knockout in amacrine cells, primary retinal ganglion cells, optic nerve crush, day 3 [CKO3]

first: Jiahui

last: Tang

address: 7 Jinsui Road

institute: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: primary retinal ganglion cell

extract_protocol:
RNA from FACS-sorted RGCs were isolated, and cDNA amplification product were prepared with Discover-sc WTA Kit V2 (Vazyme #N711), following manufacturers’ protocols. RNA quality was determined by examining A260/A280 with Agilent 2100 Bioanalyzer. RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies).
2 μg total RNAs were used for stranded RNA sequencing library preparation using  the TruePrep DNA Library Prep Kit V2 (Vazyme #TD502) and TruePrep Index Kit V2 for Illumina (Vazyme #TD202), and the manufacturer’s instructions.

value: primary retinal ganglion cell

value: ZnT3 CKO in amacrine cells

value: optic nerve crush


title: InVitro_NCU-MM1_LEN-R_DMSO

description: Gene expression in LEN-R NCU-MM1 cells after 24 h of DMSO treatment

source_name: LEN-R NCU-MM1, 24 h, DMSO

value: multiple myeloma (MM) cell line

value: after 24 h of DMSO treatment


title: random_end_hek293t_N50 biol rep 1-1


title: RNA-seq of WT cells after 30 h growth in ONA solid medium at 28°C - replicate 3

value: treptomyces ambofaciens ATCC23889


title: RNA-seq of WT cells after 30 h growth in SAF solid medium at 28°C - replicate 2

value: treptomyces ambofaciens ATCC23885


title: IF152 M12

value: sigmoid colon

value: 12 Month


title: random_end_hek293t_N25 biol rep 2-10


title: InVitro_NCU-MM1_Control_LEN10

description: Gene expression in control NCU-MM1 cells after 24 h of LEN treatment

source_name: Control NCU-MM1, 24 h, LEN

value: Female

value: after 24 h of LEN treatment


title: ZnT3 conditional knockout in amacrine cells, primary retinal ganglion cells, optic nerve crush, day 3 [CKO2]


title: IF152 M6

value: 6 Month


title: ZnT3 conditional knockout in amacrine cells, primary retinal ganglion cells, optic nerve crush, day 3 [CKO1]


title: random_end_hek293t_N25 biol rep 2-9


title: IF152 BL

value: Baseline


title: random_end_hek293t_N25 biol rep 2-8


title: wild type, primary retinal ganglion cells, optic nerve crush, day 3 [ONC3]

value: WT


title: InVitro_NCU-MM1_Control_DMSO

description: Gene expression in control NCU-MM1 cells after 24 h of DMSO treatment

source_name: Control NCU-MM1, 24 h, DMSO


title: RNA-seq of WT cells after 30 h growth in HT solid medium at 28°C - replicate 3

value: treptomyces ambofaciens ATCC23883

value: HT solid medium at 28 degree C


title: RNA-seq of WT cells after 30 h growth in SAF solid medium at 28°C - replicate 1

value: treptomyces ambofaciens ATCC23884

value: SAF solid medium at 28 degree C


title: RNA-seq of WT cells after 30 h growth in HT solid medium at 28°C - replicate 2

value: treptomyces ambofaciens ATCC23882


title: Bone marrow cells in long term culture media [BAT37Md]

value: whole bone marrow cells

value: long term culture media


title: RNA-seq of WT cells after 30 h growth in HT solid medium at 28°C - replicate 1

value: treptomyces ambofaciens ATCC23881


title: wild type, primary retinal ganglion cells, optic nerve crush, day 3 [ONC2]

value: primary retinal ganglion cell

value: optic nerve crush


title: random_end_hek293t_N25 biol rep 2-6


title: random_end_hek293t_N25 biol rep 2-7


title: IF149 BL

value: IF

value: sigmoid colon


title: wild type, primary retinal ganglion cells, optic nerve crush, day 3 [ONC1]


title: IF145 M12

value: Control

value: 12 Month


title: RNA-seq of WT cells after 30 h growth in MMM supplemented with 25 mM NAG solid medium at 28°C - replicate 2

source_name: RNA-seq of WT cells after 30 h growth in MMM (minimum medium mannitol 0.5 %) supplemented with 25 mM NAG (N-acetylglucosamine) solid medium at 28°C - replicate 2

