title: Late bud Rho-, replicate 01, bulk RNA seq

city: Dresden

first: Maximina

last: Yun

address: Fetscherstrasse 105

institute: TUD

data_processing:
basecalling:  Basecalls were done with Illumina bcl2fastq version 2.20.0.
preparation of reference:  Sequence and gene annotation of the axolotl nuclear genome assembly AmexG_v6.0-DD were downloaded from https://www.axolotl-omics.org. The gene models for the HoxA and HoxD genes were replaced with manual curated gene models (personal communication with Sergej Nowoshilow, axolotl-omics.org). Sequence and gene annotation of the mitochondrial genome assembly (NCBI GenBank, AY659991.1) and RNA spike-in control sequences (ERCC, Ambion; for quality control) were included as well.
mapping:  Reads were aligned to the axolotl reference genome AmexG_v6.0-DD using the aligner STAR (v2.7.6a) with AmexG_v6.0-DD splice sites as support (parameters:--outSAMmultNmax 1).
counts per feature:  Uniquely mapped fragments were compared based on their overlap to AmexG_v6.0-DD gene annotations using featureCounts (v2.0.1) to create a table of counts per gene and cell (parameters:  -a AmexG_v6_DD.gtf -s 0 -o bfx1406.AmexG_v6_DD.tsv -Q 1).
Assembly: AmexG_v6.0-DD
Supplementary files format and content: bfx1406.AmexG_v6_DD.tsv.gz is a tab-separated file with the output from FeatureCounts. Each row represents a gene and the columns contain the gene information followed by the sample counts and additional gene information.

extract_protocol:
Blastemas samples were collected from early (11 dpa), mid- (13 dpa), late (15 dpa)- or palette-stage (18 dpa) animals at 48 h following GalNP(Rho) injection. Samples were dissociated in 400 ml of 1x Liberase (Roche) diluted in 0.8x PBS, using mechanical disruption with forceps together with smooth pipetting at room temperature for 30 min. For live/dead staining, suspensions were incubated in 0.8X PBS supplemented with 200 nM CellTrace calcein green AM (Invitrogen) and 12.5 uM SYTOX blue (Invitrogen) at room temperature for 15 min. Subsequently, cell suspensions were filtered through a 70-mm-diameter strainer to generate single-cell suspensions and immediately subjected to FACS. Alive cells were sorted using a FACSAria III equipped with a 100 mm nozzle (BD Biosciences) according to the presence or absence of rhodamine signal using blastemas from vehicle-injected axolotls as negative controls. Single rhodamine+ cells were sorted into 2 ?l of lysis buffer (nuclease-free water, 0.2% Triton X100, 4U/?l RNase Inhibitor).
Processing of the samples for RNA-sequencing was done following a modified Smartseq-2 protocol (https://star-protocols.cell.com/protocols/1595). In brief, samples were thawed on ice and we added 0.5ul of dT-buffer to each sample, containing poly-dT oligos (final concentration of 0.5uM) for capturing mRNAs. Subsequently, we performed reverse transcription and cDNA amplification. Libraries were prepared with the Vazyme TruePrep DNA Library Prep Kit V2 (discontinued) and sequenced on an Illumina NextSeq 500 to an average of 32mio SE75bp fragments/sample.

treatment_protocol: Upper limb amputation; GalNP-rho injection; blastema collection and dissocation at 11, 13, 15 and 18 dpa; FACS separation of rhodamine negative and positive populations

value: d/d

value: Blastema

tag: animal

value: Late-bud

tag: days post_amputation

tag: rhodamine signal

value: Negative

value: Non-senescent


title: Late bud Rho+, replicate 01, bulk RNA seq

status: Public on Jul 10 2023

type: SRA

state: Saxony

department: CRTD

country: Germany

library_source: transcriptomic

molecule: polyA RNA

organism: Ambystoma mexicanum

source_name: Blastema

tag: genotype

tag: tissue

tag: regeneration stage

value: Positive

tag: cell type

value: Senescent


title: DPC17CKO2

city: University Park

first: Camilla

middle: H. K.

last: Hughes

state: PA

address: 439 Shortlidge Rd

department: Animal Science

country: USA

institute: Penn State University

data_processing:
Data were analyzed using the GenPipes pipeline, version 4.3.0 (https://pubmed.ncbi.nlm.nih.gov/31185495/) using default settings, with Ensembl v.102 annotation.
Trimming was performed with trimmomatic.
Reads were aligned using STAR.
Raw count data was obtained using HTseq.
Raw count data were analyzed in DEseq2.
Assembly: GRCm38
Supplementary files format and content: Raw count data as txt, file name CountMatrixSFAMH_raw.txt.
Supplementary files format and content: DEseq2 results in Excel docs, one document for each relevant comparison, file names: Data_S1_ED17_5_con_vs_cko.xlsx; Data_S2_PND1_con_vs_cko.xlsx; Data_S3_PND4_con_vs_cko.xlsx; Data_S4_CON_ED17_5_vs_PND1.xlsx; Data_S5_CON_PND1_vs_PND4.xlsx; Data_S6_CKO_ED17_5_vs_PND1.xlsx; Data_S7_CKO_PND1_vs_PND4.

organism: Mus musculus

source_name: Whole ovary

extract_protocol:
RNA was isolated from whole ovaries using the Arcturus PicoPure RNA Isolation Kit (Thermo), according to the manufacturer’s protocol. Following isolation, ovaries from 3-5 PND1 or PND4 or 5 ED17.5 mice were pooled together within each age and genotype group and RNA was further purified and DNase-treated using the RNA Clean & Concentrator Kit (Zymo Research), also according to the manufacturer’s protocol. RNA purity was assessed by Nanodrop and all samples had absorbance ratio of A260/280 >1.8 and A260/230 > 1.1, with all samples but two having A260/230 > 1.7. RNA quality and quality were assessed on a Biorad experion according to the manufacturers’ protocol and all samples had an RQI > 8.0, indicating high RNA quality.
An RNA input of 100 ng was used for library construction. First, mRNA was separated using oligo-dT based purification, using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). This purified mRNA was used directly as input for the Library construction with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), also conducted according to the manufacturer’s protocol.

value: Whole ovary

value: whole ovary (mixed)

value: CKO

tag: age


title: Lrrc10 KO SH-2

city: La Jolla

first: Rebecca

middle: J.

last: Salamon

state: CA

address: 9500 Gilman Drive

department: Pediatrics

institute: University of California, San Diego

description: Lrrc10 KO SH-2

data_processing:
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files of reads (ranging ~18-28Mil per sample) and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Cutadapt (Version 3.4) was used to trim adapter sequences, remove unpaired reads, and remove reads less than 36 nucleotides. The cut reads were checked for quality and adapter removal using FastQC.
Reads were aligned to the GRCm39 mouse genome using HiSAT2 (Version 2.2.1)
Gene-level counts were generated using RSEM (Version 1.1.17)
Differential gene expression analysis was performed DESeq2
Assembly: GRCm39
Supplementary files format and content: RSEM expected gene counts (txt)
Supplementary files format and content: TPM gene counts (xslx)

molecule: total RNA

source_name: full heart ventricle

extract_protocol:
Sex-balanced groups were collected at 7 days post-surgery (Sham or MI), hearts were harvested, full ventricles (above and below MI ligation) were isolated, and immediately homogenized in Trizol (Invitrogen) according to the manufacturer's protocol. Mouse tissue samples suspended in TRIzol were submitted to the University of Wisconsin Biotechnology Center (UWBC) Gene Expression Center (Research Resource Identifier - RRID:SCR_017757) for RNA extraction. Total RNA was purified following the recommendations of the Qiagen RNeasy Mini (Qiagen, Hilden, Germany) procedure, which included on-column DNase treatment.
Total RNA was used as input material and libraries were prepared by following the SMARTer Stranded Total RNA Sample Prep Kit – HI Mammalian user manual (Takara Bio USA, Mountain View, CA, USA).

value: full heart ventricle

value: Lrrc10 KO

tag: treatment

value: Sham


title: Late bud Rho+, replicate 02, bulk RNA seq


title: DPC17CKO1


title: 5274-MP-12

city: Nashville

first: Mary

last: Philip

state: TN

address: 777 PRB, 2220 Pierce Ave

department: Medicine

institute: Vanderbilt University Medical Center

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in ListeraTAG-infected mice, rep 3

data_processing:
The quality of the sequenced reads was assessed with FastQC and QoRTs.
Sequenced reads were aligned with default parameters to the mouse reference genome (GRCm38.p6) using STAR v2.7.6a.
Gene expression estimates were obtained with featureCounts v2.0.1 using composite gene models from Gencode vM25
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include raw abundance values for each sample as obtained from featureCounts

source_name: Spleen

extract_protocol:
5,000 cells were sorted directly into Trizol LS and frozen. Total RNA was extraced from sorted cells using the Rneasy Micro kit (Qiagen)and amplified using the SMART-Seq v4 UltraLow Input RNA Kit (Clontech).
Libraries were prepared using NEBNext polyA mRNA sample kits (NEB).

value: Spleen

tag: source


title: WT SH-4

description: WT SH-4

value: Lrrc10 WT


title: WT MI-1

description: WT MI-1

value: MI


title: WT MI-2

description: WT MI-2


title: PR100-FLAG-Replicate2

city: London

first: Adrian

last: Isaacs

address: Cruciform Building, Gower Street

department: Neurodegenerative Diseases

country: United Kingdom

institute: University College London

description: Crosslinked PR100-FLAG sample, protein-RNA complexes purified using SDS-PAGE and RNA extracted with Proteinase K digest

data_processing:
Multiplexed cDNA libraries were sequenced using Illumina HiSeq, generating 100-nt single-end reads.
Sequenced reads were processed by the iMaps software package (http://icount.biolab.si/), and de-multiplexed into individual libraries based on their experimental barcodes. Unique molecular identifier nucleotides were used to distinguish and collapse PCR duplicates. The barcode sequences and adaptors were removed from the 5′ and 3′ ends.
Trimmed sequences were mapped to the human genome build (GRCh38, Gencode version 27) with STAR aligner allowing two mismatches (Langmead and Salzberg, 2012). Uniquely mapping reads were kept, and the preceding aligned nucleotide was assigned as the DPR crosslinked site.
Significant crosslink sites were determined by the iCount False Discovery Rate (<0.05) algorithm by weighing the enrichment of crosslinks versus shuffled random positions (https://github.com/tomazc/iCount).
For subsequent analysis, we set a threshold of at least 300,000 unique crosslink events for each PR100-crosslinked sample, and n=4 samples met this threshold (3 purified with SDS-PAGE and 1 purified by immunoprecipitation). We analysed the number of crosslinking events for these PR100-crosslinked samples and their corresponding controls: PR100-non-crosslinked and FLAG-crosslinked.
Assembly: Human genome build (GRCh38, Gencode version 27)
Supplementary files format and content: crosslinks bed, peaks bed, grouped bed, grouped bedgraph, grouped peaks bed

organism: Homo sapiens

growth_protocol: HEK293Ts were cultured in Dulbecco’s modified Eagle medium supplemented with 10% fetal bovine serum, grown at 37°C with 5% CO2 injection, and routinely passaged.

extract_protocol:
RNA was purified using Proteinase K digestion, as previously described (Lee et al., 2021).
The iiCLIP protocol was performed as previously described (Lee et al., 2021). Transiently transfected cells induced for 24 hours were irradiated with UV once with 160 mJ/cm2 using Stratalinker 1800 at 254 nm. Protein-RNA complexes were ligated to a preadenylated, infrared dye labeled L3 adaptor and purified. RNA was isolated using proteinase K digestion and reverse-transcribed into cDNA. cDNA was subsequently purified and circularised.

treatment_protocol: PR100 (Mizielinska et al., 2014) was cloned into pcDNA5 Flp-In Expression vectors with a 3′ triple FLAG tag, generating PR100-3xFLAG (PR100-FLAG) pcDNA5 plasmid, with the 3xFLAG only vector (FLAG) also used as a control. For iiCLIP experiments, HEK293Ts were grown at ≈80% confluency in 10cm plates and transiently transfected with PR100-FLAG, FLAG pcDNA5 plasmids using Lipofectamine 2000. Expression of the constructs was induced by supplementing the media with 150 ng ml-1 of doxycycline for 24 hours.

