title: Liver macrophages, Tet2KO transplanted, rep4

first: Waihay

last: Wong

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

data_processing:
Sequence reads were filtered to remove reads containing adapters, greater than 10% undetermined bases, or greated than 50% of bases with Q score less than or equal to 5.
Trimmed sequence reads were pseudo-aligned using Salmon (version 1.2.1). Salmon index and decoys were generated using GRCm38/mm10 assembly.
Supplementary files format and content: mm10
Supplementary files format and content: Quantification files for each sample.

source_name: liver

growth_protocol: Irradiated B6.SJL mice were transplanted at 8 weeks with wild type or TET2 deficient bone marrow cells.

extract_protocol:
Animals were sacrificed at 11 weeks of diet. Livers were perfused with PBS and processed into single cell suspension by enzymatic and physical dissociation. Hepatic macrophages were sorted using fluorescently labeled antibodies.
RNA was isolated using Rneasy micro kit (Qiagen). 0.2 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit following manufacturer's protocols.
Pooled libraries were sequenced using Illumina NovaSeq 6000.

treatment_protocol: Steatohepatitis was induced by feeding with a choline-deficient, L-amino acid-defined, high-fat diet consisting of consisting of 60 kcal% fat and 0.1% methionine by weight for 11 weeks.

value: liver

tag: recipient mouse

value: Irradiated B6.SJL

value: macrophage

value: CDAHFD


title: ChOR_T60_H2BK120ub_r2

status: Public on Feb 06 2023

type: SRA

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

description:
EdU-labelled genomic DNA
ChOR_T60_H2BK120ub_RRPM_MEAN.bw

library_source: genomic

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were read into Seqmonk (v1.47.1) with MAPQ>20, ignoring duplicates, and reads extended by 250bp. Samples were normalized based on Drosphila spike-In abundance and corresponding ClickedInputs. Replicates were merged, exported as bedgraphs and converted to bigwig using UCSC BedGraphtoBigWig
Assembly: mm10
Assembly: dm6
Supplementary files format and content: bigwig files for merged replicates (RRPM-adjusted)  for the mouse genome
Library strategy: ChOR-seq

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: ESCs were grown on gelatin-coated dishes in serum+LIF conditions at 37 °C with 5 % CO2. DMEM was supplied with fetal bovine serum (15 %), home-made LIF, non-essential amino acids, penicillin/streptomycin and beta-mercaptoethanol. Cells were passaged using Trypsin-EDTA or TrypLE.

extract_protocol: After the appropriate treatment, cells were washed with cold PBS, crosslinked for 5min with 1% Formaldehyde at room temperature and subsequently quenched with 0.1M Glycin (final concentration) for 5min before harvesting. Then, nuclei were isolated and sonicated using the Covaris Chromatin Shearing Kit. ChIP-Immunoprecipation of chromatin was done using antibodies according to the manufacturers recommendation with EdU-labelled Drosophila S2 chromatin serving as Spike-In control and, where the epitope of the antibody does not recognize the Drosophila homolog (i.e. H2A.Z) , H2AV antibodies to immunoprecipitate Spike-In chromatin as well. Purified fragments were biotinylated, libraries prepared, EdU-biotinylated fragments pulled down using Streptavidin and sequenced

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min and then either collected (T0) or cultured for indicated maturation intervals (T15-T480, in minutes) in media without EdU before collection. If treated with DMSO (volume equivalent), Triptolide (10uM), Indole-3-acetic acid (500uM) and/or dTAG-13 (1uM), cells were incubated for indicated times in the description and then  collected.

tag: cell line

tag: strain

tag: genotype

value: wildtype

tag: treatment


title: AP2_F_Rapamycin_rep_3

city: Philadelphia

first: Katelyn

middle: Ann

last: Walzer

state: PA

address: 380 South University Avenue

department: Pathobiology

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Fastq files were pseudoaligned to the Cryptosporidium parvum Iowa II reference transcriptome (version 50, VEuPathDB) using Kallisto v.0.45.0
Kallisto transcript counts were imported into R using the Bioconductor package tximport
Expression data was normalized using the TMM method in the function calcNormFactors from the package edgeR
Differentially expressed genes (log2 fold-change ≥ 1 and p-value ≤ 0.01) were identified by linear modeling and Bayesian statistics using the limma package
Assembly: Version 50 of the Cryptosporidium parvum Iowa II reference from VEuPathDB
Supplementary files format and content: Tab-delimited text files include log2 counts per million (CPM) values for each sample

molecule: total RNA

organism: Cryptosporidium parvum

source_name: Cryptosporidium parvum infected HCT-8 cells

growth_protocol: HCT-8 cells grown in 24-well plates were infected with 100,000 oocysts per well for 48 hours at 5% CO2 and 37º C

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions
Libraries were prepared using the Illumina Stranded mRNA Prep, Ligation kit (20040534), according to the manufacturer’s instructions

treatment_protocol: Cultures were untreated (ethanol vehicle) or treated with 100 nM rapamycin for 48 hours

tag: background strain

value: Cryptosporidium parvum Iowa II (Bunchgrass Farms)

value: rapamycin treatment for 48 hours


title: Control.35

city: Rochester

first: Nagaswaroop

last: Kengunte Nagaraj

state: Minnesota

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by STAR-2.5.2b aligner
Gene counts were generated using Subread featureCounts (http://subread.sourceforge.net/)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Adipose

growth_protocol: MSC were cultured in standard conditions (37 °C with 5% CO2) in advanced minimum essential medium supplemented with 5% platelet lysate in T-75 flasks, then washed extensively with phosphate-buffered saline and replenished with serum-free advanced minimum essential medium for 36 hours.

extract_protocol:
After serum-starvation, MSC was centrifuged at 400 x g for 5 minutes at 20 °C to pellet cells and supernatant was aliquoted off.
RNA libraries were prepared using 200 ng of total RNA according to the manufacturer’s instructions.
TruSeq Stranded mRNA Sample Prep Kit v2

tag: tissue

value: Adipose

tag: cell type

value: Mesenchymal Stem Cells

tag: disease state

value: Control


title: Liver macrophages, Tet2KO transplanted, rep3

city: Boston

middle: J

state: MA

department: Medical Oncology


title: ChOR_T60_H2BK120ub_r1


title: AP2_F_Rapamycin_rep_2


title: Control.31


title: Liver macrophages, Tet2KO transplanted, rep2


title: Control.30


title: ChOR_T30_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T30_H2BK120ub_RRPM_MEAN.bw


title: Liver macrophages, Tet2KO transplanted, rep1


title: ChOR_T30_H2BK120ub_r1


title: AP2_F_Control_rep_3

value: untreated


title: DKD.53

value: DKD, Diabetic Nephropathy


title: AP2_F_Rapamycin_rep_1


title: ChOR_T120_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T120_H2BK120ub_RRPM_MEAN.bw


title: ChOR_T15_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T15_H2BK120ub_RRPM_MEAN.bw


title: DKD.52


title: Liver macrophages, vavCre transplanted, rep4

value: WT


title: Liver macrophages, vavCre transplanted, rep3


title: AP2_F_Control_rep_1


title: DKD.51


title: ChOR_T15_H2BK120ub_r1


title: ChOR_T0_H2BK120ub_r2

description:
EdU-labelled genomic DNA
ChOR_T0_H2BK120ub_RRPM_MEAN.bw


title: Liver macrophages, vavCre transplanted, rep2


title: DKD.50_R


title: DKD.18_smRNA

data_processing:
Base calling was performed with the Illumina bcl2fastq
The paired end reads were aligned by Bowtie aligner
Assembly: hg19
Supplementary files format and content: tab-delimited text files include Raw counts and CPM values for each microRNA per sample

extract_protocol:
After serum-starvation, MSC was centrifuged at 400 x g for 5 minutes at 20°C to pellet cells and supernatant was aliquoted off.
Small RNA libraries were prepared from 250 ng of total RNA according to manufacturer’s instructions
NEBNext Multiplex Small RNA Kit


title: Liver macrophages, vavCre transplanted, rep1


title: ChOR_T0_H2BK120ub_r1


title: WT_Rapamycin_rep_2


title: DKD.49


title: Liver, Tet2KO transplanted, rep9

extract_protocol:
Animals were sacrificed at 11 weeks of diet and livers were perfused with PBS and harvested.
RNA was isolated using Rneasy mini plus kit (Qiagen). 1.0-1.3 ug of total RNA was used for the construction of sequencing libraries.
cDNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocols.
Pooled libraries were sequenced using Illumina NovaSeq 6000.

tag: transplanted cell_type

value: TET2 deficient bone marrow cells.