value: treptomyces ambofaciens ATCC23880

value: MMM (minimum medium mannitol 0.5 percent) supplemented with 25 mM NAG (N-acetylglucosamine) solid medium at 28 degree C


title: RNA-seq of WT cells after 30 h growth in MMM supplemented with 25 mM NAG solid medium at 28°C - replicate 1

source_name: RNA-seq of WT cells after 30 h growth in MMM (minimum medium mannitol 0.5 %) supplemented with 25 mM NAG (N-acetylglucosamine) solid medium at 28°C - replicate 1

value: treptomyces ambofaciens ATCC23879

value: WT


title: random_end_hek293t_N25 biol rep 2-5


title: wild type, primary retinal ganglion cells, normal control [Ctrl2]

value: normal


title: IF145 M6

source_name: colon mucosa biopsy

value: 6 Month


title: RNA-seq of WT cells after 30 h growth in MMM (minimum medium mannitol 0.5 %) solid medium at 28°C - replicate 2

value: treptomyces ambofaciens ATCC23878

value: MMM (minimum medium mannitol 0.5 percent) solid medium at 28 degree C


title: wild type, primary retinal ganglion cells, normal control [Ctrl1]


title: random_end_hek293t_N25 biol rep 2-4


title: IF145 BL

value: Baseline


title: GSC_UNC0638

city: Hong Kong

first: Jinyue

last: Liao

address: Room 38016, 1/F Lui Che Woo Clinical Sciences Building

department: Department of Chemical Pathology

institute: The Chinese University of Hong Kong

description: scATAC on GSC treated with G9a inhibitor

data_processing:
Sequencing data were processed using the Bio-Rad ATAC-Seq Analysis Toolkit, which performed FASTQ debarcoding, read trimming, alignment, bead filtration, bead deconvolution, cell filtration and peak calling.
For generation of the fragments file, which contain the start and end genomic coordinates of all aligned sequenced fragments, sorted bam files were further process with “bap-frag” module of BAP
Genome_build: mm10
Supplementary_files_format_and_content: Fragments file

source_name: Cultured germline stem cells (GSCs)

growth_protocol: Oct4+/KIT- germ cells were FACS-sorted and cultured on Matrigel (feeder-free) or on MEF feeder layer in StemPro™-34 SFM supplemented with GDNF, bFGF and EGF. Cells were passged every one week.

extract_protocol:
Cell tagmentation was performed according to SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) User Guide (10000106678, Bio-Rad) and the protocol based on Omni-ATAC was followed (Corces et al. 2017). In brief, washed and pelleted cells were lysed with the Omni-ATAC lysis buffer containing 0.1% NP-40, 0.1% Tween-20, 0.01% digitonin, 10 mM NaCl, 3 mM MgCl2 and 10 mM Tris-HCl pH 7.4 for 3 min on ice. The lysis buffer was diluted with ATAC-Tween buffer that contains 0.1% Tween-20 as a detergent. Nuclei were counted and examined under microscope to ensure successful isolation. Same number of nuclei were subjected to tagmentation with equal ratio of cells/Tn5 transposase to minimize potential batch effect. Nuclei were resuspended in tagmentation mix, buffered with 1×PBS supplemented with 0.1% BSA and agitated on a ThermoMixer for 30 min at 37 °C. Tagmented nuclei were kept on ice before encapsulation.
Tagmented nuclei were loaded onto a ddSEQ Single-Cell Isolator (Bio-Rad). scATAC-Seq libraries were prepared using the SureCell ATAC-Seq Library Prep Kit (17004620, Bio-Rad) and SureCell ATAC-Seq Index Kit (12009360, Bio-Rad). Bead barcoding and sample indexing were performed with PCR amplification as follows: 37 °C for 30 min, 85 °C for 10 min, 72 °C for 5 min, 98 °C for 30 s, eight cycles of 98 °C for 10 s, 55 °C for 30 s and 72 °C for 60 s, and a single 72 °C extension for 5 min to finish. Emulsions were broken and products were cleaned up using Ampure XP beads. Barcoded amplicons were further amplified for 8 cycles. PCR products were purified using Ampure XP beads and quantified on an Agilent Bioanalyzer (G2939BA, Agilent) using the High-Sensitivity DNA kit (5067-4626, Agilent). Libraries were sequenced on HiSeq 2000 with 150 bp paired-end reads.