tag: cell line

tag: iclip antibody

value: Ms FLAG Sigma

tag: group


title: DPC17CON4

value: CON


title: PR100-FLAG-Replicate1


title: PR100-FLAG-Replicate3


title: Late bud Rho-, replicate 02, bulk RNA seq

value: d/d

value: Blastema


title: 5274-MP-11

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in ListeraTAG-infected mice, rep 2


title: PR100-FLAG-Replicate4

description: Crosslinked PR100-FLAG sample, protein-RNA complexes purified using immunoprecipitation with beads and RNA extracted with Proteinase K digest


title: WT SH-3

description: WT SH-3


title: SHRSP Male 14 weeks normal salt, rep1

type: RNA

city: Muenster

first: Anika

last: Witten

address: Domagkstr. 3

department: Institute of Human Genetics, Department Genetic Epidemiology

institute: University of Muenster

description:
32
direct hybridization assay

hyb_protocol: sample hybridization was performed following the WGGEX Direct Hybridization Assay Guide

scan_protocol: BAR standard

data_processing: The data were normalised using quantile normalisation and the different gene expression analysis were performed using the R packages systemsbio and limma

organism: Rattus norvegicus

source_name: Rat 14 weeks old, cardiac tissus, free wall left ventricle

label_protocol: biotin-cRNA was performed using the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip according to the manufacturer's instruction

growth_protocol: All animals were maintained under standard conditions of regular 12h diurnal cycles using an automated light switching device and climate-controlled conditions at a constant room temperature of 22°C. Animals had access to food and water ad libitum. All animal experiments were approved by the responsible local government committee in accordance with the guidelines of the Charité-Universitätsmedizin Berlin and national animal protection guidelines (Landesamt für Gesundheit und Soziales (LAGeSo) Berlin, Germany) for the use of laboratory animals. Male SHRSP and F344 rats were obtained from our colonies at the Forschungseinrichtung für Experimentelle Medizin (FEM), Charité - Universitätsmedizin, Berlin. To develop the consomic strain SHRSP-1F344 (Rat Genome Database (RGD)-ID: SHRSP-Chr 1F344/Rkb), we crossed the SHRSP strain with the F344 strain in accordance with our linkage results and introgressed the whole rat chromosome (RNO)1 from F344 into the SHRSP background.

extract_protocol: Hearts were dissected and arrested in diastole by rinsing in 1 M KCl solution and subsequently blotted dry. The atria were trimmed away and hearts and kidneys were weighed. LV tissue was separated from septum and right ventricle for determination of LV weight. RNA was isolated from the free wall LV by the TRIzol reagent according to the manufacturer's instructions and dissolved in DEPC-treated H2O. The quality and concentration of the purified total RNA were confirmed by spectroscopy.

treatment_protocol: normal salt for 14 weeks

tag: strain

value: Rat SHRSP

value: cardiac, left ventricle

tag: Sex

value: male

value: 14 weeks old


title: Late bud Rho+, replicate 03, bulk RNA seq

value: Late-bud

value: Positive

value: Senescent


title: DPC17CON3

value: Whole ovary

value: whole ovary (mixed)


title: WT SH-2

description: WT SH-2

value: full heart ventricle

value: Sham


title: 5274-MP-10

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in ListeraTAG-infected mice, rep 1

value: Spleen


title: DPC17CON2


title: WT SH-1

description: WT SH-1

value: Lrrc10 WT


title: Late bud Rho-, replicate 03, bulk RNA seq

value: Negative

value: Non-senescent


title: DPC17CON1

value: CON


title: Mid bud Rho+, replicate 01, bulk RNA seq

value: d/d

value: Blastema

value: Mid-bud


title: 5274-MP-17

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in ListeraTAG-infected mice, rep 2


title: Mid bud Rho-, replicate 01, bulk RNA seq


title: shSrebf2.Trm.Kidney.d14#2

first: Miguel

last: Reina-Campos

state: California

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Aligned with STAR 2.5.4a to mouse genome
Gene-level quantification calculated by featureCounts
Assembly: mm10
Supplementary files format and content: .tsv file of gene counts by samples matrix

source_name: kidney

extract_protocol:
Ultra-low-input RNA Seq was performed on sort purified cells, polyadenylated mRNA was converted to cDNA
Illumina adapters were added and product was PCR amplified for sequencing

value: kidney

value: P14 CD8 T cell


title: shSrebf2.Trm.Kidney.d14#1


title: 5274-MP-16

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in ListeraTAG-infected mice, rep 1


title: 5274-MP-15

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in ListeraTAG-infected mice, rep 3


title: 5274-MP-13

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in ListeraTAG-infected mice, rep 1


title: shCD19.Trm.Kidney.d14#1


title: Mid bud Rho+, replicate 02, bulk RNA seq


title: Mid bud Rho-, replicate 02, bulk RNA seq


title: 5274-MP-14

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in ListeraTAG-infected mice, rep 2


title: shSrebf2.Trm.Gut.d14#2

source_name: small intestine

value: small intestine


title: 5274-MP-18

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in ListeraTAG-infected mice, rep 3


title: shSrebf2.Trm.Gut.d14#1


title: Palette Rho+, replicate 01, bulk RNA seq

value: Palette stage

value: Positive


title: Palette Rho-, replicate 01, bulk RNA seq


title: NF-TE_mphMcrs1_RNA_rep2

city: Shanghai

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

country: China

institute: Tongji University

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: --trim-n -q 25,25 -m 75 -a AGATCGGAAGAGC -A AGATCGGAAGAGC.
All RNA-seq data were mapped to the mm10 reference genome after cutadapt using hisat2 with parameters ‘--data-cufflinks --no-discordant --no-mixed --no-unal’.
The TPM (Transcripts Per Million) of genes were obtained by StringTie.
Signal tracks for each sample were generated using the deepTools bamCoverage function with parameters  "--normalizeUsing RPKM --smoothLength 150 --extendReads 150".
Genome_build: mm10
Supplementary_files_format_and_content: *.bw are bigWig files generated using deepTools. *.exp are gene expression files generated by StringTie.

source_name: NF-TE

growth_protocol: BDF1 mice were used as oocyte donors, and the cumulus cells were used as nuclear donors. MII oocytes were enucleated in Chatot-Ziomek-Bavister (CZB) medium containing 5 μg/mL cytochalasin B (CB) by Piezo-driven pipette (PrimeT 130 ech) of an Olympus inverted microscope. The donor cells were transferred into enucleated oocytes by direct injection. The reconstructed oocytes were then cultured in CZB medium for 1h before activation treatment. The cloned constructs were activated by 6 h incubation in 1 mM SrCl2 in Ca2+-free CZB and 5 μg/mL cytochalasin B. Reconstructed embryos were thoroughly washed and cultured in G-1 PLUS medium at 37℃ under 5% CO2.

extract_protocol:
10 blastomeres were used per reaction, and three replicates were performed for each stage. All isolated blastomeres were washed three times in 0.5% BSA in PBS solution to avoid contamination. RNA-seq libraries were generated using the Covaris DNA shearing protocol for Smart-seq sequence library generation. Briefly, RNAs with a polyadenylated tail were captured, reverse transcribed and pre-amplified. DNA was sheared and purified for library construction.
Libraried were generated using the KAPA HyperPrep Kit for the Illumina platform (kk8504), following the manufacturer's instrunctions. Paired-end 150 bp sequencing was performed in NovaSeq (Illumina) platform in Berry Genomics and Novogen.

treatment_protocol: Isolated zygotes were injected with either morpholino oligonucleotides targeted at Max, Mcrs1 or 25-base random control morpholino. All morpholinos were designed and synthesized in Gene Tools (https://www.gene-tools.com/). Injected embryos were cultured in G-1 PLUS medium at 37℃ under 5% CO2. Knocking-down (KD)-efficiency was examined at morula or blastocyst stage. ICM and TE were collected for Smart-seq2.

tag: development stage

value: TE

value: morpholino targeted at Mcrs1

value: Fertilized


title: NF-TE_mphMcrs1_RNA_rep1


title: shCD19.Trm.Gut.d14#2


title: NF-TE_mphMax_RNA_rep2

value: morpholino targeted at Max


title: Palette Rho+, replicate 02, bulk RNA seq

value: Senescent


title: pk_mutant_biol_rep2_tech_rep3

city: Iowa City

first: Krishna Madhav

last: Nukala

state: Iowa

address: 129 E Jefferson

department: Department of Biology

institute: University of Iowa

description: Adult prickle-prickle mutant brains. Third technical replicate of the second biological replicate

hyb_protocol: Hybridization was performed following their standard protocol. See www.roche.com.

scan_protocol: Scanning was performed following their standard protocol. See www.roche.com.

data_processing: Raw data (.pair files) were normalized in ArrayStar software version 16.0.0 (DNASTAR, Inc, Madison, WI). The robust multichip analysis (RMA) algorithm was used for background correction, quantile normalization, and median polish summarization. A Student's t test corrected for multiple testing with the Benjamini and Hochberg false discovery rate (FDR) method was calculated for each experiment.

organism: Drosophila melanogaster

source_name: Brains of prickle-prickle adults

label_protocol: Labeling was performed following their standard protocol. See www.roche.com.

growth_protocol: Flies were maintained at 25°C in malt-based media (Archon Scientific).

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen). Double-stranded cDNA was generated using Double-Stranded cDNA Synthesis Kit with random hexamer (Invitrogen). RNA and cDNA quality were analyzed using Experion RNA and DNA analysis kits (Bio-Rad), respectively.

treatment_protocol: Adult brains were dissected in 1X PBS (pH 7.4)

value: prickle-spiny legs (pk^pk1):spontaneous mutation

tag: phenotype

value: Partially lethal, planar polarity defective

tag: developmental stage

value: Adult

value: Brain


title: Palette Rho-, replicate 02, bulk RNA seq

value: d/d

tag: animal

tag: days post_amputation

value: Negative

value: Non-senescent


title: shCD19.Trm.Kidney.d14#2

value: kidney

tag: genotype


title: Palette Rho+, replicate 03, bulk RNA seq

tag: tissue

value: Blastema

tag: rhodamine signal


title: shSrebf2.Trm.Liver.d14#2

source_name: liver

value: liver

tag: cell type

value: P14 CD8 T cell


title: Palette Rho-, replicate 03, bulk RNA seq

tag: regeneration stage

value: Palette stage


title: Lrrc10 KO SH-1

description: Lrrc10 KO SH-1

value: full heart ventricle

value: Lrrc10 KO

tag: treatment

value: Sham


title: pk_mutant_biol_rep2_tech_rep4

description: Adult prickle-prickle mutant brains. Fourth technical replicate of the second biological replicate


title: pk_mutant_biol_rep2_tech_rep2

description: Adult prickle-prickle mutant brains. Second technical replicate of the second biological replicate


title: pk_mutant_biol_rep1_tech_rep4

description: Adult prickle-prickle mutant brains. Fourth technical replicate of the first biological replicate


title: NF-TE_mphMax_RNA_rep1

value: TE

value: morpholino targeted at Max

value: Fertilized


title: shSrebf2.Trm.Liver.d14#1


title: pk_mutant_biol_rep2_tech_rep1

description: Adult prickle-prickle mutant brains. First technical replicate of the second biological replicate

value: prickle-spiny legs (pk^pk1):spontaneous mutation

value: Partially lethal, planar polarity defective


title: NF-TE_control_RNA_rep2

value: untreated


title: NF-TE_control_RNA_rep1


title: NF-ICM_mphMcrs1_RNA_rep2

source_name: NF-ICM

value: ICM

value: morpholino targeted at Mcrs1


title: shCD19.Trm.Liver.d14#2


title: shCD19.Trm.Liver.d14#1


title: shCD19.Trm.Gut.d14#1

value: small intestine


title: NF-ICM_mphMcrs1_RNA_rep1


title: pk_mutant_biol_rep1_tech_rep3

description: Adult prickle-prickle mutant brains. Third technical replicate of the first biological replicate

value: Adult

value: Brain


title: Early bud Rho+, replicate 02, bulk RNA seq

value: d/d

value: Blastema

value: Early-bud

value: Positive

value: Senescent


title: pk_mutant_biol_rep1_tech_rep2

description: Adult prickle-prickle mutant brains. Second technical replicate of the first biological replicate


title: shSrebf2.Tem.Spleen.d14#2

source_name: spleen

value: spleen

value: P14 CD8 T cell


title: Early bud Rho-, replicate 01, bulk RNA seq

value: Negative

value: Non-senescent


title: Early bud Rho+, replicate 01, bulk RNA seq


title: shSrebf2.Tem.Spleen.d14#1


title: Early bud Rho-, replicate 02, bulk RNA seq


title: shCD19.Tem.Spleen.d14#2


title: Early bud Rho-, replicate 03, bulk RNA seq


title: shCD19.Tem.Spleen.d14#1


title: shSrebf2.Trm.Gut.d7#3


title: pk_mutant_biol_rep1_tech_rep1

description: Adult prickle-prickle mutant brains. First technical replicate of the first biological replicate

value: prickle-spiny legs (pk^pk1):spontaneous mutation


title: cornea-resveratrol-day7-rep2

city: Guangzhou

first: Chenjia

last: Xu

address: Zhongshan Ophthalmic Center

institute: Zhongshan Ophthalmic Center

data_processing:
PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2.
Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cornea

extract_protocol:
RNeasy Fibrous Tissue Mini Kit (QIAGEN, Duesseldorf, Germany) was used to extract RNA from the corneas.
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.