title: ChOR_noEdU_H2AK119ub_r4

description: noEdU-labelled (control) genomic DNA


title: WT_Rapamycin_rep_1


title: Liver, Tet2KO transplanted, rep8


title: ChOR_noEdU_H2AK119ub_r3

description: noEdU-labelled (control) genomic DNA


title: DKD.48


title: AP2_F_Control_rep_2


title: ChOR_T0_H2AK119ub_r4

description: EdU-labelled genomic DNA


title: Liver, Tet2KO transplanted, rep7


title: WT_Control_rep_2


title: DKD.47_R


title: ChOR_T0_H2AK119ub_r3

description: EdU-labelled genomic DNA


title: DKD.46


title: WT_Rapamycin_rep_3


title: Liver, Tet2KO transplanted, rep6


title: WT_Control_rep_1


title: DKD.20


title: ChOR_noEdU_H2AK119ub_r2

description: noEdU-labelled (control) genomic DNA


title: Liver, Tet2KO transplanted, rep4


title: Liver, Tet2KO transplanted, rep5


title: DKD.21


title: ChOR_noEdU_H2AK119ub_r1

description: noEdU-labelled (control) genomic DNA


title: Poly I:C (10ng/mL), IFNAR, 8h

city: Los Angeles

first: Hector

middle: I

last: Navarro

state: California

address: 570 Boyer Hall

department: MIMG

institute: UCLA

data_processing:
Reads were trimmed using cutadapt (1) (cutoff q=20) and mapped to the mm10 genome.
The October 2014 version of the Ensembl database was used to extract gene annotation information.
CPM values were generated using edgeR (5) to normalize the raw counts data based on sequencing depth
Assembly: mm10
Supplementary files format and content: .xlsx

source_name: Bone Marrow

growth_protocol: Bone marrow cells were isolated from mouse femurs and cultured with 20 ng/ml GM-CSF and 10 ng/ml IL-4 to produce BMDCs with half the media being replaced on day 3 and 6 as previously reported

extract_protocol:
Collected in Invitrogen™ TRIzol™ Reagent (Cat# 15-596-018) for RNA and was extracted using Qiagen RNeasy Mini Kit
RNA was used for Illumina bead Arrays as described (Cheng et al 2017) and for RNA-seq as described (Sen et al 2020). Briefly, libraries were prepped using KAPA Stranded mRNA-Seq Kit Illumina® platform KR0960 – v3.15 using 1µg of RNA per sample measured using Qubit 2.0 fluorometer. Final libraries were checked via agarose gel and multiplexed with a maximum of 24 samples per sequencing reaction. Libraries were sequenced using Illumina HiSeq 3000 with single end 50bp reads

treatment_protocol: Cells were stimulated with CpG (0.1µM) (Invivogen ODN 1668 Cat# tlrl-1668), or Poly(I:C) HMW (10µg/mL) (Invivogen Cat#tlrl-pic) and collected at specified timepoints

value: Bone Marrow

value: BMDCs

value: IFNAR

tag: strain background

value: Poly I:C (10ng/mL)

tag: time (hr)


title: DKD.19


title: Poly I:C (10ng/mL), RelBko, 8h

value: RelBko


title: ChOR_T480_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T480_H2AK119ub_RRPM_MEAN.bw


title: Liver, Tet2KO transplanted, rep3

value: liver

value: Irradiated B6.SJL


title: Poly I:C (10ng/mL), WT, 8h


title: DKD.18


title: WT_Control_rep_3

value: wildtype


title: Liver, Tet2KO transplanted, rep2

value: CDAHFD


title: ChOR_T480_H2AK119ub_r1


title: Poly I:C (10ng/mL), IFNAR;RelBko, 8h

value: IFNAR;RelBko


title: ChOR_T180_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T180_H2AK119ub_RRPM_MEAN.bw


title: ChOR_T180_H2AK119ub_r1


title: Liver, vavCre transplanted, rep9

value: wild type bone marrow cells.


title: DKD.16

value: Adipose

value: Mesenchymal Stem Cells


title: Poly I:C (10ng/mL), RelBko, 3h


title: DKD.15


title: DKD.17


title: Poly I:C (10ng/mL), WT, 3h


title: ChOR_T120_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T120_H2AK119ub_RRPM_MEAN.bw


title: Liver, vavCre transplanted, rep8


title: Poly I:C (10ng/mL), IFNAR, 1h


title: DKD.13


title: Poly I:C (10ng/mL), IFNAR;RelBko, 1h


title: Liver, vavCre transplanted, rep7


title: Liver, vavCre transplanted, rep6


title: ChOR_T60_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T60_H2AK119ub_RRPM_MEAN.bw


title: ChOR_T120_H2AK119ub_r1


title: DKD.14


title: Poly I:C (10ng/mL), IFNAR;RelBko, 3h


title: Liver, vavCre transplanted, rep5


title: DKD.12


title: ChOR_T60_H2AK119ub_r1


title: DKD.11


title: ChOR_T30_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T30_H2AK119ub_RRPM_MEAN.bw


title: Liver, vavCre transplanted, rep4


title: Liver, Tet2KO transplanted, rep1


title: Poly I:C (10ng/mL), RelBko, 1h


title: DKD.10


title: Liver, vavCre transplanted, rep3


title: Poly I:C (10ng/mL), WT, 1h


title: ChOR_T30_H2AK119ub_r1


title: DKD.9


title: ChOR_T15_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T15_H2AK119ub_RRPM_MEAN.bw


title: Liver, vavCre transplanted, rep2


title: ChOR_T15_H2AK119ub_r1


title: DKD.8


title: CPG (.1uM), IFNAR, 8h

value: CPG (.1uM)


title: CPG (.1uM), RelBko, 8h


title: DKD.7

value: DKD, Diabetic Nephropathy


title: ChOR_T0_H2AK119ub_r2

description:
EdU-labelled genomic DNA
ChOR_T0_H2AK119ub_RRPM_MEAN.bw


title: CPG (.1uM), IFNAR;RelBko, 3h


title: Poly I:C (10ng/mL),  IFNAR, 3h


title: DKD.5


title: CPG (.1uM), IFNAR;RelBko, 8h


title: Tumor-bearing Spleen, scRNA-seq

city: Saint Louis

first: Derek

middle: Arthur George

last: Barisas

state: Missouri

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Supplementary files format and content: mm10
Supplementary files format and content: Unfiltered Cell Ranger output files

source_name: Spleen

extract_protocol:
Spleens were minced and digested in 1mg/mL Collagenase Type IV + 0.25mg/mL DNase I. Bone marrow was removed by centrifugation and digested. Digestion was quenched then filtered through a 100μm filter. Cells were pelleted, counted, and aliquoted. TruStain FcX™ PLUS was used to block samples then biotin anti-lineage antibodies were used to stain lineage cells. After washing, strepavidin magnetic beads (NEB, S1420S) were used to deplete lineage positive cells. Remaining cells were pelleted and then stained with streptavidin BV605 (Biolegend, #405229), anti-CD45 AF700, anti-PDGFRα APC, anti-CD51 PE (Biolegend, clone RMV-7), anti-CD31 PE-Cy7 (Biolegend, clone 390), anti-Sca-1 PerCP-Cy5.5 (Biolegend, clone D7), and anti-c-Kit FITC (Biolegend, clone 2B8). Cells were then washed into holding buffer (0.04% BSA in PBS), stained with DAPI, and sorted on a high modified MoFlo into five populations: Live/Lin-/CD45+/c-Kit+/Sca-1+, Live/Lin-/CD45+/c-Kit+/Sca-1-, Live/Lin-/CD45-/CD31+, Live/Lin-/CD45-/CD31-, Live/Lin-/CD45-/CD31-/CD51+, Live/Lin-/CD45-/CD31-/CD51-. These populations were combined at equal ratios and submitted for 10X Genomics 3' v3.1 Chemistry sample preparation and sequencing on a NovaSeq6000.
Library preparation was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriately sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction an Ilumina R2 primer sequence was added.

value: Hematopoietic and non-hematopoietic cells

value: Spleen

value: Tumor-bearing

tag: age

value: 8-16 weeks old


title: Control BM, scRNA-seq

description: 10x Genomics

value: Bone Marrow

value: Control


title: Control Spleen, scRNA-seq

description: 10x Genomics


title: CPG (.1uM), IFNAR;RelBko, 1h

value: BMDCs


title: DKD.4


title: ChOR_totalChIP_H2BK120ub_TPL_r1

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were read into Seqmonk (v1.47.1) with MAPQ>20, ignoring duplicates,  reads extended by 250bp and normalized to the number of million of reads (RPM). Replicates were merged, exported as bedgraph and converted to bigwig using UCSC BedGraphToBigWig
Broad Peaks were called on bam files with MACS2 (v2.2.6) using pooled Inputs as control with parameters --nomodel, FDR q=0.05, read extension 250bp, -b (broad option) with cutoff q=0.1
Peak sets of individual replicates were concatanated, sorted using BEDtools SortBED, overlapping and adjacent peaks (<500bp) merged using BEDtools Merge. From this resulting peakset only peaks were kept that overlap the peakset of individual replicates.
Assembly: mm10
Assembly: dm6
Supplementary files format and content: bigwig files, bed files for called Peak regions for the mouse genome

extract_protocol: After the appropriate treatment, cells were washed with cold PBS, crosslinked for 5min with 1% Formaldehyde at room temperature and subsequently quenched with 0.1M Glycin (final concentration) for 5min before harvesting. Then, nuclei were isolated and sonicated using the Covaris Chromatin Shearing Kit. ChIP-Immunoprecipation of chromatin was done using antibodies according to the manufacturers recommendation. Libraries were prepared from purified fragments  and sequenced.

treatment_protocol: If cells were treated, they were incubated with DMSO (volume equivalent) or Triptolide (10uM) for indicated times in the description before collection.

value: Triptolide (10uM) for 10min


title: Ovary SRSF1-cKO rep3 [cKO3]

city: Beijing

first: Jiali

last: Liu

address: 2 West Yuanmingyuan Road

country: China

institute: China Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2 v2.0.5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Ovary

growth_protocol: All mice were bred and housed under specific pathogen-free conditions with controlled temperature (22 ± 1℃) and exposed to a constant 12-hour light-dark cycle in the animal facilities of China Agricultural University. All experiments were conducted following the guidelines and with the approval of the Institutional Animal Care and Use Committee of China Agricultural University