treatment_protocol: For G9a inhibition, cells were treated with 1uM UNC0638.

tag: strain

tag: cell source

value: Oct4-GFP+ germ cell in vitro culture

value: Postnatal day 5.5

value: Cultured on MEF, treated with UNC0638


title: random_end_hek293t_N25 biol rep 2-3


title: random_end_hek293t_N25 biol rep 2-2


title: shArl4c_2

city: Fukuoka

first: Kana

last: Hasegawa

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

institute: Kyushu University

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: mDE6,  expressing shArl4c, rep2

extract_protocol:
Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols MGIEasy RNA Directional Library Prep Set (MGI).


title: shArl4c_3

source_name: mDE6,  expressing shArl4c, rep3


title: GSC_untreated

description: scATAC on GSC under normal condition

value: Cultured on MEF


title: IF139 M12

value: IF


title: IF149 M6

value: sigmoid colon


title: random_end_hek293t_N25 biol rep 2-0


title: IF141 M6

value: Control


title: IF141 BL


title: GSC_EMT

description: scATAC on GSC undergoing EMT-like process

value: Feeder-free culture


title: shControl_3

source_name: mDE6,  expressing shControl, rep3

value: shControl


title: GSC_ML_ATAC_2

data_processing:
Raw reads were pre-processed with trim-galore for trimming Illumina adaptor sequences.
RNA-Seq: Counts were assigned to genes defined by the Ensembl (release 67) annotation using RSEM.
ATAC-Seq: Reads were processed using the ENCODE ATAC-seq pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags. RNA-seq: text file with TPM value.

extract_protocol:
Genomic DNA was extracted by nuclear isolation followed by Tn5 tagmentation.
ATAC libraries was generated using Vazyme TruePrep DNA Library Prep Kit V2 according Omni-ATAC protocol with modifications.

treatment_protocol: For G9a inhibition, cells were treated with UNC0638 for 48 hours.

value: Cultured on Matrigel at 10ug/cm2


title: random_end_hek293t_N25 biol rep 1-12

description: Polysome profiling of the random-end N25 5'UTR library in HEK293T, replicate 1


title: shArl4c_1

source_name: mDE6,  expressing shArl4c, rep1


title: wild type, primary retinal ganglion cells, normal control [Ctrl3]

value: primary retinal ganglion cell

tag: genotype


title: IF139 M6

tag: sample group


title: random_end_hek293t_N25 biol rep 1-11


title: shControl_2

source_name: mDE6,  expressing shControl, rep2


title: random_end_hek293t_N25 biol rep 1-10


title: RNA-seq of WT cells after 30 h growth in MMM (minimum medium mannitol 0.5 %) solid medium at 28°C - replicate 1

value: treptomyces ambofaciens ATCC23877

value: WT


title: IF141 M12

tag: time point

value: 12 Month


title: shControl_1

source_name: mDE6,  expressing shControl, rep1

tag: cell line


title: GSC_ML_ATAC_1


title: random_end_hek293t_N25 biol rep 2-1


title: IF138 M12


title: GSC_EL_ATAC_1

value: Cultured on Matrigel at 0.1ug/cm2


title: GSC_UNC0638_2

extract_protocol:
RNA was extracted by Qiagen RNeasy Micro Kit according to manufacturer's instructions.
Low input RNA-Seq library preparation was conducted using the modified protocol of Smart-seq2 and Vazyme TruePrep DNA Library Prep Kit V2.

value: Cultured on MEF, treated with UNC0638 at 2uM


title: Con A+MSC 12h rep2

city: Hangzhou

first: Fen

last: Zhang

state: State...

address: Qingchun Road

institute: Zhejiang University

description: Con A+MSC 12h.csv

data_processing:
Illumina Casava1.7 software used for basecalling.
The sequencing data was filtered with SOAPnuke (v1.5.2) and the clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by StringTie (v2.1.2)
Genome_build: GRCm39  The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html)
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL  chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 150 bases reads were generated on DNBSEQ-G400 platform (TSINGKE, China).