treatment_protocol: SD rats as donors and Wistar rats as recipients to establish allograft corneal transplantation models.Postoperative intraperitoneal injection with resveratrol solution or saline daily until 7 days postoperatively.

value: cornea

value: Wistar

value: resveratrol i.p.


title: NT-TE_RNA_rep6

source_name: NT-TE

value: TE

value: untreated

value: NT


title: Hepatocellular carcinoma cell_48hr_0μM_rep2

city: Zhanjiang

first: z

middle: z

last: p

state: Guangdong

address: wenmingdonglu

department: school of pharmacy

institute: GuangDongMedicialUniversity

description:
Gene expression in PLC/PRF/5 cell treated with 0μM ELT for 48hr
[Con2,normalized]

hyb_protocol: 22.5 uL 2X Hybridization buffer (Agilent) was mixed with the completed labeling reaction to a final volume of 45 uL. The mixture was heated at 100°C for 5 min and chilled immediately to 0°C. 45 uL labeled sample mix was hybridized onto a microarray at 55°C for 20 hrs. The slides were washed at room temperature in 6X SSC with 0.005% Triton X-102 for 10 min, then in 0.1X SSC with 0.005% Triton X-102 for 5 min.

scan_protocol: The slides were scanned on an Agilent G2505C microarray scanner.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The raw intensities were log2 transformed and quantile normalized. After normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 1 out of 4 samples were retained. Multiple probes from the same small RNA (miRNA/tsRNA/pre-miRNA/tRNA/ snoRNA) were averaged and consolidated into one RNA level. Differentially expressed small RNAs between two comparison groups were identified by filtering at the indicated fold change (FC) and statistical significance (p-value) thresholds. Hierarchical clustering, scatter plots, and volcano plots were generated by R software.

source_name: PLC/PRF/5 cell, 48h,concentration of 0μM ELT

label_protocol: For Small RNA Microarray profiling, 100 ng total RNA was firstly dephosphorylated with 3 units T4 polynucleotide kinase (T4 PNK) at 37°C for 40 min to remove both (P) and (cP) chemical groups from the 3' end of RNAs to form a 3-OH end. The reaction was terminated at 70°C for 5 min and cooled immediately to 0°C. 7 uL of DMSO was added and heated to 100°C for 3 min to denature the RNAs and chilled immediately to 0°C. RNA end labeling was performed by adding ligase buffer, BSA, final 50 mM pCp-Cy3, and 15 units T4 RNA ligase in a 28 uL reaction at 16°C overnight.

growth_protocol: The human HCC cell line PLC/PRF/5 was obtained from the Cell Bank of Chinese Academy of Sciences (Shanghai, China), maintained in DMEM medium and supplemented with 10% (v/v) fetal bovine serum in a 37 °C, 5% CO2 and 95% air humidity incubator. Cell passage was carried out when the cell density achieved 80-90%

extract_protocol: The total cellular RNA of each sample was respectively extracted by Trizol and was mixed by three cell culture dishes to minimize errors.RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity (quality) was assessed by Bioanalyzer 2100 or denaturing gel electrophoresis.

treatment_protocol: PLC/PRF/5 cell was seeded in cell culture dish and then cultured for 12 h. Different concentrations of ELT were then added and incubations continued for 48 h.

value: liver tumor

tag: gender

value: female

value: 0μM ELT


title: NT-TE_RNA_rep5


title: NF-ICM_mphMax_RNA_rep1

value: ICM

value: morpholino targeted at Max

value: Fertilized


title: NF-ICM_control_RNA_rep1


title: Hepatocellular carcinoma cell_48hr_8μM_rep1

description:
Gene expression in PLC/PRF/5 cell treated with 8μM ELT for 48hr
[E4-1,normalized]

source_name: PLC/PRF/5 cell, 48h,concentration of 8μM ELT

value: 8μM ELT


title: NF-ICM_control_RNA_rep2


title: Hepatocellular carcinoma cell_48hr_0μM_rep1

description:
Gene expression in PLC/PRF/5 cell treated with 0μM ELT for 48hr
[Con1,normalized]


title: Early bud Rho+, replicate 03, bulk RNA seq

value: d/d

value: Blastema

value: Early-bud

value: Positive

value: Senescent


title: cornea-resveratrol-day7-rep1

value: cornea

value: Wistar


title: Hepatocellular carcinoma cell_48hr_8μM_rep2

description:
Gene expression in PLC/PRF/5 cell treated with 8μM ELT for 48hr
[E4-2,normalized]


title: 10-day-fructose-fermentation biol rep 3

city: Fuzhou

first: Long-Bin

last: zhang

state: Fujian

address: Jianping Road

department: College of Biological Science and Engineering

institute: Fuzhou University

description: Sample 12

data_processing:
Basecalls performed using Illumina CASAVA1.7 software.
Fragments blasted using HISAT2 software.
The raw reads were filtered and normalized as fragments per kilobase of exon per million fragments mapped (FPKM) using the software program Cufflinks.
Genes were annotated by mapping to the C.unicolor 87613 genome.
The DAVID tool (https://david.ncifcrf.gov/) was used for the enrichment of DEGs into different categories according to their annotated function
Assembly: The reference sequences are available at Sequence Read Archive (SRA) GenBank database, deposited under the Accession Number No. SRR23097119 (BioProject: PRJNA924695).
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

organism: Cerrena unicolor

source_name: strain

growth_protocol: C.unicolor 87613 were incubated in a potato dextrose medium with altered carbon sources and shaked at 200 rpm, 30 ℃ for 6 or 10 days.

extract_protocol:
Total RNA was extracted from three replicate cultures under each treatment, using the RNAiso Plus Reagent (TaKaRa, Dalian, China), according to the manufacturer’s instructions.
For high-throughput sequencing, the extracted RNA was used for library construction with the NEBNext Ultra RNA library Prep kit (NEB, Ipswich, Massachusetts, USA), as per manufacturer’s recommendations.

treatment_protocol: The carbon source was alternative with either glucose or fructose.

value: strain

tag: cell line

value: strain 87613

value: hyphae

value: WT

value: incubated with fructose as single carbon source for 10 days


title: 6-day-fructose-fermentation biol rep 3

description: Sample 9

value: incubated with fructose as single carbon source for 6 days


title: 6-day-fructose-fermentation biol rep 1

description: Sample 7


title: 10-day-fructose-fermentation biol rep 2

description: Sample 11


title: 10-day-fructose-fermentation biol rep 1

description: Sample 10


title: cornea-resveratrol-day7-rep3

value: resveratrol i.p.


title: 10-day-Glucose-fermentation biol rep 3

description: Sample 6

value: incubated with glucose as single carbon source for 10 days


title: 6-day-fructose-fermentation biol rep 2

description: Sample 8


title: NT-TE_RNA_rep4

value: TE

value: untreated

value: NT


title: cornea-control-day7-rep3

value: saline i.p.


title: shSrebf2.Trm.Gut.d7#1

value: small intestine

value: P14 CD8 T cell


title: shCD19.Trm.Gut.d7#3


title: 10-day-Glucose-fermentation biol rep 2

description: Sample 5


title: shSrebf2.Trm.Gut.d7#2


title: NT-TE_RNA_rep3


title: cornea-control-day7-rep2


title: 10-day-Glucose-fermentation biol rep 1

description: Sample 4


title: shCD19.Trm.Gut.d7#1


title: 6-day-Glucose-fermentation biol rep 3

description: Sample 3

value: incubated with glucose as single carbon source for 6 days


title: shCD19.Trm.Gut.d7#2


title: shSrebf2.Trm.Kidney.d7#2

value: kidney


title: cornea-control-day7-rep1

value: cornea

value: Wistar


title: shSrebf2.Trm.Kidney.d7#1


title: 6-day-Glucose-fermentation biol rep 1

description: Sample 1

value: strain

value: strain 87613


title: 6-day-Glucose-fermentation biol rep 2

description: Sample 2

value: hyphae

value: WT


title: shCD19.Trm.Kidney.d7#1


title: gestational day 19.5, 3

city: Stillwater,

first: Khursheed

last: Iqbal

state: OK

address: 310 N Monroe St,

institute: Oklahoma state university

library_source: transcriptomic single cell

data_processing:
The Cell Ranger-atac Single-nuclei Software Suite was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. Downstream processing was done using Signac (version 1.1.1)
Assembly: rn6
Supplementary files format and content: filtered_peak_bc_matrix.h5, singlecell.csv, fragments.tsv.gz, fragments.tsv.gz.tbi, barcodes.tsv,  matrix.mtx,  peaks.bed

source_name: Uterine tissue

extract_protocol: Rats timed pregnancies were obtained by mating adult males (>10 weeks of age) and adult females (8-12 weeks of age). Uterine-placental interface tissue (also called metrial glands) were dissected from gd 15.5 (n=3 pregnancies) and 19.5 rat placentation sites (n= 3pregnancies) and put in ice cold Hank’s balanced salt solution (HBSS). Tissues were minced into fine pieces with a razor blade and digested in Dispase II (1.25 units/mL), 0.4 mg/mL collagenase IV , and DNase I (80 units/mL,) in HBSS for 30 min. Red blood cells were lysed using ACK lysis buffer. Samples were washed with HBSS supplemented with 2% fetal bovine serum (FBS, Thermo-Fisher), and DNase1  and passed through a 100 ìm cell strainer. Following enzymatic digestion, cell debris was removed using MACS Debris Removal Solution. Cells were isolated from gd 15.5 and 19.5 uterine-placental interface tissue as described above, and nuclei were isolated from the cell suspension according to the 10X Genomics Nuc  lei Isolation protocol. Briefly, cells were washed with HBSS supplemented with 2% FBS (Thermo-Fisher) and cell number determined. Approximately 500,000 cells were centrifuged, and 100 mL 10X Genomics Nuclei Isolation Lysis Buffer was added. The suspension was incubated for 3 min, then 10X Genomics Nuclei Isolation Wash Buffer was added. Cells were passed through a 40 mm cell strainer and centrifuged. Cells were resuspended in 50 mL chilled 10X Genomics Nuclei Isolation Buffer. Single nuclei were captured using the Chromium Controller into 10X barcoded gel beads. Libraries were generated using Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 (10X Genomics) and sequenced in a NovaSeq6000 sequencer at the KUMC Genome Sequencing Core.