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit v3-cBot-HS was used with 0.4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Conditional knockout

value: Ovary

value: 16.5 days post-coitus

value: Conditional knockout type


title: CPG (.1uM), IFNAR, 1h

value: IFNAR


title: DKD.3


title: Ovary SRSF1-cKO rep2 [cKO2]


title: ChOR_totalChIP_H2AK119ub_r2

value: wildtype


title: DKD.2

value: Adipose


title: CPG (.1uM), IFNAR, 3h


title: Tumor-bearing BM, scRNA-seq

description: 10x Genomics


title: Ovary SRSF1-cKO rep1 [cKO1]


title: ChOR_totalChIP_H2AK119ub_r1


title: Ovary WT rep3 [Control6]

value: wild type


title: DKD.6

value: Mesenchymal Stem Cells


title: ChOR_T0_H2AK119ub_r1


title: CPG (.1uM), RelBko, 3h

value: RelBko

value: CPG (.1uM)


title: DKD.1

value: DKD, Diabetic Nephropathy


title: ChOR_panH3_totalChIP_rep1


title: ChOR_totalChIP_H2BK120ub_TPL_r2


title: CPG (.1uM), RelBko, 1h


title: ChOR_panH2A_totalChIP_rep2


title: Ovary WT rep2 [Control5]


title: CPG (.1uM), WT, 8h

value: WT


title: A549_UV+_n3

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

description: replicate 1

data_processing:
Fastq files were generated using bcl2fastq. RNA-seq reads of good quality were trimmed in their 5' and 3’-ends with the cutadapt software to remove uninformative nucleotides due to primer sequences. Trimmed reads of 100 bp or more were aligned on the Human genome (hg19) using Tophat2. Only reads with a mapping quality score of 20 or more were retained (samtools) for downstream analysis.
Gene coordinates were obtained on the basis of overlapping Refseq transcripts with the same gene symbol. For each gene, two 500 bp regions located upstream and downstream the polyadenylation site (PAS) at the end of the gene were defined (genes with downstream region overlapping another gene were discarded), and reads located in the upstream and downstream regions were counted in each sample. A table of counts was built with the featureCounts software (R version 3.4.0). Only genes with at least 10 reads in both regions in either condition were kept for further analysis. In total, 4,208 genes passed all these steps and were used for subsequent analysis. The differential analysis between the UV+ and UV- conditions was done using two independent biological replicates per condition. For each gene, the fold regulation of the downstream region (that is the ratio of normalized read counts between conditions) was compared to the fold regulation of the upstream region using a Wald test implemented in DESeq2 (Love et al., 2014).
Assembly: hg19
Supplementary files format and content: xls

source_name: Non-small cell lung cancer cell line

growth_protocol: A549 cells were cultured in DMEM (Eurobio) containing 10% FCS (Pan Biotech) and L-Glutamine (Eurobio) at 37°C in 5% CO2.

extract_protocol:
Cell pellets were resuspended in approximately 3 x cell pellet volume of lysis Buffer A (10 mM HEPES pH 7.9, 15 mM MgCl2, 10 mM KCl, 0.1% NP40, 1 mM DTT) containing RNAseOut (Thermo Scientific) and incubated on ice for 15 min. Cells were then pelleted at 3000 rpm for 5 min at 4°C and the supernatant retained for cytoplasmic RNA. Nuclear pellets were washed in 2 x 1 mL Lysis Buffer A at 3000 rpm for 5 min at 4°C, resuspended in 2 x pellet volume with Nuclear Lysis Buffer B (20 mM HEPES pH 7.9, 400 mM NaCl, 1.5 M MgCl2, 0.2 mM EDTA, 5 mM DTT) containing RNAseOut and incubated on ice for 30 min. Nuclear debris was pelleted at 13 000 rpm for 15 min at 4°C and supernatants placed in Trizol Reagent for RNA extraction. RNA was extracted with TRIzol Reagent (ThermoFischer Scientific) according to the manufacturer’s instructions, and 1 µl of GlycoBlue (ThermoFisher Scientific) was added for RNA precipitation.
RNA was treated with TURBO DNase I (ThermoFisher Scientific), quantified and analyzed using an RNA 2100 Bioanalyzer (Agilent). 500 ng of good quality RNA (RIN > 9) were used for Illumina compatible library preparation using the Stranded total RNA protocol allowing to take into account strand information. A first step of ribosomal RNA depletion was performed using the RiboZero Gold kit (Illumina). After fragmentation, cDNA synthesis was performed and resulting fragments were used for dA-tailing followed by ligation of TruSeq indexed adapters. PCR amplification was finally achieved to generate the final barcoded cDNA libraries. Libraries were equimolarly pooled. Sequencing was carried out on a HiSeq instrument (Illumina) to obtain around 40 million raw single-end reads of 100 nucleotides per sample.

treatment_protocol: Cells were washed with PBS and irradiated with 40 J/m2 UV (254 nm; Stratalinker), placed in fresh media and harvested on ice after 16h of recovery at 37°C.

value: UVC irradiation

tag: extract

value: Nucleus


title: ChOR_panH2A_totalChIP_rep1


title: CPG (.1uM), WT, 3h

value: Bone Marrow


title: A549_UV+_n4

description: replicate 2


title: A549_UV-_n2

description: replicate 2

value: No irradiation


title: ChIP_410_H2BK120ub_r3

description: H2Bub_replicated_final_noblacklist_n21676.bed


title: CPG (.1uM), WT, 1h

value: BMDCs


title: A549_UV-_n1

description: replicate 1


title: RNA-Seq-8cell-3

city: Austin

first: Can

last: Cenik

state: TX

address: Moffett Molecular Biology Building 2.122 2500 Speedway

department: Molecular Biosciences

institute: The University of Texas at Austin

description:
RNA
cds_counts.csv.gz

data_processing:
For ribosome profiling experiments (conventional ribosome profiling and Ribo-ITP), 5’ adapters are of the form  NNNNNNNNNNNNXXXX where Ns correspond to the UMIs and Xs correspond to the nucleotides to be discarded. The sequence of the 3’ adapters is AAAAAAAAAACAAAAAAAAAA.   5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses.   After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools 56 version 1.11 for processing BAM files.   We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools version 1.1.1 with the following parameters: “umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex ”.  The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. Conventional ribosome profiling samples did not include UMIs.   Next we clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA, from the Ribo-ITP data, using cutadapt version 1.18 with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only”. For conventional ribosome profiling data, we removed the poly-A tails and the first three nucleotides of the reads using “cutadapt -u 3 -a AAAAAAAAAA --overlap=4 --trimmed-only”.  After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 version 2.3.4.3. The unaligned reads were mapped to a manually-curated transcriptome. We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools when applicable. In deduplication of external libraries without UMIs, a set of reads with the same length that are mapped to an identical nucleotide position are collapsed into a single read. As the last step, .ribo files are created using RiboPy version 0.0.1. All subsequent analyses used ribosome footprints that were 29-35 nucleotides in length.   For analyses involving nucleotide resolution data, we determined the A-site offset for each ribosome footprint length using translation stop site metagene plots. Specifically, for each read length, we identified the highest peak upstream of the translation stop site and used the distance to the annotated stop site as the offset.
For RNA-Seq experiments, 5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses. After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools version 1.11 for processing BAM files.
Supplementary_files_format_and_content: .ribo files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format. Number of reads mapping to CDS are given in the csv file cds_counts.csv.gz.

source_name: 8-cell Embryo

growth_protocol: Sperm was frozen from CAST/EiJ male mice and stored in liquid nitrogen. For in vitro fertilization, oocytes were isolated from C57BL/6J female mice approximately 15 h after hCG injection, and IVF was performed using thawed CAST/EiJ sperm 50. 1-cell, 2-cell, 4-cell, and 8-cell embryos were collected 21.5, 39, 62, and 69 h after hCG injection, respectively. Fertilized oocytes were cultured overnight to the 2-cell stage in a 150 µL drop of HTF medium (Cytospring, mH0113). For development to the 4-cell and 8-cell stages, 2-cell embryos were cultured in KSOM medium (Cytospring, K0114). Embryos were placed individually into 0.2 mL PCR tubes and flash-frozen in liquid nitrogen. All samples were processed with Ribo-ITP within 48 h of collection.

extract_protocol:
A working lysis buffer solution was prepared by adding 1 µL of the MNase (NEB) [1:50 dilution] per 5 µL lysis buffer. To lyse the mouse samples, 6 µL of working lysis buffer was added directly to the frozen cell-containing droplet. Digestion was immediately performed for 30 minutes at 37 °C in a thermal cycler with a heated lid. 1 µL EGTA was added to a final concentration of 10 mM to inhibit further digestion. Samples were placed on ice until processing through Ribo-ITP.
Total RNA sequencing libraries were prepared with Smart-seq3, with modifications. Unfertilized mouse samples (GV, MII) and in vitro fertilized mouse samples (1, 2, 4, and 8-cell stage) were lysed and reverse transcribed as described. cDNA was pre-amplified with 13 PCR cycles and bead purified with AMPure XP (1.8x) with a final elution in 5 µL nuclease-free water. 1 µL of pre-amplified cDNA was assessed by Bioanalyzer High Sensitivity DNA kit to confirm successful pre-amplification and proper size profile. Another 1 µL was assessed on Qubit using the dsDNA HS assay to quantify the pre-amplified cDNA. Samples were diluted with nuclease-free water and normalized to 600 pg inputs [100 pg/µL] and subjected to tagmentation and post-tagmentation PCR. The tagmentation and subsequent PCR were scaled up 6x: precisely,, 600 pg pre-amplified cDNA was tagmented with 6 µL of Tagmentation Mix, 9 µL of Nextera Index primers were added, and 18 µL of Tagmentation PCR mix was used. 16 PCR cycles were performed followed by equivolume sample pooling (12 µL of each PCR product) and AMPureXP purification at a 1x ratio. The final library size distribution and concentration was assessed with the HS DNA Bioanalyzer. Sequencing was performed with Nova Seq 6000 with paired-end reads (using 100 cycle kits: 60+40).