value: liver

value: wild type

value: with MSC


title: random_end_hek293t_N25 biol rep 1-8


title: IF138 BL

value: Baseline


title: Con A+MSC 12h rep1

description: Con A+MSC 12h.csv


title: GSC_UNC0638_1

value: Oct4-GFP+ germ cell in vitro culture

value: Postnatal day 5.5

value: Cultured on MEF, treated with UNC0638 at 1uM


title: IF136 M12

value: IF

value: sigmoid colon


title: random_end_hek293t_N25 biol rep 1-7


title: GSC_UNC0638_05

value: Cultured on MEF, treated with UNC0638 at 0.5uM


title: IF136 M6

value: 6 Month


title: GSC_control

value: Cultured on MEF, treated with DMSO (control)


title: random_end_hek293t_N25 biol rep 1-5


title: random_end_hek293t_N25 biol rep 1-6


title: GSC_EL_ATAC_2


title: Con A+MSC 6h rep2

description: Con A+MSC 6h.csv


title: IF136 BL


title: IF139 BL


title: random_end_hek293t_N25 biol rep 1-4


title: Con A+MSC 6h rep1

description: Con A+MSC 6h.csv


title: IF135 M12


title: random_end_hek293t_N25 biol rep 1-9


title: GSC_Oct4_high

value: Cultured on Matrigel at 10ug/cm2, FACS-sorted Oct4-high cells


title: GSC_Oct4_mid

value: Cultured on Matrigel at 10ug/cm2, FACS-sorted Oct4-GFP mid cells


title: random_end_hek293t_N25 biol rep 1-3


title: Con A+MSC 12h rep3

description: Con A+MSC 12h.csv


title: IF138 M6

value: Control


title: IF135 M6


title: Con A 12h rep1

description: Con A 12h.csv

value: without MSC


title: Con A 12h rep2

description: Con A 12h.csv


title: GSC_Oct4_low

value: Cultured on Matrigel at 10ug/cm2, FACS-sorted Oct4-GFP low cells


title: IF135 BL


title: IF133 M12

value: 12 Month


title: random_end_hek293t_N25 biol rep 1-1


title: random_end_hek293t_N25 biol rep 1-2


title: Con A+MSC 6h rep3

description: Con A+MSC 6h.csv

value: liver

value: wild type


title: Con A 6h rep3

description: Con A 6h.csv


title: GSC_ML

value: Cultured on Matrigel at 10ug/cm2


title: random_end_hek293t_N25 biol rep 1-0


title: Con A 6h rep2

description: Con A 6h.csv


title: IF133 M6


title: GSC_D9

value: Oct4-GFP+ germ cell in vitro culture

value: 9 days after transfering from MEF to Matrigel


title: IF133 BL

value: Baseline


title: GSC_EL

value: Postnatal day 5.5

value: Cultured on Matrigel at 0.1ug/cm2


title: GSC_D4

value: 4 days after transfering from MEF to Matrigel


title: defined_end_tcell biol rep 2-12

description: Polysome profiling of the defined-end N50 5'UTR library in T cells, replicate 2

source_name: T cell

value: T cell


title: IF130 M12

value: IF

value: sigmoid colon


title: defined_end_tcell biol rep 2-11


title: defined_end_tcell biol rep 2-10


title: GSC_D0

value: Cultured on MEF


title: H3K36me3_WT

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

institute: CNRS

data_processing:
TRIM ADAPTER SEQUENCES + READS FILTERING AND QUALITY CONTROL  Trim Galore version: 0.4.0 cutadapt 1.8.3 FastQC_v0.11.7 python-2.7.2
READS INDEX   bwa-0.7.15
READS ALIGNMENT   bwa-0.7.15
ALIGNED READS FILTERING  bash
ALIGNED READS FILTERING  samtools-1.3.1
ALIGNED READS SORTING  samtools-1.3.1
CONVERT TO BIGWIG FORMAT  python-3.4.3 / deepTools-2.5.3
QUANTIFICATION MATRIX  python-3.4.3 / deepTools-2.5.3
Genome_build: dm6 r6.13
Supplementary_files_format_and_content: Bigwig files containing chip-seq reads coverage
Supplementary_files_format_and_content: Normalized ChIP-seq reads coverage

organism: Drosophila melanogaster

source_name: Late embryonic derived S2 cells

growth_protocol: Schneider 2 (S2) Drosophila cells were cultured in Schneider Drosophila medium complemented with 10% heat-inactivated FBS and 1% pen-strep

extract_protocol:
Chromatin was digested as described (Lhoumaud et al., 2014). Library preparation was from total nucleosomes or purified nucleosomes (following ChIP using anti-H3K27me3, anti-H3K36me2, anti-H3K36me3 antibodies). ChIP samples were prepared for sequencing using standard Illumina protocols of ChIP sample prep kits from 12 ng of starting precipitated DNA to generate sequencing libraries
ChIP samples were prepared for sequencing using standard Illumina protocols of TruSeq ChIP sample prep kits from 100 ng of starting precipitated DNA to generate sequencing libraries

treatment_protocol: S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis of double-stranded RNAs (dsRNA) specific for Mes-4/NSD, Hypb/dSET2 or luciferase were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 4 days and cells were then harvested.