value: Uterine tissue

value: gestational day 19.5


title: gestational day 19.5, 1


title: gestational day 15.5, 3

value: gestational day 15.5


title: gestational day 19.5, 2


title: gestational day 15.5, 2


title: shSrebf2.Te.Spleen.d7#2

value: spleen


title: NT-TE_RNA_rep1

value: TE

value: untreated


title: NT-ICM_RNA_rep6

source_name: NT-ICM

value: ICM

value: NT


title: NT-TE_RNA_rep2


title: NT-ICM_RNA_rep5


title: NT-ICM_RNA_rep2


title: NT-ICM_RNA_rep4


title: NT-ICM_RNA_rep3


title: gestational day 15.5, 1


title: shCD19.Trm.Kidney.d7#2

value: P14 CD8 T cell


title: shSrebf2.Te.Spleen.d7#1


title: young_shoots_myc2_mRNA_seq_rep3

city: Wuhan

first: Li

last: Deng

address: Shizishan 1

institute: Huazhong Agricultural University

data_processing:
RNA-seq raw reads were processed using fastp with default parameters. Clean reads were aligned to TAIR10 genome using hisat2 with "--dta-cufﬂinks" parameters. Thereafter, we used SAMtools to filter out sequences with low alignment quality (-q 30). FPKM values were calculated using StringTie with default parameters.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis accession Columbia (Col-0) and myc2 were grown at 22 °C under a 16 h light/8 h dark photoperiod.

extract_protocol:
Total RNA was isolated using the RNeasy Plant Mini Kit (QIAGEN, 74904)
Approximately 1 μg of RNA was used for library preparation using an Illumina TruSeq RNA kit, according to the manufacturer’s instructions.

treatment_protocol: The aerial part of two-week-old seedlings were immediately frozen in liquid nitrogen and stored at -80°C for RNA-seq assay.

value: Shoots of two-week-old seedlings

tag: time

value: two-week-old


title: young_shoots_myc2_mRNA_seq_rep1


title: young_shoots_Col-0_mRNA_seq_rep3

value: Col-0 (wild-type)


title: young_shoots_myc2_mRNA_seq_rep2


title: young_shoots_Col-0_mRNA_seq_rep2


title: NT-Morula_RNA_rep6

source_name: NT-Morula

value: Morula


title: young_shoots_Col-0_mRNA_seq_rep1


title: P5d-1

description: Sort-purified (live CD8+CD90.1+CD44+) 5d tumor-exposed transgenic TCRTAG CD8 T cells isolated and parked in tumor-free B6 mice for 5d, from spleen, rep 1

library_source: genomic

data_processing:
The quality of the sequenced reads was assessed with FastQC.
Reads were aligned to the mouse reference genome (GRCm38.p6) with BWA-backtrack (Heng Li and Durbin 2009). Post-alignment filtering was done with samtools and Picard tools to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates.
Coverage files (BigWig) per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 . Blacklisted genomic regions were excluded (https://sites.google.com/site/anshulkundaje/projects/blacklists).
Assembly: GRCm38.p6
Supplementary files format and content: BigWig files for each sample

molecule: genomic DNA

source_name: Spleen

extract_protocol:
CD8 T cells were FACS-sorted into FCS containing tubes and after sort 10% DMSO were added, mixed and stored at -80°C until all samples were collected. Profiling of Chromatin was performed by ATAC-seq. Cells were thawed and washed in cold PBS and lysed.
After cell lysis, transposition happened at 42ºC for 45 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), material was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5x ratio.

value: Spleen


title: NT-Morula_RNA_rep5


title: P1d-3

description: Sort-purified (live CD8+CD90.1+CD44+) 24h tumor-exposed transgenic TCRTAG CD8 T cells isolated and parked in tumor-free B6 mice for 5d, from spleen, rep 3


title: P1d-2

description: Sort-purified (live CD8+CD90.1+CD44+) 24h tumor-exposed transgenic TCRTAG CD8 T cells isolated and parked in tumor-free B6 mice for 5d, from spleen, rep 2


title: NT-Morula_RNA_rep4


title: shCD19.Te.Spleen.d7#2


title: NT-Morula_RNA_rep3


title: T47D_RBKO_siPRMT5_2

city: Dallas

first: Chang-Ching

last: Lin

state: TX

address: 4554 Glenwick Ln, Apt 2203

department: Harold C. Simmons Comprehensive Cancer Center

institute: UT Southwestern Medical Center

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4).
The trimmed reads were then aligned to the human genome (GRCH38) using STAR (2.7.3a).
The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: MCF-7_RBKO and T47D_RBKO cells were maintained respectively in DMEM and RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Maxwell RSC simply RNA kit (Promega).
mRNA libraries were prepared using TruSeq Stranded mRNA Library prep kit (Illumina).

treatment_protocol: Cells were transfected with a PRMT5 siRNA or control siRNA

value: ER+ breast cancer cells

value: RB1 knockout


title: T47D_RBKO_siPRMT5_1


title: P1d-1

description: Sort-purified (live CD8+CD90.1+CD44+) 24h tumor-exposed transgenic TCRTAG CD8 T cells isolated and parked in tumor-free B6 mice for 5d, from spleen, rep 1


title: 5274-MP-4

description: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in liver tumors, rep 1

source_name: Liver

value: Liver

tag: source


title: P5d-2

description: Sort-purified (live CD8+CD90.1+CD44+) 5d tumor-exposed transgenic TCRTAG CD8 T cells isolated and parked in tumor-free B6 mice for 5d, from spleen, rep 2


title: NT-ICM_RNA_rep1


title: P10d-1

description: Sort-purified (live CD8+CD90.1+CD44+) 10d tumor-exposed transgenic TCRTAG CD8 T cells isolated and parked in tumor-free B6 mice for 5d, from spleen, rep 1


title: T47D_RBKO_siPRMT5_3


title: NT-Morula_RNA_rep2


title: T47D_RBKO_siNG3

value: siNG


title: HT183_sCAD

city: Tucson

first: Yong

last: Liu

state: AZ

address: The University of Arizona

department: Physiology

institute: University of Arizona

data_processing:
Raw sequence reads were trimmed to remove adapter sequence/low quality sequence with Trim Galore for Illumina sequence with pair.
Trimmed sequence reads were mapped to human GRCh38 with STAR. BAM file was generated.
Read counts per gene were generated with htseq-count (parameter settings: --stranded=yes --idattr=gene_id --type=exon --mode=union --format=bam)
Gene differential expression analysis was performed with cuffdiff and BAM files from STAR (parameter settings: -library-norm-method geometric -library-type fr-secondstrand)
Assembly: GRCh38 (hg38)
Supplementary files format and content: Excel file including raw counts for each gene for each sample.

source_name: coronary plaque

extract_protocol:
Total RNA were extracted with TRIzol. Using 20ug glycogen for coprecipation and precipitated overnight at -20°C. About 5ng of total RNA was used for SMART-seq library preparation.
RNA libraries for RNA-seq were prepared using SMART-Seq Stranded Kit following manufacture's protocol for 5ng total RNA input.

tag: disease state

value: sCAD patient

value: coronary plaque


title: HT180_sCAD


title: HT179_sCAD


title: HT185_sCAD


title: NT-Morula_RNA_rep1


title: NT-8cell_RNA_rep6


title: N-6

description: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells from spleen, rep 6


title: T47D_RBKO_siNG2


title: HT177_sCAD


title: N-5

description: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells from spleen, rep 5


title: shCD19.Te.Spleen.d7#1

value: spleen


title: T47D_RBKO_siNG1


title: HT151_sCAD


title: N-4

description: Sort-purified (live CD8+CD90.1+CD44-) transgenic TCRTAG CD8 T cells from spleen, rep 4


title: HT149_sCAD


title: NT-8cell_RNA_rep5


title: MCF-7_RBKO_siPRMT5_3


title: NT-8cell_RNA_rep4


title: MCF-7_RBKO_siPRMT5_2


title: HT113_sCAD


title: NT-8cell_RNA_rep3


title: L5d-3

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 5d post activation in liver tumors, rep 3


title: H275_sCAD


title: L5d-2

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 5d post activation in liver tumors, rep 2


title: NT-8cell_RNA_rep2


title: MCF-7_RBKO_siPRMT5_1


title: NT-8cell_RNA_rep1


title: H255_sCAD


title: L5d-1

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 5d post activation in liver tumors, rep 1


title: H193_sCAD


title: HT103_sCAD


title: L1d-2

description: Sort-purified (live CD8+CD90.1+CD69+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in liver tumors, rep 2


title: L1d-3

description: Sort-purified (live CD8+CD90.1+CD69+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in liver tumors, rep 3


title: L5d-4

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 5d post activation in liver tumors, rep 4


title: MCF-7_RBKO_siNG1


title: H265_sCAD


title: NT-4cell_RNA_rep4


title: NT-4cell_RNA_rep5


title: Pemrametostat3

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4).
The trimmed reads were then aligned to the human genome (GRCH38) using STAR (2.7.3a).
The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package.
RNA splicing analysis was conducted using SUPPA2 and IRFinder.
Assembly: hg38
Supplementary files format and content: CSV file includes events of alternative splicing determined by SUPPA2
Supplementary files format and content: TSV file includes events of intron retention determined by IRFinder

growth_protocol: MCF-7_RBKO cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

treatment_protocol: Cells were treated with DMSO or 500 nM pemrametostat.

value: pemrametostat


title: NT-4cell_RNA_rep2

value: untreated


title: L10d-3

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 10d post activation in liver tumors, rep 3


title: HT158_ACS

value: ACS patient


title: HT184_ACS


title: Pemrametostat1


title: MCF-7_RBKO_siNG2


title: HT154_ACS


title: L10d-2

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 10d post activation in liver tumors, rep 2


title: MCF-7_RBKO_siNG3


title: Vehicle3

value: DMSO


title: L10d-1

description: Sort-purified (live CD8+CD90.1+CD44+) transgenic TCRTAG CD8 T cells isolated 10d post activation in liver tumors, rep 1


title: NT-4cell_RNA_rep1

value: NT


title: L6-3

description: L6-3: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in liver tumors, rep 3

data_processing:
The quality of the sequenced reads was assessed with FastQC.
Reads were aligned to the mouse reference genome (GRCm38.p6) with BWA-backtrack (Heng Li and Durbin 2009). Post-alignment filtering was done with samtools and Picard tools to remove unmapped reads, improperly paired reads, non-unique reads, and duplicates. To identify regions of open chromatin represented by enrichments of reads, peak calling was performed with MACS2. For every replicate, the narrowpeak results of MACS2 were used after filtering for adjusted p-values smaller than 0.01. Only peaks called in at least two replicates of each condition were retained and a consensus peak set was produced with DiffBind v3.0.13.
Coverage files (BigWig) per replicate normalized for differences in sequencing depths between the different samples were generated with bamCoverage of the deepTools suite (Ramìrez et al. 2016) using the following parameters: -bs 10 --normalizeUsing RPGC --effectiveGenomeSize 2652783500 --ignoreForNormalization chrX chrY --ignoreDuplicates --minFragmentLength 40 . Blacklisted genomic regions were excluded (https://sites.google.com/site/anshulkundaje/projects/blacklists). Merged coverage files were created with UCSC bigWigMerge.
Assembly: GRCm38.p6
Supplementary files format and content: BigWig files for each sample


title: HT153_ACS


title: NT-l2cell_RNA_rep5


title: NT-l2cell_RNA_rep6


title: Vehicle2


title: HT148_ACS


title: Vehicle1


title: NF-ICM_mphMax_RNA_rep2

value: ICM

value: morpholino targeted at Max

value: Fertilized


title: NT-4cell_RNA_rep3


title: Pemrametostat2


title: L1d-1

description: Sort-purified (live CD8+CD90.1+CD69+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in liver tumors, rep 1


title: L6-2

description: L6-2: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in liver tumors, rep 2


title: NT-l2cell_RNA_rep4


title: HT147_ACS


title: HT146_ACS


title: Input_DMSO

data_processing:
Aligning sequencing reads using Bowtie2 with default parameters.
Peaks were called using Model-based Analysis of ChIP-Seq (MACS) software.
Assembly: hg19
Supplementary files format and content: bigWig files for each sample
Supplementary files format and content: Peak calls (except for input samples)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quencing and cell lysis, chromatin was sonicated using a microtip sonicator (Branson 150) to an average fragment size of 100-300 bp.
Kapa HyperPlus Kit (Roche).