treatment_protocol: No treatment

tag: Stage

value: 8-cell Embryo

value: C57BL/6J x CAST/EiJ


first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

description:
ribominus RNA
Ribo-seq_cpeb1bmutant+lowdoseMO_22h_replicate_2

data_processing:
Low-quality bases were trimmed and filtered by cutadapt (V 1.13) and Trimmomatic (V 0.36). Processed reads were mapped to zebrafish rRNA transcriptome using bowtie and retain unmapped reads.
The remaining reads were mapped to zebrafish genome (Zv9) using TopHat (v2.1.1) with ‘‘–bowtie1’’. The expression levels of mRNAs were evaluated by Cufflinks v2.2.1 with ‘‘-p x -u -G’’. Translation efficiency of each mRNA was calculated by the ratio of RPFs and mean expression of mRNA input replicates.
Assembly: Zv9
Supplementary files format and content: fpkm for samples

organism: Danio rerio

extract_protocol:
The zebrafish embryos were incubated in 100 mg/ml cycloheximide (Selleck) buffer (5 mM NaCl, 0.2 mM KCl, 0.3 mM CaCl2, 0.3 mM MgSO4) for 5 min at 28°C. The embryos were then transferred into ice-cold lysis buffer. After triturating the embryos through the needle, the lysate was clarified by recovering the soluble supernatant after centrifugation for 10 min at 20,000 g at 4°C. 3 μl of RNase I (100 U/µl) was added to 600 μl of lysate. After a 45 min incubation at room temperature with gentle mixing, 10 µl of SUPERase·In RNase inhibitor (Invitrogen) was added to stop the nuclease digestion. MicroSpin S-400 HR columns (GE Healthcare) were equilibrated with 3 ml of polysome buffer by gravity flow and emptied by centrifugation at 600 g for 4 min. Immediately 100 µl of the digested lysate was loaded on the column and eluted by centrifugation at 600 g for 2 min. RNA was extracted from the flow-through using Trizol reagent (Invitrogen). Ribosomal RNA fragments were removed using the RiboZero Kit (Illumina) and were separated on a 17% denaturing urea-PAGE gel (National Diagnostics).
RNA fragments sized 27 nt to 30 nt were cut out from the gel, and were subjected to library preparation using the Smarter smRNA-Seq kit (Clontech).

value: zebrafish embryos

value: cpeb1b mutant

value: 22 hpf


title: RNA-Seq-8cell-2

description:
RNA
cds_counts.csv.gz


title: ChIP_410_H2BK120ub_r2

value: wildtype


title: Control, IFNAR, 1h

value: IFNAR

value: Control


title: Control, RelBko, 1h

value: RelBko


title: ChIP_410_H2AZ_r2

description: H2AZ_replicated_final_noblacklist_n19677.bed


title: Control, IFNAR;RelBko, 1h

value: IFNAR;RelBko


title: ChIP_410_H2BK120ub_r1


title: RNA-Seq-8cell-1

description:
RNA
cds_counts.csv.gz


title: Ribo-seq_wt+lowdoseMO_22h_replicate_2

description:
ribominus RNA
Ribo-seq_wt+lowdoseMO_22h_replicate_2

value: wild type


title: ChIP_410_H2AZ_r1


title: Control, WT, 1h

value: WT


title: RNA-Seq-4cell-2

description:
RNA
cds_counts.csv.gz

source_name: 4-cell Embryo

value: 4-cell Embryo


title: RNA-Seq-8cell-4

description:
RNA
cds_counts.csv.gz


title: Ovary WT rep1 [Control4]

value: Ovary

value: 16.5 days post-coitus


description:
ribominus RNA
Ribo-seq_cpeb1bmutant+lowdoseMO_22h_replicate_1


title: RNA-Seq-2cell-4

description:
RNA
cds_counts.csv.gz

source_name: 2-cell Embryo

value: 2-cell Embryo


title: ChIP_522_H3K27me3_r1

description: H3K27me3_replicated_final_noblacklist_n11502.bed

value: wildtype (untreated)

value: DMSO


title: RNA-Seq-4cell-1

description:
RNA
cds_counts.csv.gz

value: C57BL/6J x CAST/EiJ


description:
ribominus RNA
Ribo-seq_cpeb1bmutant+lowdoseMO_16h_replicate_1

value: zebrafish embryos

value: 16 hpf


title: RNA-Seq-2cell-3

description:
RNA
cds_counts.csv.gz


title: B16 Wild-type 0ng/ml IFNg Rep 3

first: Stephanie

last: Dougan

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

data_processing:
Quantification of transcripts from reads was performed using Salmon (v1.8.0) with the mouse GRCm39 reference genome and Gencode transcript release v27
The R package tximport (v1.18.0) was used to quantify transcript abundance and DESeq2 (v1.30.1) was used to identify differentially expressed genes.
Assembly: GRCm39; Gencode transcript release v27
Supplementary files format and content: Comma-separated file of raw, un-normalized read counts from tximport following Salmon

source_name: Tumor

extract_protocol:
Qiagen RNeasy Plus Kit
RNA libraries were prepared for sequencing at Genewiz using standard Illumina protocols

treatment_protocol: 0 or 100ng/ml IFNg for 24 hours at 37C

value: Tumor

value: Melanoma

value: Wild-type

value: 0 ng/ml IFNg


title: B16 Wild-type 100ng/ml IFNg Rep 3

value: 100 ng/ml IFNg


title: ChIP_410_H2AK119ub_r3

description: H2Aub_replicated_final_noblacklist_4703.bed

value: wildtype


title: Ribo-seq_wt+lowdoseMO_16h_replicate_2

description:
ribominus RNA
Ribo-seq_wt+lowdoseMO_16h_replicate_2

value: wild type


title: RNA-Seq-2cell-2

description:
RNA
cds_counts.csv.gz


title: ChIP_410_H2AK119ub_r2


title: Ribo-seq_wt+lowdoseMO_22h_replicate_1

description:
ribominus RNA
Ribo-seq_wt+lowdoseMO_22h_replicate_1

value: 22 hpf


title: B16 Wild-type 0ng/ml IFNg Rep 2


title: Ribo-seq_wt+lowdoseMO_16h_replicate_1

description:
ribominus RNA
Ribo-seq_wt+lowdoseMO_16h_replicate_1


title: ChIP_410_H2AK119ub_r1


title: ChIP_410_H3K27me3_r2.


title: RNA-Seq-2cell-1

description:
RNA
cds_counts.csv.gz


description:
ribominus RNA
Ribo-seq_cpeb1bmutant+lowdoseMO_8h_replicate_2

value: cpeb1b mutant

value: 8 hpf


title: B16 STAT1-/- 100ng/ml IFNg Rep 3


title: RNA-Seq-1cell-4

description:
RNA
cds_counts.csv.gz

source_name: 1-cell Embryo

value: 1-cell Embryo


description:
ribominus RNA
Ribo-seq_cpeb1bmutant+lowdoseMO_8h_replicate_1


title: ChIP_Input_r3


description:
ribominus RNA
Ribo-seq_cpeb1bmutant+lowdoseMO_16h_replicate_2


title: Ribo-seq_wt+lowdoseMO_8h_replicate_2

description:
ribominus RNA
Ribo-seq_wt+lowdoseMO_8h_replicate_2


title: RNA-Seq-1cell-3

description:
RNA
cds_counts.csv.gz


title: ChIP_Input_r2


title: RNA-Seq-1cell-2

description:
RNA
cds_counts.csv.gz


title: Ribo-seq_wt+lowdoseMO_8h_replicate_1

description:
ribominus RNA
Ribo-seq_wt+lowdoseMO_8h_replicate_1


title: B16 Wild-type 100ng/ml IFNg Rep 2


title: B16 STAT1-/- 0ng/ml IFNg Rep 3


title: RNA-Seq-1cell-1

description:
RNA
cds_counts.csv.gz


title: SCAR_410_strandedInput_MCM2Series_T0_r3

description: EdU-labelled genomic DNA

data_processing:
adapters and low quality reads were filtered with TrimGalore (v0.0.6)
reads were mapped to the genome with bowtie2 (v2.4.2) and uniquely mapped peaks kept using samtools (v1.12)
duplicate reads were removed with picard (version 2.26.10)
bam files were split into forward and reverse strands according to the SAM flag, using samtools view (version 1.5) -F 20 and -f 16, respectively
For each strand the SCAR normalized signal (CPM) was computed in 1kb bins and smoothed in a uniform blur considering the neighboring 30 bins on each side. For each 1kb window, the signal from its corresponding SCAR input was subtracted and negative values were set to zero
Assembly: mm10
Supplementary files format and content: SCAR-seq Partition scores in bigwig format
Library strategy: SCAR-Seq

extract_protocol: After the appropriate treatment, cells were collected by scraping and nuclei were isolated. Chromatin was digested with MNase. Sequentially, mononucleosomal fragments were immunoprecipitated, purified fragments were biotinylated, libraries were prepared, EdU-biotin fragments were pulled-down and sequenced.

treatment_protocol: Cells were incubated in EdU media (f.c. 10 µm)  for 10 min and then either collected (T0) or cultured for indicated maturation intervals (T30; T3; T8) in media without EdU before collection. If treated with DMSO or Indole-3-acetic acid (IAA), cells were incubated for 1h50 with 500uM IAA or DMSO prior to incubation with EdU for 10 min and then either collected (T0) or cultured for indicated timed in media without EdU but continuously with IAA or DMSO


description:
ribominus RNA
RNA-seq_cpeb1bmutant+lowdoseMO_22h_replicate_2

data_processing:
Low-quality bases were trimmed and filtered by cutadapt (V 1.13) and Trimmomatic (V 0.36)
Processed reads were mapped to zebrafish genome (Zv9) from Ensembl annotation using hisat2 (V 2.0.5) with default parameters. After mapping quality (≥ 20) filtering using SAMtools (V1.9), read counts and corresponding RPKM were calculated. The final RPKM of each transcript is the average of RPKMs in replicates.
Assembly: Zv9
Supplementary files format and content: rpkm for samples

extract_protocol:
The entire embryo was used for RNA-seq. The RNA-seq was performed in duplicates, and each group had 10 embryos per replicate. Total RNA was extracted from the embryos at different developmental stages by TRIzol reagent (Invitrogen) .
The RNA was purified using RiboMinus Eukaryote Kit v2.