value: S2 (Schneider 2) cell line

value: WT

tag: passages

tag: antibody

value: ChIP-seq anti-H3K36me3 (Abcam, ab9050)


title: H3K36me2_WT

value: ChIP-seq anti-H3K36me2 (Upstate #07-369)


title: Con A 6h rep1

description: Con A 6h.csv

value: liver

value: without MSC


title: IF130 BL


title: IF130 M6

value: 6 Month


title: defined_end_tcell biol rep 2-9


title: defined_end_tcell biol rep 2-8


title: IF129 M12

value: 12 Month


title: defined_end_tcell biol rep 2-7


title: IF129 M6


title: H3K27me3_M_Rep2

value: Mes-4 KD

value: ChIP-seq anti-H3K27me3 (Upstate #07-449)


title: defined_end_tcell biol rep 2-6


title: H3K27me3_H_Rep2

value: HypB KD


title: defined_end_tcell biol rep 2-5


title: IF129 BL

value: Baseline


title: H3K27me3_WT_Rep2


title: IF128 M12

value: Control


title: IF128 M6


title: H3K27me3_input_Rep1

value: none, ChIP-seq input


title: IF128 BL


title: H3K27me3_H_Rep1


title: defined_end_tcell biol rep 2-2

value: T cell


title: defined_end_tcell biol rep 2-3


title: IF122 M12

value: IF

value: sigmoid colon


title: TBNW_14.1e

city: Oxford

first: David

last: Church

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

hyb_protocol: Affymetrix protocols

scan_protocol: Affymetrix protocols

data_processing: robust multi array (RMA) averaged using R Oligo package

label: biotin

source_name: PR-Cre, Pten fl/fl, Fbxw7 R482Q/+

label_protocol: Affymetrix protocols

growth_protocol: Mice were housed under standard conditions

extract_protocol: Qiagen Rneasy blood and tissue as per manufacturer protocol

treatment_protocol: Untreated

value: uterus at 8 weeks age

value: PR-Cre, Pten fl/fl, Fbxw7 R482Q/+


title: TBNW_1.2g


title: defined_end_tcell biol rep 2-4


title: H3K27me3_input_Rep2

value: S2 (Schneider 2) cell line

value: WT


title: Con A 12h rep3

description: Con A 12h.csv

value: liver

value: wild type


title: H3K27me3_M_Rep1


title: TBNW_23.1c


title: defined_end_tcell biol rep 2-1


title: TBNW_17.2g


title: TBNW_23.1d


title: IF122 M6

value: 6 Month


title: TBNW_15.1e


title: H3K27me3_WT_Rep1


title: defined_end_tcell biol rep 2-0


title: TBNW_1.1g


title: T727_48h_rep3

city: Nankang, Taipei

first: Hung-Che

last: Lin

address: 128 Academia Road, Section 2

country: Taiwan

institute: Academia sinica

data_processing:
Adapter trimming and quality filtering of pair-end raw reads with Fastp version 0.14.1 (fastp  -l 100 -f 0 -F 0 -t 10 -T 10 -i R1.fastq.gz -I R2.fastq.gz)
Mapping and quantification of reads against a reference transcriptome of A. oligospora TWF154 was done with Salmon v0.9.1 (salmon quant -i Ao_TWF154_Salmon_Index -l A --numBootstraps 200 -1 R1_filtered.fastq.gz -2 R2_filtered.fastq.gz
Transcript abundance estimates from Salmon were converted to a Sleuth-compatible format using the Wasabi package version 0.2
Likelihood ratio and Wald tests were performed to establish overall and differential expression for each transcript using the Sleuth program
Supplementary files format and content: Spreedsheet table with all the betas, normalized TPMs, and statistics from LTR tests merged toegher.