tag: chip antibody

value: input


title: L6-1

description: L6-1: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in liver tumors, rep 1


title: L12-3

description: L12-3: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in liver tumors, rep 3


title: NT-l2cell_RNA_rep2

tag: development stage


title: HT145_ACS


title: pSer2 Pol II_Pem_1

value: Abcam (ab5095)


title: L12-2

description: L12-2: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in liver tumors, rep 2


title: HT94_ACS


title: NT-l2cell_RNA_rep1


title: NT-e2cell_RNA_rep6


title: HT114_ACS


title: E6-3

description: E6-3: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in ListeraTAG-infected mice, rep 3

value: Spleen


title: HT112_ACS


title: HT111_ACS


title: pSer2 Pol II_DMSO_2

value: ER+ breast cancer cells

value: RB1 knockout


title: NT-l2cell_RNA_rep3


title: L12-1

description: L12-1: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in liver tumors, rep 1

value: Liver


title: HT109_ACS


title: NT-e2cell_RNA_rep4


title: pSer2 Pol II_DMSO_1


title: E6-2

description: E6-2: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in ListeraTAG-infected mice, rep 2


title: NT-e2cell_RNA_rep5


title: NT-e2cell_RNA_rep3


title: E24-3

description: E24-3: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in ListeraTAG-infected mice, rep 3


title: E6-1

description: E6-1: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 6h post activation in ListeraTAG-infected mice, rep 1


title: pSer2 Pol II_Pem_2


title: HT107_ACS


title: E24-2

description: E24-2: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in ListeraTAG-infected mice, rep 2


title: T47D_RBKO3

growth_protocol: MCF-7 and T47D cells were maintained respectively in DMEM and RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using Maxwell RSC simply RNA kit (Promega).
mRNA libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (NEW ENGLAND BioLabs).


title: NT-e2cell_RNA_rep1


title: NT-14h_RNA_rep6


title: T47D_RBKO2


title: E24-1

description: E24-1: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 24h post activation in ListeraTAG-infected mice, rep 1


title: NT-14h_RNA_rep5


title: NT-e2cell_RNA_rep2


title: E12-2

description: E12-2: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in ListeraTAG-infected mice, rep 2


title: T47D_WT3

value: RB1 WT


title: NT-14h_RNA_rep4


title: E12-3

description: E12-3: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in ListeraTAG-infected mice, rep 3


title: T47D_WT2


title: Input_Pem


title: MC38_til2

description: Biological replicate 2

data_processing:
Reads were aligned to the mm10 genome using cellranger count and final data matrices for all samples were generated with cellranger aggr.
Assembly: mm10
Supplementary files format and content: .h5 processed file contain the filtered feature bc gene expression aggregrate of all samples, including P14 from the tumor (til) and spleen profiled in two independent biological replicates.

source_name: tumor

extract_protocol:
Tumors were minced into small pieces and then incubated in RPMI with 1.2 mg/mL HEPES, 292 µ/mL L-glutamine, 1 mM MgCl2, 1 mM CaCl2, 5% fetal bovine serum, and 100 U/mL collagenase (Worthington) at 37°C for 30 min. After enzymatic incubations tumors were further dissociated over a 70-μm nylon cell strainer (Falcon). Lymphocytes were separated on a 44%/67% Percoll density gradient. Spleens and lymph nodes were processed with the frosted ends of microscope slides. Red blood cells were lysed with ACK buffer (140 mM NH4Cl and 17 mM Tris-base, pH 7.4).
P14 from tumors and spleens of mice were profiled by scRNAseq in two independent repeats. For each repeat, 2 x 105 P14 cells coming from pooled spleens and MC38-GP33-41 tumors from three independent mice were sorted into T cell culture media. Samples were spun down at 500 rcf for 5 minutes and then resuspended in PBS + 0.04% (w/v) bovine serum albumin. Samples were then loaded into Chromium Chip B (10X Genomics) and partitioned into Gel Bead In-Emulsions (GEMs) in a chromium controller (10X) Genomics). Single cell RNA libraries were generated according to the Chromium Single Cell 3’ Reagent Kits v3 User Guide and sequenced on a HiSeq 4000.

value: tumor

value: P14 CD8 T cells


title: T47D_WT1


title: E12-1

description: E12-1: Sort-purified (live CD8+CD90.1+CFSEhi) transgenic TCRTAG CD8 T cells isolated 12h post activation in ListeraTAG-infected mice, rep 1


title: Colon DSS and mutant E.coli vs WT E.coli

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

institute: Charité Universitätsmedizin

hyb_protocol: Whole mouse genome 4x44k microarrays were done according to the supplier’s protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5 µm resolution and extended range (XDR) using a DNA microarray laser scanner (Agilent Technologies)

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.11.5.1.1, Agilent). Data was background-corrected and intra-array normalized using R package limma.

source_name: colon epithelial cells, DSS, mutant infection

label_protocol: RNA labeling was performed with the Quick-Amp Labeling Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: All animals were maintained in autoclaved micro-isolator cages and provided with sterile drinking water or DSS as indicated and chow ad libitum. Male, 6–8 week-old mice were used for this study.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method according the manufacturer´s protocol.

treatment_protocol: Enterobacteriaceae-free , Axin2CreErt2/Rosa26-tdTomato mice were treated for 48 h with 2 mg/ml streptomycin in drinking water. Streptomycin was replaced by drinking water 24 h before infection. Mice were infected with 1x 109 CFU of M1/5 E. coli, a pks+ E.coli strain and its isogenic Δ clbR mutant via oral gavage. At 5 days post-infection, mice were treated with 2% DSS as drinking water for 7 days. After DSS treatment, mice were changed to normal drinking water and allowed to recover. Mice were treated with Tamoxifen (Sigma) by  intraperitoneally injection into mice (4 mg/25 g bodyweight, diluted in 200 µl corn oil) after DSS treatment to induce TdTomato expression. Mice were allowed to recover for 4 weeks.

tag: agent

value: DSS and E.coli mutant infection

source_name: colon epithelial cells, DSS, WT infection

value: DSS and E.coli WT infection


title: Colon WT vs Rspo KI

source_name: colon epithelial cells WT

value: WT

source_name: colon epithelial cells Rspo KI

value: Rspo Knock-in


title: GUIDE seq enEbPO1

first: chen

last: peng

address: College of Life Sciences, Wuhan University

department: College of Life Sciences

institute: Wuhan University

data_processing:
Thecleandatawasgeneratedbytrimminglowqualitybasesatbothendsofreadandremoveshortfragments,thisworkwascompletedbysequencingcompany
ForGUIDEseq,thesequencingdatawasprocessedbycorrespondingsoftware,Links to software and other resources for computational analysis of GUIDE-seq data will be made available at http:// jounglab.org/guideseq.the human genome version used in the analysis is hg19;

source_name: embryonic kidney

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to GUIDE-seq methods. Briefly, Genomic DNA was sheared to length of about 250 bp, added Y adapter, and amplified by two rounds of nested anchored PCR. The last PCR products were GUIDE-seq libraries and sent to the company for sequencing using an Illumina sequencer

value: embryonic kidney

value: Epithelial cells

value: wild type

value: Guide seq


title: GUIDE seq enEbNLRC4


title: GUIDE seq enEbB2M


title: GUIDE seq enEbCLIC4


title: GUIDE seq enEbCTLA4


title: NT-14h_RNA_rep1

value: untreated

value: NT


title: NT-14h_RNA_rep2


title: MC38_til1

description: Biological replicate 1


title: Colon DSS and WT E.coli vs. mutant E.coli


title: GUIDE seq enEbDNMT1


title: MCF-7_RBKO3


title: Colon Rspo KI vs WT


title: NT-6h_RNA_rep6


title: MCF-7_RBKO2


title: MC38_spl2

description: Biological replicate 2

source_name: spleen

value: spleen


title: T47D_RBKO1

value: ER+ breast cancer cells


title: NT-14h_RNA_rep3


title: NT-6h_RNA_rep5


title: MC38_spl1

description: Biological replicate 1


title: MCF-7_RBKO1

value: RB1 knockout


title: NT-6h_RNA_rep4


title: MCF-7_WT3


title: GUIDE seq lbCTLA4


title: GUIDE seq lbB2M


title: NT-6h_RNA_rep3


title: MCF-7_WT2


title: GUIDE seq lbPO1


title: NT-6h_RNA_rep1


title: GUIDE seq lbCLIC4


title: NT-6h_RNA_rep2


title: MCF-7_WT1


title: GUIDE seq lbNLRC4


title: GUIDE seq lbDNMT1


title: cumulus cell-CC_RNA_rep3

source_name: cumulus cell-CC

value: CC

value: cumulus cell


title: GUIDE seq enEbsite5


title: cumulus cell-CC_RNA_rep2


title: RNAseq (polyA RNA) of vph1∆ cells grown in SDC biol. rep. #2

city: South San Francisco

first: Voytek

last: Okreglak

address: 1170 Veterans Blvd

institute: Calico Life Sciences

data_processing:
Reads generated from the Illumina Nova-seq and were demultiplexed with bcl2fastq based on the barcode sequence of each sample. Reads were pseudo-aligned and then quantified using Salmon by deploying the mapping based mode using a Salmon generated index.
RNA-seq data was quantified using Salmon-0.8.1 with two separate annotation indices: •open-reading frames (ORFs) as defined by SGD‘complex transcriptome’ index created by aggregating ORFs, their longest annotated UTRs + all non-canonical and non- coding transcripts pulled from SGD. Salmon was run using the ‘quant’ command with the following settings:‘libType’: ‘ISR’, ‘useVBOpt’: [], ‘numBootstraps’: ‘30’, and 549 ‘incompatPrior’: ‘0’. 550 Salmon quantification was prepared and processed for differential expression analysis using Tximport . Differential gene expression analysis was performed with DESEQ2 using a Wald test
Assembly: sacCer3
Supplementary files format and content: tables with TPM values for each gene in all samples (polyA_TPMs.txt). One file per sample.

organism: Saccharomyces cerevisiae

source_name: vph1∆::NatMX SAL1+ HAP1+ CAT5(91M) MIP1(661T) MKT1(30G) RME1(INS-308A) TAO3(1493Q)

growth_protocol: Samples were grown at room-temp  in synthetic defined medium containing yeast nitrogen base, dextrose and amino acids to a low (0.05 OD600) to minimize confounding effects of media acidification

extract_protocol:
Duplicate cultures on two separate days (4 replicates total) were grown in the appropriate media to OD600=0.05, harvested by filtration onto MF Membrane filters (Milipore, HAWP02500) and snap frozen in liquid nitrogen. Frozen cells were processed as described in76. Briefly, cells were resuspended in 200 µL of Lysis buffer (10 mM Tris [pH 8.0], 0.5% SDS, 10 mM EDTA) and separated from the filter disks. 200 µL Acid Phenol [pH 4.3] was added and the samples were vortexed for 30 s. The samples were incubated at 65°C for 1 hr in a Thermomixer with intermittent shaking (2000 RPM for 1 min every 15 min). 400 µL of 100% ethanol was added and the RNA was purified using the Direct-zol RNA Miniprep Plus kit (Zymo research) according to the manufacturer’s protocol including the DNase digestion step.
No-selection libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit (#PNE7760L, Illumina) without the polyA selection step. Given the concentration of RNA is much higher for total unselected RNA,10 ng of total RNA was input and the fragmentation time was increased to 20 minutes (vs. 15 min standard) to ensure efficient fragmentation of rRNA and proceeded with the vendor’s protocol.