title: RNA-Seq-MII-4

description:
RNA
cds_counts.csv.gz

source_name: MII-stage Oocyte

growth_protocol: Oocytes were collected from superovulated C57BL/6J female mice as previously described in (Chen, J. et al. Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition. Genes Dev. 25, 755–766, 2011). One hour after human Chorionic Gonadotropin (hCG) injection, the ovaries were placed in a 3 cm dish containing FHM medium (Cytospring, F1114), and Germinal vesicle (GV)-stage oocytes were released by scraping the surface of the ovaries with #5 Dumont forceps (Roboz). Meiosis II (MII)-stage oocytes were isolated from the oviducts approximately 14 h after hCG injection. Cumulus cells were removed from the oocytes by treatment with 1 mg/mL Hyaluronidase (Sigma H3884) in FHM medium. Both GV- and MII-stage oocytes were rinsed through three drops of FHM medium and then through three drops of 20 mg/mL BSA (Sigma A3311) in PBS (Hyclone SH30028.02). The oocytes were placed individually in 0.2 mL PCR tubes using a finely pulled glass pipette under a stereomicroscope and flash-frozen in liquid nitrogen. The liquid volume transferred with the oocytes was less than 0.5 µL.

value: MII-stage Oocyte


title: single cells KO_1_lungs

city: Augusta

first: Kebin

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Augusta University

data_processing:
Sequencing : Illumina NextSeq 500 platform under the following sequencing protocol: 28 bp (Read 1), 8 bp (indexing Run), and 91 bp (RNA Read 2)
Mapping: STAR aligner in Cell Ranger 3.1.0 pipeline
Genome_build: mm10 Mouse Genome
Supplementary_files_format_and_content: matrix, barcodes and features of rawcounts

source_name: Tumor-bearing Lung

extract_protocol:
Balb/c mice were injected i.v. with 2.5*105 4T1 WT or PDL1-KO cells. After fourteen days, mice were sacrificed, lungs were perfused with PBS and harvested. Following collagenase digestion, leukocytes were positively selected using CD45 magnetic nanobeads (Biolegend).
Chromium Single Cell 3’ Reagent Kit v3

tag: cell line injected

value: 4T1.PD-L1 KO

value: Balb/c


title: B16 Wild-type 100ng/ml IFNg Rep 1


title: B16 Wild-type 0ng/ml IFNg Rep 1


title: RNA-Seq-MII-3

description:
RNA
cds_counts.csv.gz


description:
ribominus RNA
RNA-seq_cpeb1bmutant+lowdoseMO_22h_replicate_1


title: single cells WT_2_lungs


title: B16 STAT1-/- 100ng/ml IFNg Rep 1


title: RNA-seq_wt+lowdoseMO_22h_replicate_2

description:
ribominus RNA
RNA-seq_wt+lowdoseMO_22h_replicate_2


title: RNA-Seq-MII-2

description:
RNA
cds_counts.csv.gz


title: ChIP_Input_r1


title: RNA-seq_wt+lowdoseMO_22h_replicate_1

description:
ribominus RNA
RNA-seq_wt+lowdoseMO_22h_replicate_1


title: single cells WT_1_lungs


title: B16 IFNgR1-/- 100ng/ml IFNg Rep 3


title: B16 STAT1-/- 0ng/ml IFNg Rep 1


description:
ribominus RNA
RNA-seq_cpeb1bmutant+lowdoseMO_16h_replicate_1


title: B16 STAT1-/- 100ng/ml IFNg Rep 2


title: RNA-Seq-GV-4

description:
RNA
cds_counts.csv.gz

source_name: GV-stage Oocyte

value: GV-stage Oocyte


title: RNA-Seq-MII-1

description:
RNA
cds_counts.csv.gz


title: single cells KO_2_lungs


description:
ribominus RNA
RNA-seq_cpeb1bmutant+lowdoseMO_16h_replicate_2

value: zebrafish embryos


title: B16 IFNgR1-/- 100ng/ml IFNg Rep 2


title: B16 IFNgR1-/- 0ng/ml IFNg Rep 3


title: RNA-seq_wt+lowdoseMO_16h_replicate_2

description:
ribominus RNA
RNA-seq_wt+lowdoseMO_16h_replicate_2

value: 16 hpf


title: Dam_Met4_2

city: Edinburgh

first: Frederic

last: Li Mow Chee

address: Crewe Road

department: Edinburgh Cancer Centre

country: United Kingdom

institute: University of Edinburgh

description: DamID-seq data from untethered Dam-expressing Met4 cSCC cells

data_processing:
Library strategy: DamID-Seq
Nextera adaptor trimming was performed using TrimGalore (version 0.6.3; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the minimum required overlap with the adaptor sequence set to 5
Single-end read binning against the human reference genome (GRCh38) was performed using BBSplit, part of the BBMap package (version 38.11; https://sourceforge.net/projects/bbmap/)
Binned reads were aligned to the human reference genome using Bowtie2 (version 2.3.4.3)
Mapped reads were sorted and indexed using SAMtools (version 1.6)
The human reference genome was binned into GATC motifs fragments and expanded by 250 bp on either side (500-bp fragment window)
Single-end reads were imported as a GenomicRanges object in R, and the average number of reads within the 500-bp GATC window tilling the entire human chromosomes was computed
Read values were normalised to the total number of mapped reads (excluding decoy chromosomes). Ratios of Dam-lamin B1 versus untethered Dam control normalised reads were calculated and binary-logarithm-transformed
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph

source_name: Cutaneous squamous cell carcinoma

growth_protocol: Human cSCC Met4 and Met4 Mena-/- cells were cultured in RM+ medium consisting of high-glucose Dulbecco’s modified Eagle’s medium (DMEM; Sigma-Aldrich, #D6546) and Ham’s F-12 nutrient mixture (Life Technologies, #21765-037) (3:1 DMEM:Ham’s F-12 ratio) supplemented with 10% (v/v) foetal bovine serum (FBS; Life Technologies, #10270-106), 0.4 μg/ml hydrocortisone (STEMCELL Technologies, #7904), 3 mM L-glutamine (#200049), 5 μg/ml transferrin (#T2252), 1 × 10^−10 M cholera toxin (#C8052), 10 ng/ml epidermal growth factor (#E2644), 5 μg/ml insulin (#I9278) and 0.2 M liothyronine (all Sigma-Aldrich, #T6397)

extract_protocol:
Genomic DNA (gDNA) extraction was performed using a DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer instructions
For methylated GATC library preparation, gDNA (300 ng) was digested using DpnI (New England Biolabs) for 6 h at 37°C, followed by DpnI inactivation for 20 min at 80°C. dsAdR adaptor ligation was performed using T4 DNA ligase (New England Biolabs) overnight at 16°C, followed by ligase inactivation for 10 min at 65°C. Digestion using DpnII (New England Biolabs) was then performed for 1 h at 37°C, followed by DpnII inactivation for 20 min at 65°C. The reaction mixture was purified using a PCR purification kit (Qiagen) and eluted in RNase-free water. Initial PCR amplification was performed using AdR_PCR primers and SYBR Select master mix (PCR cycles 1–5), with the extension temperature was set at 72°C. The optimum number of remaining cycles was determined by plotting linear Rn (passive reference dye-normalised reporter signal) versus cycle number and calculating the number of cycles corresponding to 10× initial fluorescence intensity to avoid PCR duplication. Methylated GATC gDNA fragments were purified using solid-phase reversible immobilisation beads and eluted in RNase-free water. GATC gDNA fragments (50 ng) were treated with Nextera Tn5 transposase (Illumina) for 5 min at 37°C with shaking. The transposase reaction was stopped by adding binding buffer from the PCR purification kit, and tagged DNA fragments were eluted in RNase-free water. DNA fragments were indexed and barcoded and PCR-amplified using Ad1_noMX and Ad2.n primers and SYBR Select master mix, with initial holding temperature of 72°C (5 min) followed by 98°C (30 s). The optimum number of cycles was determined by qPCR (as above) at a denaturing temperature of 98°C (10 s), annealing temperature of 63°C (30 s) and extension temperature of 72°C (1 min). Library fragments were purified using solid-phase reversible immobilisation beads and eluted in RNase-free water

treatment_protocol: Met4 and Met4 Mena-/- cells in 6-well plates were transduced with lentivirus for Dam-lamin B1 or untethered Dam, transferred to 15-cm dishes and incubated for 60 h

tag: tumor stage

value: Metastatic cSCC

value: Met4 malignant keratinocyte

tag: genetic modificaton

value: Parental

tag: construct

value: Untethered Dam


title: Dam_Met4_Mena_null_2

description: DamID-seq data from untethered Dam-expressing Met4 Mena-/- cSCC cells