organism: Orbilia oligospora

growth_protocol: Fungal mycelium were plated on low nutritent medium (LNM) agar plates for 5 days at 25 °C

extract_protocol:
Total RNA was extracted from lyophilized samples via a Trizol-chloroform based protocol
Library preparation for total RNA samples (Genomic Core Facility, Institute of Molecular Biology, Academia Sinica) were carried out using the Illumina TruSeq stranded mRNA library preparation kit.

treatment_protocol: Approximately 2500 to 3000 C. elegans N2 strain at L4 larval stage were placed on each fungal plate, and hyphal collections were taken at 2, 4, 10, 24, and 48 hours after exposure, with worms being washed for 2 and 4 hours prior to collection for the 2 and 4 hpe samples, respectively. The fungal mycelium was immediately collected with a cell scraper, frozen in liquid nitrogen, and lyophilized.


title: defined_end_tcell biol rep 1-10

description: Polysome profiling of the defined-end N50 5'UTR library in T cells, replicate 1


title: IF122 BL

extract_protocol: oligo-dT


title: T727_48h_rep2


title: IF118 M6


title: defined_end_tcell biol rep 1-9


title: TBNW_15.1f

source_name: PR-Cre, Pten fl/fl

value: PR-Cre, Pten fl/fl


title: defined_end_tcell biol rep 1-8


title: IF118 BL


title: TBNW_16.2i


title: defined_end_tcell biol rep 1-7


title: IF116 M6


title: T727_24h_rep2


title: T727_24h_rep3


title: IF116 BL


title: TBNW_16.2f


title: TBNW_18.2e


title: T727_24h_rep1


title: IF113 M12

value: 12 Month


title: defined_end_tcell biol rep 1-5


title: IF113 M6


title: T727_10h_rep3


title: defined_end_tcell biol rep 1-4


title: TBNW_10.1f


title: T727_10h_rep2


title: TBNW_10.1i


title: IF113 BL


title: defined_end_tcell biol rep 1-3


title: TBPW_8.1h

source_name: PR-Cre, Fbxw7 R482Q/+

value: PR-Cre, Fbxw7 R482Q/+


title: T727_10h_rep1


title: IF111 M12


title: T727_48h_rep1


title: defined_end_tcell biol rep 1-6


title: T727_04h_rep3


title: TBPW_8.2c


title: IF111 M6


title: T727_04h_rep2


title: defined_end_tcell biol rep 1-2


title: TBPW_1.1l


title: IF111 BL


title: defined_end_tcell biol rep 1-1


title: TBPW_1.1k


title: T727_04h_rep1


title: defined_end_tcell biol rep 1-0


title: IF105 M12


title: defined_end_hepg2 biol rep 1-12

description: Polysome profiling of the defined-end N50 5'UTR library in HepG2


title: IF105 M6


title: T727_02h_rep3


title: TBPW_8.1e

source_name: PR-Cre

value: PR-Cre


title: defined_end_hepg2 biol rep 1-10


title: IF105 BL

value: Baseline


title: TBPW_8.2h


title: T727_02h_rep1


title: TBPW_8.2f


title: IF101 M12

value: Control


title: TBPW_8.2g


title: HiC_S2_HYPB_KD_rep2

data_processing:
alignment: Juicer version 1.6; BWA 0.7.17-r1188; openjdk version 1.8.0_302
Assembly: genome_version : dm6-r6.32
Supplementary files format and content: HiC contact matrix (.hic format)

source_name: S2 (Schneider 2)

extract_protocol:
ARIMA HiC Kit
KAPA hyperprep

treatment_protocol: S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for Mes4/NSD, Hypb/dSET2 or luc were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 4 days and cells were then harvested.

value: S2 (Schneider 2)

value: Late embryonic derived S2 cells

value: HypB KD


title: HiC_S2_HYPB_KD_rep1


title: defined_end_hepg2 biol rep 1-9


title: TPRW_1.3h


title: T727_00h_rep2


title: IF101 M6

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.45 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

value: sigmoid colon


title: T727_00h_rep3


title: T727_02h_rep2


title: defined_end_hepg2 biol rep 1-8


title: defined_end_hepg2 biol rep 1-11


title: defined_end_hepg2 biol rep 1-7


title: TBNW_10.1g

value: uterus at 8 weeks age


title: defined_end_hepg2 biol rep 1-6


title: IF101 BL


title: HiC_S2_MES4_KD_rep2

value: Mes4 KD