value: parental line is DHY211 (see Harvey et al. 2018)

value: budding yeast

value: vph1{delta}::NatMX SAL1+ HAP1+ CAT5(91M) MIP1(661T) MKT1(30G) RME1(INS-308A) TAO3(1493Q)


title: ROI11 tail vein retroperitoneal

city: Boston

first: April

last: Apfelbaum

state: MA

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

description:
DSP-1012550008322-H-A12
ROI11 from tail vein injection-derived CHLA10 retroperitoneal tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx

data_processing:
*library strategy: Nanostring GeoMx Seq Code
GeoMx DSP NGS pipeline (version 2.3.4).
FASTQ files generated for each lane (L001  L002)  paired (R1 R2).
parameters: dcc-metadata = false
save-interim-files = false
quality-trim-score = 20
2color-trimming = True
adapter1 = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2 = AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length = 10
adapter-trim-max-mismatch = 3
barcode-max-mismatch = 1
stitching-max-mismatch = 2
dedup-hd = 1
threads = 4
Assembly: NA
Supplementary files format and content: GeoMx NGS pipeline output including sample annotations, quality control, and Q3 normalized target-level count matrix

source_name: Cell line xenograft

growth_protocol: Tumor specimens were generated as follows: subcutaneous injection of 4x10^5 CHLA10 cells in 50% Matrigel, primary tumors collected 54 days post-injection (ROIS 1-4); tail vein injection of 7x10^5 CHLA10 cells injected in PBS, tumors collected 28 days post-injection (NSG immunocompromised mice) (ROIS 5-8, liver tumor, ROIS 9-12 retroperitoneal tumor).

extract_protocol:
Hybridization of the Human NGS Whole Transcriptome Atlas probe library (HWTA v1.0) was performed according to manufacturer instructions overnight at 37C. Each probe is tagged with a photocleavable unique molecular identifier (UMI) for NGS-based readout. Slides were blocked for 30’ before staining with morphology markers and SYTO DNA dye. After slide scanning, 12 ROIs comprising >1000 SYTO+ nuclei each were selected, UV-cleaved, and collected for NGS sequencing to quantify probe counts. Library preparation and Illumina NGS were carried out by NanoString. The NanoString GeoMx NGS data analysis pipeline was used (version 2.3.4) to assess probe counts, including probe and count-level QC steps using the GeoMxTools R package. Gene level count data were normalized using the quartile 3 (Q3) method comparing the upper quartile of counts in each segment with the geometric mean of negative control probes.
NanoString GeoMx pipeline

treatment_protocol: no treatment

value: Cell line xenograft

value: Ewing sarcoma tumor cell line


title: ROI12 tail vein retroperitoneal

description:
DSP-1012550008322-H-B01
ROI12 from tail vein injection-derived CHLA10 retroperitoneal tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: RNAseq (polyA RNA) of fab1∆ cells grown in SDC biol. rep. #3

source_name: fab1∆::NatMX SAL1+ HAP1+ CAT5(91M) MIP1(661T) MKT1(30G) RME1(INS-308A) TAO3(1493Q)

value: fab1{delta}::NatMX SAL1+ HAP1+ CAT5(91M) MIP1(661T) MKT1(30G) RME1(INS-308A) TAO3(1493Q)


title: RNAseq (polyA RNA) of fab1∆ cells grown in SDC biol. rep. #4


title: GUIDE seq lbsite5

value: embryonic kidney


title: cumulus cell-CC_RNA_rep1

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: --trim-n -q 25,25 -m 75 -a AGATCGGAAGAGC -A AGATCGGAAGAGC.
All RNA-seq data were mapped to the mm10 reference genome after cutadapt using hisat2 with parameters ‘--data-cufflinks --no-discordant --no-mixed --no-unal’.
The TPM (Transcripts Per Million) of genes were obtained by StringTie.
Signal tracks for each sample were generated using the deepTools bamCoverage function with parameters  "--normalizeUsing RPKM --smoothLength 150 --extendReads 150".
Genome_build: mm10
Supplementary_files_format_and_content: *.bw are bigWig files generated using deepTools. *.exp are gene expression files generated by StringTie.

extract_protocol:
10 blastomeres were used per reaction, and three replicates were performed for each stage. All isolated blastomeres were washed three times in 0.5% BSA in PBS solution to avoid contamination. RNA-seq libraries were generated using the Covaris DNA shearing protocol for Smart-seq sequence library generation. Briefly, RNAs with a polyadenylated tail were captured, reverse transcribed and pre-amplified. DNA was sheared and purified for library construction.
Libraried were generated using the KAPA HyperPrep Kit for the Illumina platform (kk8504), following the manufacturer's instrunctions. Paired-end 150 bp sequencing was performed in NovaSeq (Illumina) platform in Berry Genomics and Novogen.


title: ROI10 tail vein retroperitoneal

description:
DSP-1012550008322-H-A11
ROI10 from tail vein injection-derived CHLA10 retroperitoneal tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: RNAseq (polyA RNA) of fab1∆ cells grown in SDC biol. rep. #2


title: RNAseq (polyA RNA) of vph1∆ cells grown in SDC biol. rep. #4


title: ROI9 tail vein retroperitoneal

description:
DSP-1012550008322-H-A10
ROI9 from tail vein injection-derived CHLA10 retroperitoneal tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: GUIDE seq AsCTLA4

value: Epithelial cells


title: RNAseq (polyA RNA) of vph1∆ cells grown in SDC biol. rep. #3


title: Fertilized-PN5_input_rep2

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: --trim-n -q 25,25 -m 75 -a AGATCGGAAGAGC -A AGATCGGAAGAGC.
Then, All ULI-NChIP-seq and input data reads were aligned to the mm10 reference genome used BWA with mem command.
Signal tracks for each sample were generated using the deepTools bamCoverage function with normalized to RPKM (Reads Per Kilobase Million) and removed PCR duplicates.
The alignment files were first merged using SAMtools, then removed PCR duplicates and down-sample to same number of reads (60 million) using Picard tools
The H3K9me3 peaks were called by MACS2 with “--broad” parameters and over input data.
Genome_build: mm10
Supplementary_files_format_and_content: *.bw are bigWig files generated using deepTools. *.broadPeak are peak files generated by MACS2.

growth_protocol: BDF1 mice were used as oocyte donors, and the cumulus cells were used as nuclear donors. The reconstructed oocytes were then cultured in CZB medium for 1h before activation treatment. The cloned constructs were activated by 6 h incubation in 1 mM SrCl2 in Ca2+-free CZB and 5 μg/mL cytochalasin B. Reconstructed embryos were thoroughly washed and cultured in G-1 PLUS medium at 37℃ under 5% CO2. MII oocytes were retrieved from the dissected oviducts of super-ovulated B6D2F1 female mice at 13 h post hCG injection for subsequent SCNT procedure. To get fertilized embryos, the super-ovulated C57BL/6 female mice were mated with C57BL/6 male mice. Then, the zygotes were collected from the oviducts of the female mice at 20 h after hCG injection and were cultured in G-1 PLUS medium until PN5.

extract_protocol:
All samples were washed three times in 0.5% bovine serum albumin in phosphate-buffered saline (BSA-PBS). Chromatin was fragmented by MNase and was incubated with antibody bound beads at 4℃ for 2 hours. Captured DNA was wahed and isolated by isopropanol.
Libraried were generated using the KAPA HyperPrep Kit for the Illumina platform (kk8504), following the manufacturer's instrunctions. Paired-end 150 bp sequencing was performed in NovaSeq (Illumina) platform in Berry Genomics and Novogen.

treatment_protocol: 1 μg antibody was incubated with protein A-beads per sample at 4℃ for 2 hours.

value: Fertilized


title: ROI8 tail vein liver

description:
DSP-1012550008322-H-A09
ROI8 from tail vein injection-derived CHLA10 liver tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: GUIDE seq AsB2M

value: wild type

value: Guide seq


title: RNAseq (polyA RNA) of fab1∆ cells grown in SDC biol. rep. #1


title: ROI7 tail vein liver

description:
DSP-1012550008322-H-A08
ROI7 from tail vein injection-derived CHLA10 liver tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: Fertilized-PN5_input_rep1


title: RNAseq (polyA RNA) of atg18∆ cells grown in SDC biol. rep. #4

source_name: atg18∆::NatMX SAL1+ HAP1+ CAT5(91M) MIP1(661T) MKT1(30G) RME1(INS-308A) TAO3(1493Q)

value: atg18{delta}::NatMX SAL1+ HAP1+ CAT5(91M) MIP1(661T) MKT1(30G) RME1(INS-308A) TAO3(1493Q)


title: RNAseq (polyA RNA) of atg18∆ cells grown in SDC biol. rep. #3


title: RNAseq (polyA RNA) of vph1∆ cells grown in SDC biol. rep. #1


title: ROI6 tail vein liver

description:
DSP-1012550008322-H-A07
ROI6 from tail vein injection-derived CHLA10 liver tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: RNAseq (polyA RNA) of atg18∆ cells grown in SDC biol. rep. #2


title: GUIDE seq AsCLIC4


title: NT-TE_input_rep2

source_name: NT-TE

value: TE

value: NT


title: NT-TE_input_rep1


title: NT-ICM_input_rep2

source_name: NT-ICM

value: ICM


title: RNAseq (polyA RNA) of atg18∆ cells grown in SDC biol. rep. #1


title: NT-ICM_input_rep1


title: ROI5 tail vein liver

description:
DSP-1012550008322-H-A06
ROI5 from tail vein injection-derived CHLA10 liver tumor
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: GUIDE seq AsDNMT1


title: GUIDE seq Assite5


title: ROI3 subcutaneous

description:
DSP-1012550008322-H-A04
ROI3 from subcutaneous CHLA10 xenograft
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: ROI4 subcutaneous

description:
DSP-1012550008322-H-A05
ROI4 from subcutaneous CHLA10 xenograft
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: NT-Morula_input_rep5

source_name: NT-Morula

value: Morula


title: GUIDE seq AsNLRC4


title: RNAseq (polyA RNA) of wild-type cells grown in SDC biol. rep. #3


title: RNAseq (polyA RNA) of wild-type cells grown in SDC biol. rep. #4


title: ROI2 subcutaneous

description:
DSP-1012550008322-H-A03
ROI2 from subcutaneous CHLA10 xenograft
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: ROI1 subcutaneous

description:
DSP-1012550008322-H-A02
ROI1 from subcutaneous CHLA10 xenograft
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: NT-Morula_input_rep4


title: RNAseq (polyA RNA) of wild-type cells grown in SDC biol. rep. #1


title: GUIDE seq AsPO1


title: NT-Morula_input_rep3


title: NT-Morula_input_rep2


title: young_shoots_myc2_ChIA-PET_2_H3K4me3_rep2

data_processing:
library strategy: ChIA-PET
Fastp fitered the raw reads
The cleaned reads were analysed with ChIA-PET Tool V3.
Assembly: TAIR10
Supplementary files format and content: long-range interaction bedpe

source_name: Shoots of two-week-old seedlings (myc2)

extract_protocol:
About 2 g of sample was used for each ChIA-PET assay. Tissues were ground to fine powder in liquid nitrogen and lysed in 10 ml of Buffer S (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) for 20 min at 4 °C. The homogenate was mixed with 20 ml of Buffer F (50 mM HEPES-KOH (pH 7.5), 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and the chromatin was fragmented into 1–3 kb by sonication using a Bioruptor (Diagenode). The lysates were centrifuged at 20,000 × g for 5 min at 4 °C and 20 ml of Buffer F were added to the supernatant for ChIP. ChIP was performed using antibodies against the following: H3K4me3 (ABclonal, A2357). Antibody (50–80 g) was added to Dynabeads® protein G beads (Life Technologies, 10003D) and incubated for 6 h on a rotator at 4 °C. Beads were washed with phosphate-buffered saline with Tween® (PBST) twice and incubated with sonicated chromatin overnight at 4 °C with rotation. Subsequently, beads were washed twice for 5 min each at 4 °C in 5 ml low-salt buffer (50 mM HEPES-KOH, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), followed by two washes in 5 ml high-salt buffer (low salt ChIP buffer in which 150 mM NaCl was replaced with 350 mM NaCl), one wash in 5 ml LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 1 mM EDTA, 0.1% sodium deoxycholate), and one wash in TE buffer (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA). ChIP DNA on beads was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F) and Klenow enzyme (NEB, cat. no. M0212L).
Proximity ligation of ChIP DNA was performed using biotinylated bridge-linker, Forward strand: 5′-[5Phos]CGCGATATC/iBIOdT/TATCTGACT-3′, Reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′). Proximity ligation DNA was reverse cross-linked, and the ChIA-PET libraries were prepared using Tn5 transposase (VAHTS; cat. no. TD501). DNA fragments containing the bridge-linker at ligation junctions were captured by Dynabeads™ M-280 Streptavidin (Invitrogen, 11205D), and used as templates for PCR amplification.