tag: cell line

value: Mena knockout


title: B16 STAT1-/- 0ng/ml IFNg Rep 2

value: Tumor

value: Melanoma

tag: genotype

value: 0 ng/ml IFNg


title: LMNB1_Met4_Mena_null_2

description: DamID-seq data from Dam-lamin B1-expressing Met4 Mena-/- cSCC cells

value: Dam-lamin B1


title: RNA-Seq-GV-2

description:
RNA
cds_counts.csv.gz

tag: strain


title: RNA-Seq-GV-3

description:
RNA
cds_counts.csv.gz


title: B16 IFNgR1-/- 0ng/ml IFNg Rep 2

tag: treatment


title: RNA-seq_wt+lowdoseMO_16h_replicate_1

description:
ribominus RNA
RNA-seq_wt+lowdoseMO_16h_replicate_1

tag: tissue

value: wild type


title: B16 IFNgR1-/- 100ng/ml IFNg Rep 1

tag: cell type

value: 100 ng/ml IFNg


title: DamID-seq data from untethered Dam-expressing Met4 Mena-/- cSCC cells

description:
Dam_Met4_Mena_null
MenaKO.bedgraph

data_processing:
Library strategy: DamID-Seq
Nextera adaptor trimming was performed using TrimGalore (version 0.6.3; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the minimum required overlap with the adaptor sequence set to 5
Single-end read binning against the human reference genome (GRCh38) was performed using BBSplit, part of the BBMap package (version 38.11; https://sourceforge.net/projects/bbmap/)
Binned reads were aligned to the human reference genome using Bowtie2 (version 2.3.4.3)
Mapped reads were sorted and indexed using SAMtools (version 1.6)
The human reference genome was binned into GATC motifs fragments and expanded by 250 bp on either side (500-bp fragment window)
Single-end reads were imported as a GenomicRanges object in R, and the average number of reads within the 500-bp GATC window tilling the entire human chromosomes was computed
Read values were normalized to the total number of mapped reads (excluding decoy chromosomes). Ratios of Dam-lamin B1 versus untethered Dam control normalized reads were calculated and binary-logarithm-transformed
Genome_build: GRCh38
Supplementary_files_format_and_content: bedgraph

extract_protocol:
Genomic DNA (gDNA) extraction was performed using a DNeasy Blood & Tissue Kit (Qiagen) according to manufacturer instructions
For methylated GATC library preparation, gDNA (300 ng) was digested using DpnI (New England Biolabs) for 6 h at 37°C, followed by DpnI inactivation for 20 min at 80°C. dsAdR adaptor ligation was performed using T4 DNA ligase (New England Biolabs) overnight at 16°C, followed by ligase inactivation for 10 min at 65°C. Digestion using DpnII (New England Biolabs) was then performed for 1 h at 37°C, followed by DpnII inactivation for 20 min at 65°C. The reaction mixture was purified using a PCR purification kit (Qiagen) and eluted in RNase-free water. Initial PCR amplification was performed using AdR_PCR primers and SYBR Select master mix (PCR cycles 1–5), with the extension temperature was set at 72°C. The optimum number of remaining cycles was determined by plotting linear Rn (passive reference dye-normalized reporter signal) versus cycle number and calculating the number of cycles corresponding to 10× initial fluorescence intensity to avoid PCR duplication. Methylated GATC gDNA fragments were purified using solid-phase reversible immobilisation beads and eluted in RNase-free water. GATC gDNA fragments (50 ng) were treated with Nextera Tn5 transposase (Illumina) for 5 min at 37°C with shaking. The transposase reaction was stopped by adding binding buffer from the PCR purification kit, and tagged DNA fragments were eluted in RNase-free water. DNA fragments were indexed and barcoded and PCR-amplified using Ad1_noMX and Ad2.n primers and SYBR Select master mix, with initial holding temperature of 72°C (5 min) followed by 98°C (30 s). The optimum number of cycles was determined by qPCR (as above) at a denaturing temperature of 98°C (10 s), annealing temperature of 63°C (30 s) and extension temperature of 72°C (1 min). Library fragments were purified using solid-phase reversible immobilisation beads and eluted in RNase-free water


title: RNA-Seq-GV-1

description:
RNA
cds_counts.csv.gz


description:
ribominus RNA
RNA-seq_cpeb1bmutant+lowdoseMO_8h_replicate_2

value: cpeb1b mutant

value: 8 hpf


title: DamID-seq data from untethered Dam-expressing Met4 cSCC cells

description:
Dam_Met4
Met4.bedgraph


title: Ribo-ITP-8cell-4

description:
RNA from Ribosome Protected Footprint
mouse-itp_v5.ribo

data_processing:
Library strategy: Ribo-ITP
For ribosome profiling experiments (conventional ribosome profiling and Ribo-ITP), 5’ adapters are of the form  NNNNNNNNNNNNXXXX where Ns correspond to the UMIs and Xs correspond to the nucleotides to be discarded. The sequence of the 3’ adapters is AAAAAAAAAACAAAAAAAAAA.   5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses.   After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools 56 version 1.11 for processing BAM files.   We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools version 1.1.1 with the following parameters: “umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex ”.  The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. Conventional ribosome profiling samples did not include UMIs.   Next we clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA, from the Ribo-ITP data, using cutadapt version 1.18 with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only”. For conventional ribosome profiling data, we removed the poly-A tails and the first three nucleotides of the reads using “cutadapt -u 3 -a AAAAAAAAAA --overlap=4 --trimmed-only”.  After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 version 2.3.4.3. The unaligned reads were mapped to a manually-curated transcriptome. We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools when applicable. In deduplication of external libraries without UMIs, a set of reads with the same length that are mapped to an identical nucleotide position are collapsed into a single read. As the last step, .ribo files are created using RiboPy version 0.0.1. All subsequent analyses used ribosome footprints that were 29-35 nucleotides in length.   For analyses involving nucleotide resolution data, we determined the A-site offset for each ribosome footprint length using translation stop site metagene plots. Specifically, for each read length, we identified the highest peak upstream of the translation stop site and used the distance to the annotated stop site as the offset.
For RNA-Seq experiments, 5’ adapter sequence “ATTGCGCAATG” was clipped from the first read in the pair using cutadapt version 1.18. Clipped reads shorter than 8 nucleotides were removed using: “cutadapt -j 4 --trimmed-only -m 8  -g ATTGCGCAATG”. We then extracted the next 8 nucleotides corresponding to the UMIs from the first read in the pair and appended them to the headers (of FASTQ files) of both read pairs using UMI-tools with the following parameters: “umi_tools extract --bc-pattern NNNNNNNN”.  After UMI extraction, we used the second read in the pair (40 nt) for all subsequent analyses. After filtering out reads aligning to a reference of ribosomal and tRNAs, the remaining reads were aligned to a transcriptome reference where SNPs were masked with Ns (see the next section for details); thereafter, we retained only the alignments with mapping quality greater than 2. We then collapsed reads that align to the same transcript using their respective UMIs: “umi_tools dedup --per-contig --per-gene”. For each transcript, we counted the number of reads aligning to the coding sequence. We used bowtie2 for all alignments and samtools version 1.11 for processing BAM files.
Supplementary_files_format_and_content: .ribo files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format. Number of reads mapping to CDS are given in the csv file cds_counts.csv.gz.

extract_protocol:
A working lysis buffer solution was prepared by adding 1 µL of the MNase (NEB) [1:50 dilution] per 5 µL lysis buffer. To lyse the mouse samples, 6 µL of working lysis buffer was added directly to the frozen cell-containing droplet. Digestion was immediately performed for 30 minutes at 37 °C in a thermal cycler with a heated lid. 1 µL EGTA was added to a final concentration of 10 mM to inhibit further digestion. Samples were placed on ice until processing through Ribo-ITP.
For 100-cell human K562 cells and all mouse samples, Ribo-ITP outputs were immediately processed through the D-Plex Small RNA-seq Kit (Diagenode C05030001) with minor modifications as detailed here. The dephosphorylation reaction was supplemented with 0.5 µL T4 PNK (NEB) and the reaction was incubated for 25 minutes. For reverse transcription, the template switching oligo (TSO) was diluted 1:2 in nuclease-free water. All 100-cell human samples and three of the MII-stage oocytes were processed using the single index (SI) module; while the other mouse samples were processed using the unique dual index (UDI) module. Half of the cDNA was amplified for 17 PCR cycles and a 1:4 dilution of the resulting library was assessed by Agilent Bioanalyzer High Sensitivity DNA kit. The concentrations of the target peaks were used to pool samples with approximately equimolar representation. AMPure XP bead cleanup (1.8x) was performed followed by size-selection using 3% agarose, dye-free gel cassettes with internal standards (Sage Science BDQ3010) on the BluePippin platform. Tight parameter settings of 173-207 bp range were used for samples prepared with the SDI module. Tight parameter settings of 183-217 bp range were used for samples prepared with the UDI module. Samples were sequenced on a Illumina NovaSeq 6000.

value: 8-cell Embryo

value: C57BL/6J x CAST/EiJ


description:
ribominus RNA
RNA-seq_cpeb1bmutant+lowdoseMO_8h_replicate_1

value: zebrafish embryos


title: Ribo-ITP-8cell-3


title: B16 IFNgR1-/- 0ng/ml IFNg Rep 1


title: RNA-seq_wt+lowdoseMO_8h_replicate_2

description:
ribominus RNA
RNA-seq_wt+lowdoseMO_8h_replicate_2


title: DamID-seq data from Dam-lamin B1-expressing Met4 Mena-/- cSCC cells

description:
LMNB1_Met4_Mena_null
MenaKO.bedgraph


title: Ribo-ITP-8cell-2


title: RNA-seq_wt+lowdoseMO_8h_replicate_1

description:
ribominus RNA
RNA-seq_wt+lowdoseMO_8h_replicate_1


title: Ribo-ITP-8cell-1


title: DamID-seq data from Dam-lamin B1-expressing Met4 cSCC cells

description:
LMNB1_Met4
Met4.bedgraph


title: LMNB1_Met4_2

description: DamID-seq data from Dam-lamin B1-expressing Met4 cSCC cells


title: Flag_Cpeb1b_replicate_2

data_processing:
The quality of raw sequencing reads was processed using FastQC and low-quality bases were trimmed and filtered by cutadapt (V 1.13) (11) and Trimmomatic (V 0.36) (12). Processed reads were mapped to the zebrafish genome (Zv9) using TopHat (v2.1.1) (18) with ‘‘–bowtie1’’.
The target binding regions of Cpeb1b were identified using MACS2 software (version 2.0.10). The target genes were annotated based on Ensembl (release 79) gene annotation information by applying BEDTools’ intersectBed (version 2.16.2).
Assembly: Zv9
Supplementary files format and content: rpkm for samples

extract_protocol:
Flag-cpeb1b mRNA injected embryos were collected at 16 hpf and lysed in NETN lysis buffer (150 mM NaCl, 0.5% NP-40, 50 mM Tris-HCl, pH 7.4, RNase inhibitor, Roche cocktail protease inhibitor). The lysate was incubated with anti-FLAG M2 Magnetic Beads (Merck) for 4 h at 4 °C. Then, the beads were washed five times with the lysis buffer and five times with TBS buffer. For RIP-seq assay, the bead-bound RNA was extracted and then fragmented by RNA Fragmentation Reagent (Ambion).
The fragmented RNA was subjected to library construction using the SMARTer smRNA-Seq kit (Clontech).