treatment_protocol: The aerial part of two-week-old seedlings were dual cross-linked with 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min and 1% formaldehyde (SIGMA, F8775) for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature. Harvested samples were stored at -80 °C for ChIA-PET assay.

value: Shoots of two-week-old seedlings

tag: age

value: two-week old seedlings


title: No template control

description:
DSP-1012550008322-H-A01
Nanostring no template control
Wrenn_Apfelbaum_CHLA10_xenograft_DSP.xlsx


title: NT-8cell_input_rep4


title: CHLA9 (HTO1), CHLA10 (HTO2), TC32 (HTO3)

description:
Sample 4-6 RNA, HTO, ADT
mRNA, protein
poly A RNA, Antibody-derived oligonucleotide (ADT), Hashtag-derived oligonucleotide (HTO)
rna_counts_processed.csv
adt_counts_processed.csv
metadata.csv

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT and HTO barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT and HTO sequences were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis).
Assembly: hg38
Supplementary files format and content: normalized RNA and ADT count matrices, cell metadata
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing) with HTO (hashtag oligos)

source_name: CHLA9, CHLA10, TC32

growth_protocol: Cell culture conditions in paper methods section.

extract_protocol:
500,000 cells were resuspended in PBS + 1% FBS and spun at 300g for 10 minutes at 4oC and then resuspended in 25 uL Biolegend staining buffer (420201, San Diego, CA). 2.5 uL human TruStain FcX (422301, San Diego, CA) was added per sample and incubated at 4oC for 10 minutes. Hash-Tag Antibodies, used to label the  samples  and  minimize  batch  effects,  were  added  at  250  ng/sample  (0.5 uL/sample) and incubated at 4oC for 30 minutes. Cells were washed twice in 1 mL staining buffer and spun at 300g for 5 minutes at 4oC.
Samples were pooled 1:1 at 1000 cells/uL and libraries  were  generated  using  the  3’  V3  10X  Genomics  Chromium  Controller following the manufacturer’s protocol (CG000183, Pleasanton, CA). Final library quality was assessed using the Tapestation 4200 (Agilent, Santa Clara, CA) and libraries were quantified by Kapa qPCR (Roche).Pooled libraries were then subjected to paired-end sequencing according  to  the  manufacturer’s  protocol

value: CHLA9, CHLA10, TC32

value: Ewing sarcoma cell line


title: TC71 (HTO1), RDES (HTO2), PDX305 (HTO3)

description:
Sample 7-9 RNA, HTO, ADT
mRNA, protein
poly A RNA, Antibody-derived oligonucleotide (ADT), Hashtag-derived oligonucleotide (HTO)
rna_counts_processed.csv
adt_counts_processed.csv
metadata.csv

source_name: TC71, RDES, PDX305

value: TC71, RDES, PDX305


title: young_shoots_myc2_ChIA-PET_2_H3K4me3_rep1


title: A673 (HTO1), A4573 (HTO2), SKNMC (HTO3)

description:
Sample 1-3 RNA, HTO, ADT
mRNA, protein
poly A RNA, Antibody-derived oligonucleotide (ADT), Hashtag-derived oligonucleotide (HTO)
rna_counts_processed.csv
adt_counts_processed.csv
metadata.csv


title: NT-8cell_input_rep3


title: young_shoots_Col-0_ChIA-PET_2_H3K4me3_rep1

source_name: Shoots of two-week-old seedlings (Col-0)

value: Col-0 (wild-type)


title: HCC-TAMs, DMSO-treated 2

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: School of Basic Medical Sciences, Peking University

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to  short reads (Raw data) by base calling and these short reads are recorded in FASTQ format (Chen, S. , et al 2018), which contains sequence information and corresponding  sequencing quality information.
Sequence artifacts, including reads containing adapter contamination, low-quality  nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the  subsequent reliable bioinformatics analysis. Hence quality control is an essential step  and applied to guarantee the meaningful downstream analysis. we used Fastp (version  0.23.1) (Chen, S. , et al 2018) to perform basic statistics on the quality of the raw reads.  The steps of data processing were as follows:  (1) Discard a paired reads if either one read contains adapter contamination;  (2) Discard a paired reads if more than 10% of bases are uncertain in either one read;  (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over  50% in either one read.
Assembly: hg38
Supplementary files format and content: normalized (the upperquartile method) by edgeR

source_name: HCC-TAMs

growth_protocol: HepG2 (ATCC) cells were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS). THP-1 (ATCC) cells were kindly donated by Professor Tan Huanran (School of Basic Medicine at Peking University) and grown in RPMI 1640 medium supplemented with 2-mercaptoethanol to a final concentration of 0.05 mM and 10% FBS. Cells were incubated at 37°C in a 95% humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Sequencing  libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA,  Catalog #: E7530L) following manufacturer’s recommendations and index codes were  added to attribute sequences to each sample.
The qualified libraries were pooled and sequenced on Illumina platforms with PE150  strategy in Novogene Bioinformatics Technology Co., Ltd (Beijing, China), according to  effective library concentration and data amount required.

treatment_protocol:
A total of 1×106/ml THP-1 cells were differentiated into M0 macrophages by 24 h incubation with 150 mM phorbol-12-myristate 13-acetate.  The culture supernatant after HepG2 cell starvation treatment was harvested for 36 h to use as TCM for developing HCC tumor-associated macrophages (TAMs). M0 macrophages were cultured with different concentration gradients of TCM for 24 h to be induced to HCC-TAMs. For MIF inhibitor treatment, 20 μM 4-IPP were added to TCM at the step of TAM induction for 24 h induction to investigate the effect of MIF on HCC-TAMs.
The lentiviral vector containing SPP1 shRNA was GV115 with the sequence of components hU6-MCS-CMV-EGFP.  2×105/ml THP-1 cells were inoculated in a 24-well plate, and the cells were transfected with 3×107 TU/ml virus and A solution, centrifuged at 1000 rpm for 1 hour at room temperature, placed in a cell culture incubator, and the solution was changed after 13 hours. After one week of culture, cells with strong positive expression of GFP were sorted out by flow cytometry.

value: HCC-TAMs

value: THP-1 cells

value: DMSO  treated

value: HCC conditional medium induced


title: NT-8cell_input_rep2


title: young_shoots_myc2_H3K4me3_ChIP_seq_rep2

data_processing:
The quality of raw reads was evaluated and trimmed using fastp. The parameters of fastp were as follows: the window size option shared by sliding (-W) was set to 4, the mean quality requirement option shared by sliding (-M) was set to 20, the quality threshold for a qualified base (-q) was set to 15, the percentage of bases allowed to be unqualified (-u) was set to 40%, and one read’s N base number (n) was set to 5. Clean reads were mapped to the Arabidopsis genome (TAIR10) using Burrows-Wheeler Aligner (BWA)-mem with default parameters. Duplicate reads were filtered using SAMtools. Low-quality reads were filtered using SAMtools with the mapping quality (-q) set to 30. Peak calling was performed using the MACS2 tool. The parameters of MACS2 for a narrow peak model were as follows: -f BAMPE -B -g 119667750 -q 0.00001.
Assembly: TAIR10
Supplementary files format and content: bigWig

growth_protocol: Arabidopsis myc2 mutant were grown at 22 °C under a 16 h light/8 h dark photoperiod.

extract_protocol:
Approximately 0.2 g of tissue was used for ChIP-seq assay. The fragmented chromatin was incubated with antibodies against H3K4me3 (ABclonal, A2357), which has verified the specificity.
ChIP DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (New England BioLabs, E7645).

treatment_protocol: For ChIP-seq assay, the aerial part of two-week-old myc2 seedings were crosslinked with 1% formaldehyde for 10 min, quenched with 0.2 M glycine at room temperature, and then stored at -80°C until use.

value: H3K4me3 (ABclonal, A2357)


title: RNAseq (polyA RNA) of wild-type cells grown in SDC biol. rep. #2

value: parental line is DHY211 (see Harvey et al. 2018)

value: budding yeast


title: NT-8cell_input_rep1


title: young_shoots_myc2_H3K4me3_ChIP_seq_rep1


title: HCC-TAMs, DMSO-treated 1


title: NT-Morula_input_rep1


title: HCC-TAMs, shSPP1 2

value: SPP1 knockdown


title: NT-4cell_input_rep3

value: NT


title: young_shoots_Col-0_ChIA-PET_2_H3K4me3_rep2


title: Mouse Cpxm2 KO DOCA_11

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions by Charité-Universitätsmedizin Berlin

scan_protocol: Arrays were scanned following manufacturers instructions by Charité-Universitätsmedizin Berlin

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis Console version 4.0 (TAC 4.0) using Affymetrix default analysis settings and Analysis Type Gene Expression. Summarization: Gene Level -RMA.

label: biotin

source_name: Mouse 20 weeks old, cardiac tissus, free wall left ventricle

label_protocol: Following manufacturers instructions

growth_protocol: All animals were maintained under standard conditions of regular 12h diurnal cycles using an automated light switching device and climate-controlled conditions at a constant room temperature of 22°C. Animals had access to food and water ad libitum. All animal experiments were approved by the responsible local government committee in accordance with the guidelines of the Charité-Universitätsmedizin Berlin and national animal protection guidelines (Landesamt für Gesundheit und Soziales (LAGeSo) Berlin, Germany) for the use of laboratory animals. Cpxm2-Knockout (KO) mice were obtained as heterozygous B6;129S5-Cpxm2tm1Lex/Mmucd/rk and were inbred to receive homozygous KO (Cpxm2-/-) and wild type (WT) mice (Cpxm2+/+). Baseline phenotypic characterization of all mice under control conditions was performed at about 12 weeks of age. Animals were subsequently followed for 8 weeks under either DOCA-salt or SHAM conditions.

extract_protocol: Hearts were dissected and arrested in diastole by rinsing in 1 M KCl solution and subsequently blotted dry. The atria were trimmed away and hearts and kidneys were weighed. LV tissue was separated from septum and right ventricle. RNA was isolated from the free wall LV by the TRIzol reagent according to the manufacturer's instructions and dissolved in DEPC-treated H2O. The quality and concentration of the purified total RNA were confirmed by spectroscopy.

treatment_protocol: At 12 weeks of age unilateral nephrectomy was performed in WT and KO mice and a pellet containing deoxycorticosterone acetate (DOCA) was implanted in each mouse subcutaneously. Subsequently, these mice were exposed to salt by adding 1% NaCl in drinking water (DOCA groups). Unilateral nephrectomy was also performed in an additional group of WT and KO mice but these animals received no DOCA pellet and were exposed to normal drinking water (SHAM groups). Animals were treated for overall 8 weeks.