value: 16 hpf


title: Flag_Cpeb1b_replicate_1


title: Ribo-ITP-4cell-3

value: 4-cell Embryo


title: RNA-Seq FZX_Fr_M3

city: Guangzhou

first: Liu

last: Hailun

address: Tianhe District

description:
FZX_Fr_M3
Mock treatment

data_processing:
Illumina Casava1.8 software used for basecalling.
Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
GO analysis was performed by the GO Annotation of TAIR.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
Assembly: 'Feizixiao'. Feizixiao Genome sequencing and assembly can be found in the NCBI database under accession number PRJNA747875.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

organism: Litchi chinensis

source_name: fruits

growth_protocol: Lychee trees were planted in National lychee Germplasm Nursery located in Institute of Fruit Tree Research Guangdong Academy of Agricultural Sciences.

extract_protocol:
Total RNA was extracted from the treated leaves by Plant RNA Kit (Promega, LS1040).
In the construction of Strand-specific RNA-seq (removal of ribosomal RNA), the epicenter Ribo-ZeroTM kit was used to remove the ribosomal RNA. Then, rRNA-depleted RNA was fragmented and used as a template to construct the cDNA library.The qualities of the library was further tested following these steps: 1) Initial quantification was performed using Qubit 2.0, and the insert size of the library was tested using Agilent 2100. 2) The Q-PCR method was used to accurately quantify the effective concentration of the library (effective library concentration > 2 nM). After the library's quality tests were passed, the library performed pooling according to the amount of target data, followed by sequencing on the Illumina NovaSeq platform.
ssRNA-Seq (stranded RNA-seq)

treatment_protocol: Lychee leaves and fruits were inoculated with P.litchii (1 × 104 spores·mL−1) or mock (sterile water).

value: fruits

value: mock

value: Feizixiao

value: Sterile water (Mock-inoculation)

tag: time


title: RNA-Seq FZX_Fr_M2

institute: Guangdong Academy of Agricultural Sciences

description:
FZX_Fr_M2
Mock treatment


title: RNA-Seq FZX_Fr_C3

description:
FZX_Fr_C3
P.litchii treatment

value: Peronophythora litchii

value: Inoculation with P.litchii ( 1 x 10^4 spores ml ^-1)


title: RNA-Seq FZX_Fr_M1

description:
FZX_Fr_M1
Mock treatment


title: Acute HS (40oC), TP medium, T3b, Replicate B

city: St. Louis

first: Ru

last: Zhang

address: 95 N Warson Rd

institute: Donald Danforth Plant Science Center

data_processing:
From the Illumina sequencing reads, common cassette sequences were trimmed using Geneious v10.1.3, leaving only the unique DNA barcodes.
The number of reads from each unique DNA barcode was quantified, and the total number of reads for each sample was normalized to 100 million.
Supplementary files format and content: .csv files containing the CLiP mutant library barcode and the corresponding number of normalized reads present in the sample. Each DNA sample has 2 processed files, one for 5' barcodes and one for 3' barcodes
Library strategy: genome-wide pooled mutant screens

organism: Chlamydomonas reinhardtii

source_name: Asynchronous single cells

growth_protocol: All Chlamydomonas liquid cultivation used in this paper were conducted in photobioreactors (PBRs) as described before (Zhang et al. 2022a) with minor modifications.  Algal cultures were grown in standard Tris-acetate-phosphate (TAP, with acetate, an organic carbon source) or Tris-phosphate (TP, without acetate) medium with modified trace elements (Kropat et al. 2011) in 1-L PBRs (Photon System Instruments, FMT 150/1000-RB). Cultures were illuminated with constant 100 µmol photons m2 s−1 light (50% red: 50% blue) and mixed by bubbling with filtered air. After inoculation, cultures grew to a target cell density of 2×106 cells/mL in log-phase growth at 25°C. Then, the target cell density was maintained turbidostatically using OD680 (monitored every 1 min automatically) by allowing the culture to grow to 8% above the target cell density before being diluted to 8% below the target cell density with fresh medium provided through peristaltic pumps. Through the turbidostatic mode, the PBR cultures had constant nutrient supply, controlled cell density, and exponential growth between dilution events. The OD680 measurements during exponential growth phases in between dilution events were log2 transformed, and the relative growth rate was calculated using the slope of log2(OD680) while the inverse of the slope yielded the doubling time of the culture (Zhang et al. 2022a). OD680 is a non-disruptive, efficient, and automatic measurement with 1-min resolution and high sensitivity, which is well suited for algal growth measurement under our cultivation conditions with turbidostatic control and constant dilutions. We used a small OD680 range for turbidostatic control. OD680 data is sensitive enough to quantify algal growth during each short exponential growth phase. The growth rates calculated by OD680 was mostly for us to estimate the stress level of different high temperature treatments. Different treatments (different temperatures and medium type) were conducted in individual PBRs. For WT CC-5325 cultures, cells were first acclimated at 25°C for 2-days until reaching steady growth rates before treatments at different high temperatures. Each high temperature treatment was conducted in individual PBRs with replicates.

extract_protocol:
Genomic DNA was extracted for DNA barcode amplification as described before (Li et al. 2016) with minor modifications. Frozen cell pellets (from one copy of 50 mL cultures) were mixed with 800 µL of SDS-EDTA buffer (1% SDS, 200 mM NaCl, 20 mM EDTA, 50 mM Tris-HCL, pH 8) and separated into two equal aliquots for downstream processing. Then, 500 µL of 24:25:1 phenol:chloroform:isoamyl alcohol (Sigma, P2069-400ML) was added to each tube. Samples were vortexed for 2 min, centrifuged for 5 min at 10,000 g, and the aqueous phase was aliquoted into a new PhaseLock tube (VWR, Cat No. 10847-800), added with 1.6 µL of 100 mg/µL RNaseA (ThermoFisher Scientific, Cat. No. 1209102), and incubated at 37oC for 30 min. The phenol/chloroform DNA extraction was repeated three additional times. After the final extraction, samples were transferred to a new 1.5 mL tube and 2.5 volumes cold 100% ethanol was added. Samples were incubated in a -20oC freezer for 1 h then centrifuged at 16,000 g for 20 min at 4oC. Supernatant was decanted and pellets were washed in 1 mL cold 70% ethanol. Supernatant was decanted, pellets dried for 30 min at room temperature and DNA pellets were resuspended in 50 µL molecular grade water. Like samples were combined into a single tube then quantified by high sensitivity DNA Qubit (ThermoFisher scientific, Cat. No. Q32854).
Because samples were pooled together for sequencing, barcode amplification primers contained unique indexes for downstream identification in the data analysis pipeline (Supplemental Dataset 1b). Prior to sequencing, eight DNA samples were pooled together for a total of 23.75 ng of each DNA sample in a final volume of 25 µL. Samples were sequenced at the Department of Energy Joint Genome Institute (DOE JGI) using the Illumina Hi-seq platform. The prepared libraries were quantified using KAPA Biosystems' next-generation sequencing library qPCR kit and ran on a Roche LightCycler 480 real-time PCR instrument. Sequencing of the flowcell was performed on the Illumina NextSeq500 sequencer using NextSeq500 Mid Output kits, v2, following a 1 x 50 indexed run recipe utilizing a custom sequencing primer. Reads were mapped to each DNA sample using the index code contained in the PCR amplification primer. Each DNA sample had an average of 27 million reads and the minimum number of reads was 8 million.

treatment_protocol: For pooled screens, the CLiP mutant library was pooled as described before (Fauser et al. 2022) with minor modifications. The CLiP library was replicated using a Singer RoToR robot (Singer Instruments, 704) on 384-format 1.5% TAP agar plates and grown in the dark. Five-day-old fresh plates with the CLiP mutant library were pooled using sterile glass spreaders in liquid TAP medium, vortexed to break the colonies, grown on a shaker in the dark at room temperature overnight before being inoculated into PBRs the next day. This gave cells time to acclimate from solid agar to liquid cultures before inoculation to PBRs. Pooled CLiP liquid cultures were diluted using TAP or TP medium before being inoculated into PBRs at 25°C in TAP or TP medium (initial cell density around 1x106 cells mL-1) and acclimated at 25°C in the light for 2 days to reach steady growth rates with turbidostatic control before the start of heat treatments. Acclimation at 25°C in the light was used to reduce false-positive heat-sensitive mutants that have difficulty adjusting from growth on solid to liquid medium or from dark to light conditions. The heat of 35°C lasted 4 (TAP) or 5 (TP) days and the heat of 40°C lasted 2 days because the algal cultures would not survive if heated at 40°C for longer. After 40oC heat, cultures recovered at 25oC for 3 days.  Algal cultures of pooled mutants (2 x 50 mL) were harvested before and after the heat treatments or by the end of recovery using centrifugation at 4°C for 5 min. Cell pellets were stored at -80oC before DNA extraction and barcode amplification.