value: cardiac, left ventricle

tag: Sex

value: male

value: Cpxm2 knock-out

value: 20 weeks

value: unilateral nephrectomy, subcutaneous DOCA pellet, 1% NaCl in drinking water


title: young_shoots_Col-0_ATAC_seq_rep2

data_processing:
The quality of raw reads was evaluated and trimmed using fastp. The parameters of fastp were as follows: the window size option shared by sliding (-W) was set to 4, the mean quality requirement option shared by sliding (-M) was set to 20, the quality threshold for a qualified base (-q) was set to 15, the percentage of bases allowed to be unqualified (-u) was set to 40%, and one read’s N base number (n) was set to 5. Clean reads were mapped to the Arabidopsis genome (TAIR10) using Burrows-Wheeler Aligner (BWA)-mem with default parameters. Duplicate reads were filtered using SAMtools. Low-quality reads were filtered using SAMtools with the mapping quality (-q) set to 30. Peak calling was performed using the MACS2 tool. The parameters of MACS2 for a ATAC-seq peak model was as follows: --nomodel --shift -100 --extsize 200 -f BAM -B -q 0.01 -g 119667750.
Assembly: TAIR10
Supplementary files format and content: bigWig

growth_protocol: Arabidopsis accession Columbia (Col-0) were grown at 22 °C under a 16 h light/8 h dark photoperiod.

extract_protocol:
Approximately 1 g of tissue was used for each ATAC-seq assay. The samples were chopped with a razor blade in 1×PBS buffer to obtain the intact nuclei. After filtration through Miracloth, Triton X-100 was added and the samples were incubated for 12 min on ice. The nuclei were pelleted by centrifugation and were resuspended in 20 μl TTBL buffer (VAHTS, TD501). Approximately 10,000 nuclei were treated with Tn5 (VAHTS, TD501) at 37 °C for 30 min.
Then, the sample was immediately purified using a Qiagen MinElute kit and the purified fragments were amplified for 7-10 cycles to construct a library, according to the instructions (VAHTS, TD501).

treatment_protocol: The aerial part of two-week-old seedlings were immediately frozen in liquid nitrogen and stored at -80°C for ATAC-seq assay.

value: Shoots of two-week-old seedlings


title: Mouse Cpxm2 KO DOCA_10


title: HCC-TAMs, shSPP1 1


title: Mouse Cpxm2 WT DOCA_09

value: Cpxm2 wildtype


title: HCC-TAMs, shControl 2

value: WT


title: Mouse Cpxm2 WT DOCA_07


title: young_shoots_Col-0_ATAC_seq_rep1


title: NT-4cell_input_rep1


title: HCC-TAMs, shControl 1

value: HCC-TAMs


title: S1KO_Toxo_Sp_CD4_IFNg_RNAseq_rep2

city: Bethesda

first: Stephen

middle: R

last: Brooks

state: MD

address: 50 SOUTH DR, RM 1140

department: Biodata Mining and Discovery Section

institute: NIAMS/NIH

data_processing:
RNAseq FASTQ alignment with Tophat 2.1.1
Gene expression read count data were generated using htseq-count
Assembly: mm9
Supplementary files format and content: Excel table of RNA-seq gene expression count data

growth_protocol: 18 hour re-stimulation

extract_protocol:
Total RNA  isolated with TRIzol and  phenol/chloroform, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra II Library Prep Kit for Illumina (E7645L, New England Biolabs)
Total RNA  isolated with TRIzol and  phenol/chloroform, then mRNA enriched with NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra II Library Prep Kit for Illumina (E7645L, New England Biolabs)

treatment_protocol: WT and STAT1 T-KO mice were infected with Toxplasma gondii for 7 days. Then, splenic single cell suspensions were re-stimulated overnight (18h) with solumble Toxoplasma antigen, processed for IFN-g capture assay and 50-100K CD4+ IFN-g+ T cells purified by cell sorting

value: spleen

tag: strain

value: Th1 Effector CD4+ T cell

value: Stat1 flox/flox Cd4-Cre+/-

tag: sorting strategy

value: Sorted viable, CD4+ IFN-g+ T cells


title: young, shoots, Col-0, ChIA-PET, RNAPII, rep2

first: Qiangwei

last: Zhou

state: Hubei

address: Hongshan district, shizishan #1

institute: Huazhong Agricultural university

description: ATCP-012_023-peak.cluster.FDRfiltered.intra4inter6.txt

data_processing:
Fastp fitered the raw reads
The cleaned reads were analysed with ChIA-PET Tool V3.
Assembly: TAIR10
Supplementary files format and content: tab-delimited bedpe text files include clusters for each sample

growth_protocol: Arabidopsis accession Columbia (Col-0) was grown at 22°C under a 16 h light/8 h dark photoperiod.

extract_protocol:
About 5 g of tissues were used for each ChIA-PET assay. Tissues were ground to fine powder in liquid nitrogen and lysed in 10 ml of Buffer S (50mM HEPES-KOH (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1% SDS) for 20 min at 4°C. The homogenate was mixed with 20 ml of Buffer F (50mM HEPES-KOH (pH7.5), 150mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate), and the chromatin was fragmented into 1–3 kb by sonication using a Bioruptor (Diagenode). The lysates were centrifuged at 20,000 × g for 5 min at 4°C and 20 ml of Buffer F was added to the supernatant for ChIP. ChIP was performed using antibodies against the following: H3K4me1 (ABclonal, A2355), H3K4me3 (ABclonal, A2357), H3K9me2 (Abcam, ab1220), H3K27me3 (ABclonal, A2363), and RNAPII (BioLegend, 920102). Antibody (50–80 mg) was added to Dynabeads® protein G beads (Life Technologies, 10003D) and incubated for 6 h on a rotator at 4°C. Beads were washed with PBST twice and incubated with sonicated chromatin overnight at 4°C with rotation. Subsequently, beads were washed two times for 5 min at 4°C in 5 ml of low-salt buffer (50 mM HEPES-KOH, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), followed by two washes in 5 ml of high-salt buffer (low salt ChIP buffer replaced 150 mM NaCl with 350 mM NaCl), one wash in 5 ml of LiCl wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% NP-40, 1 mM EDTA, 0.1% sodium deoxycholate), and one wash in TE buffer (10 mM Tris-HCl, pH 8.0, and 1 mM EDTA). ChIP DNA on beads was used for end-repair and A-tailing using T4 DNA polymerase (Promega, cat. no. M421F) and Klenow enzyme (NEB, cat. no. M0212L). Proximity ligation of ChIP DNA was performed using biotinylated bridge-linker, Forward strand: 5′-[5Phos]CGCGATATC/iBIOdT/TATCTGACT-3′, Reverse strand: 5′-[5Phos]GTCAGATAAGATATCGCGT-3′).
Proximity ligation DNA was reverse cross-linked and the ChIA-PET libraries were prepared by using Tn5 transposase (VAHTS; cat. no. TD501). DNA fragments contained the bridge-linker at ligation junctions were captured by Dynabeads™ M-280 Streptavidin (Invitrogen, 11205D), and used as templates for PCR amplification.

treatment_protocol: Shoots of two-week-old seedlings were dual cross-linked with 1.5 mM ethylene glycol bis (succinimidylsuccinate) (Thermo Fisher Scientific, 21565) for 30 min and 1% formaldehyde (SIGMA, F8775) for 10 min, and quenched with 0.2 M glycine at room temperature. Harvested samples were stored at -80°C for ChIA-PET assay.

value: two-weeks old

tag: tissue

tag: ecotype

tag: antibody

value: RNAPII


title: Mouse Cpxm2 WT DOCA_08

first: Anika

last: Witten

address: Domagkstr. 3

institute: University of Muenster

tag: genotype


title: young, shoots, Col-0, ChIA-PET, RNAPII, rep1


title: NT-2cell_input_rep2

first: Qianshu

last: Zhu

address: Siping Road

institute: Tongji University

tag: cell type


title: HCC-TAMs, 4IPP-1-treated 2

value: THP-1 cells

value: 4IPP-1 treated

value: HCC conditional medium induced

tag: treatment


title: Mouse Cpxm2 KO SHAM_04

value: cardiac, left ventricle

value: male

value: unilateral nephrectomy


title: Mouse Cpxm2 KO SHAM_05

value: Cpxm2 knock-out

value: 20 weeks


title: NT-2cell_input_rep1

value: NT


title: S1KO_Toxo_Sp_CD4_IFNg_RNAseq_rep1


title: Mouse Cpxm2 WT SHAM_13

value: Cpxm2 wildtype


title: Mouse Cpxm2 KO SHAM_06


title: Mouse Cpxm2 WT SHAM_02


title: HCC-TAMs, 4IPP-1-treated 1

value: HCC-TAMs

tag: cell line


title: WT_Toxo_Sp_CD4_IFNg_RNAseq_rep2

value: spleen

value: Wild type


title: NT-4cell_input_rep2


title: young, shoots, Col-0, ChIA-PET, h3k9me2, rep2

description: ATCP-013_026-peak.cluster.FDRfiltered.intra5inter7.txt

value: Shoots of two-week-old seedlings


title: young, shoots, Col-0, ChIA-PET, h3k9me2, rep1


title: NT-14h_input_rep4


title: CHLA10_CD73_positive_rep3

data_processing:
Reads were trimmed for quality and adapter sequence using TrimGalore v0.6.7.
Trimmed reads were aligned to the reference genome using STAR 2.7.9a using "--twopassMode Basic".
Gene counts were generated by STAR using the "--quantMode GeneCounts" option.
Assembly: Hg38
Supplementary files format and content: Tab-delimited read count table output by STAR.  After four summary header rows, there are four columns, with the first being gene ID, the second being unstranded read counts, the third being counts for the first strand being aligned to the RNA, and fourth being counts for the second strand being aligned to the RNA.

growth_protocol: A673 was maintained in RPMI 1640 media (Gibco) supplemented with 10% FBS (Atlas Biologicals) and 2mmol/L-glutamine (Life Technologies). CHLA10 was maintained in IMDM media (Fisher scientific) supplemented with 20% FBS, 2mmol/L-glutamine, and 1X Insulin-Transferrin-Selenium (Gibco). Cells were cultured at 37°C with 5% CO2 and were split according to ATCC and COG recommendations.

extract_protocol:
RNA was extracted with Qiagen Rneasy kit
Libraries were prepared with NEBNext Ultra II  RNA Library Prep kit

value: Ewing sarcoma cell line

value: Sorted CD73 positive


title: young, shoots, Col-0, ChIA-PET, h3k4me3, rep1

description: ATCP-001_002_010_049-peak.cluster.FDRfiltered.intra6inter8.txt

value: two-weeks old


title: young, shoots, Col-0, ChIA-PET, h3k4me3, rep2


title: NT-14h_input_rep2


title: CHLA10_CD73_positive_rep2


title: KLRG1lo P14 shCbx4 CD8 T cell, shCD4 control cells, LCMV 8 DPI, rep2

city: Rio de Janeiro

first: Renata

last: Meirelles Pereira

state: RJ

address: Av. Carlos Chagas Filho, 373, Sala D1-035

department: Instituto de Microbiologia Paulo de Goes

country: Brazil

institute: Universidade Federal do Rio de Janeiro

description: KLRG1_P14_shCD4_vs_P14_shCbx4_Log2FC.xlsx

data_processing:
Reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls.
The reads were then aligned to UCSC mm10 reference genome using TopHat (1.4.1). DUST scores were calculated with PRINSEQ Lite (v  0.20.3) and low-complexity reads (DUST > 4) were removed from the BAM files.
Read counts to each genomic feature were obtained with htseq-count (0.6.0 using the "union" option).
After removing absent features (zero counts in all samples), the raw counts were normalized with DESeq2, followed by differentially expression analysis with DESeq2.
Assembly: mm10
Supplementary files format and content: DESeq2 Log2FoldChange excel sheet

source_name: Spleen

extract_protocol:
Sort-purified P14 CD8 T cells total RNA was extracted using SMARTer Ultra Low Input RNA Kit for Sequencing-v3 according to the manufactorer's instructions
RNA-seq libraries were prepared using  SMARTer Ultra Low Input RNA Kit for Sequencing-v3 according to the manufacturer’s instructions.

value: Spleen

value: Primary

value: P14 CD8 T cells

tag: shRNA

value: shRNA knockdown, Cbx4


title: NT-14h_input_rep1


title: KLRG1lo P14 shCbx4 CD8 T cell, shCD4 control cells, LCMV 8 DPI, rep1