value: Asynchronous single cells

value: CLiP mutant library

value: vegatative

value: 40oC, TP medium


title: Acute HS (40oC), TP medium, T3b, Replicate A


title: RNA-Seq FZX_Fr_C2

description:
FZX_Fr_C2
P.litchii treatment


title: Ribo-ITP-4cell-2


title: Ribo-ITP-4cell-1


title: Acute HS (40oC), TP medium, T1, Replicate B


title: Ribo-ITP-2cell-3

value: 2-cell Embryo


title: Acute HS (40oC), TP medium, T1, Replicate A


title: RNA-Seq FZX_Fr_C1

description:
FZX_Fr_C1
P.litchii treatment


title: RNA-Seq FZX_Le_M3

description:
FZX_Le_M3
Mock treatment

source_name: leaves

value: leaves


title: Ribo-ITP-2cell-2


title: RNA-Seq FZX_Le_M2

description:
FZX_Le_M2
Mock treatment


title: Moderate HS (35oC), TP medium, T3b, Replicate A

value: 35oC, TP medium


title: Moderate HS (35oC), TP medium, T3b, Replicate B


title: RNA-Seq FZX_Le_M1

description:
FZX_Le_M1
Mock treatment


title: Moderate HS (35oC), TP medium, T1, Replicate B


title: Ribo-ITP-1cell-5

value: C57BL/6J x CAST/EiJ


title: Ribo-ITP-1cell-4

value: 1-cell Embryo


title: Control 25oC, TP medium, T3b, Replicate A

value: 25oC control, TP medium


title: RNA-Seq FZX_Le_C2

description:
FZX_Le_C2
P.litchii treatment


title: RNA-Seq FZX_Le_C3

description:
FZX_Le_C3
P.litchii treatment


title: mimic miR-146a-5p

type: RNA

city: Kyoto City

first: Hiromi

last: Nishigaki

address: 465 Kajii-Cyo, Hirokouji, Kawaramachi doori, Kamigyo-ku

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Following fragmentation, Biotinylated cRNA were hybridized for 16 hr at 45℃ on ClarionTM S Array. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChipTM Scanner 3000 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console 4.0 (TAC 4.0) using robust multi-array analysis (RMA).

label: biotin

source_name: THP-1 cell (JCRB0112.1)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.

growth_protocol: THP-1 cells were cultuerd in RPMI1640 medium containing 100ng/ml PMA for 2 days to differentiate into macrophage-like cells.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The mimic of hsa-let-7a-5p or negative contorl were mixed with lepofectamine RNAiMAX and added for 24hr to the THP-1 cells.

value: lymphocyte-like cells


title: RNA-Seq FZX_Le_C1

description:
FZX_Le_C1
P.litchii treatment


title: Ribo-ITP-1cell-3


title: Ribo-ITP-1cell-2


title: Control 25oC, TP medium, T1, Replicate B


title: mimic miR-130a-3p


title: mimic let-7e-5p


title: miRNA-Seq FZX_Fr_M3

description:
FZX_Fr_M3
Mock treatment

extract_protocol:
Total RNA was extracted from the treated leaves by Plant RNA Kit (Promega, LS1040).
The small RNA library (sRNA library) was constructed according to the manufacturer’s instruction of TrueSeq small RNA library prep kit (Illumina San Diego CA, USA), and 2.5 ng RNA per sample was used as the initial amount. The T4 RNA Ligase 1 was ligated to the 3′ end of the RNA, followed by the ligation of T4 RNA Ligase 2 (truncated) to the 5′ adapter. After that, the RNA was reverse transcribed to synthesize cDNA. Finally, small RNA libraries were obtained by screening these recovered fragments using gel separation technology. The qualities of the library was further tested following these steps: 1) Initial quantification was performed using Qubit 2.0, and the insert size of the library was tested using Agilent 2100. 2) The Q-PCR method was used to accurately quantify the effective concentration of the library (effective library concentration > 2 nM). After the library's quality tests were passed, the library performed pooling according to the amount of target data, followed by sequencing on the Illumina Nova platform.

value: fruits


title: mimic let-7d-3p


title: Control 25oC, TP medium, T1, Replicate A


title: Ribo-ITP-2cell-1


title: Ribo-ITP-1cell-1


title: mimic miR-151a-3p


title: mimic NC 2


title: Moderate HS (35oC), TP medium, T1, Replicate A


title: Ribo-ITP-MII-5

value: MII-stage Oocyte


title: Acute HS (40oC), TAP medium, T3b, Replicate B

value: 40oC, TAP medium


title: mimic miR-151a-5p


title: mimic miR-27b-3p


title: mimic let-7d-5p


title: miRNA-Seq FZX_Fr_M1

description:
FZX_Fr_M1
Mock treatment

value: mock

value: Feizixiao

value: Sterile water (Mock-inoculation)


title: Control 25oC, TP medium, T3b, Replicate B

value: Asynchronous single cells


title: Ribo-ITP-MII-4


title: Acute HS (40oC), TAP medium, T3b, Replicate A

value: CLiP mutant library


title: mimic Neg Control


title: miRNA-Seq FZX_Fr_C3

description:
FZX_Fr_C3
P.litchii treatment

value: Peronophythora litchii

value: Inoculation with P.litchii ( 1 x 10^4 spores ml ^-1)


title: miRNA-Seq FZX_Fr_C2

description:
FZX_Fr_C2
P.litchii treatment


title: Ribo-ITP-MII-3


title: Acute HS (40oC), TAP medium, T1, Replicate B

value: vegatative


title: Ribo-ITP-MII-2


title: Ribo-ITP-MII-1


title: Acute HS (40oC), TAP medium, T1, Replicate A


title: Moderate HS (35oC), TAP medium, T3a, Replicate B

value: 35oC, TAP medium


title: miRNA-Seq FZX_Le_M3

description:
FZX_Le_M3
Mock treatment

value: leaves


title: Ribo-ITP-GV-5

value: GV-stage Oocyte


title: miRNA-Seq FZX_Fr_M2

description:
FZX_Fr_M2
Mock treatment


title: miRNA-Seq FZX_Le_M2

description:
FZX_Le_M2
Mock treatment


title: Ribo-ITP-GV-4


title: miRNA-Seq FZX_Le_C3

description:
FZX_Le_C3
P.litchii treatment


title: miRNA-Seq FZX_Le_M1

description:
FZX_Le_M1
Mock treatment


title: Ribo-ITP-GV-3


title: Moderate HS (35oC), TAP medium, T1, Replicate B


title: Ribo-ITP-GV-2


title: Q77A_19_3

city: Berkeley

first: Yangnan

last: Gu

state: CA

address: 371 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

data_processing:
Clean mRNA-seq reads were aligned to the Arabidopsis thaliana reference genome (TARI10) using HISAT2 (v2.2.0) with default parameters.
Gene-level read counts were calculated with featureCount (v2.0.1) at exon level.
DEGs were analyzed using R package DESeq2 (v1.30.1) with dafault parameters.
Differential alternative splicing events were identified by rMATS (v4.1.1) with the specific parameter ‘-t paired –cstat 0.0001 --read length 150’ based on BAMs generated by STAR (v2.7.9a).
Intron Retention Scores were calculated by sam2irs based on SAMs generated by HISAT (v2.2.0).
Assembly: TAIR 10
Supplementary files format and content: tab-delimited text file include count values for each Sample
Supplementary files format and content: comma-seperated values file include LFC/p/p.adj value for each Sample
Supplementary files format and content: tab-delimited text file include IncLevelDifference values for each Sample
Supplementary files format and content: xlsx file include IRS values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedling plants

growth_protocol: seedlings grown on 1/2 MS mediate with 1% sucrose

extract_protocol:
Total RNA was extracted from about 50 mg samples of 7-day-old seedlings using the Direct-zol RNA Miniprep kit. (Genesee Scientific, cat#11-330)
mRNA-Seq (polyA enrichment)  libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

value: whole seedlings

value: MAC3BQ77A/D81AGFP mutant


title: Ribo-ITP-GV-1


title: Q77A_19_1


title: Col-0_2

value: wild type


title: miRNA-Seq FZX_Le_C2

description:
FZX_Le_C2
P.litchii treatment


title: Moderate HS (35oC), TAP medium, T1, Replicate A


title: miRNA-Seq FZX_Le_C1

description:
FZX_Le_C1
P.litchii treatment


title: Control 25oC, TAP medium, T3b, Replicate A

value: 25oC control, TAP medium


title: Col-0_1


title: miRNA-Seq FZX_Fr_C1

description:
FZX_Fr_C1
P.litchii treatment

value: fruits


title: GeneBody_K36me3_WT

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

description: CUT&Tag DNA

data_processing:
Library strategy: CUT&Tag
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample.

source_name: pancreatic tumor cell

extract_protocol: CUT&Tag libraries were prepared for sequencing using standard illumina protocols.

value: PDAC cell line

value: Wild type

tag: antibody


title: GeneBody_K36me3_KO

description: CUT&Tag DNA

value: Setd2 knockout


title: Control 25oC, TAP medium, T3a, Replicate B


title: Control 25oC, TAP medium, T3a, Replicate A


title: GeneBody_K27me3_WT

description: CUT&Tag DNA


title: E coli PCR scRNAseq sample

city: Chapel Hill

first: Adam

last: Rosenthal

state: NC

address: 125 Mason Farm Marsico Hall rm6201

department: Microbiology and Immunology

institute: UNC

description:
RNA hybridizing probes
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V7.1  and using custom scripts available from the Sahand Hormoz lab (https://gitlab.com/hormozlab/bacteria_scrnaseq)
Assembly: Probe-based genome builds for B subtilis, E coli and C perfringens are deposited alongside GTF files in the Hormoz lab github: https://gitlab.com/hormozlab/bacteria_scrnaseq
Supplementary files format and content: H5 files

organism: Escherichia coli

source_name: Bacterial cells in suspension

extract_protocol:
Freshly collected bacterial cells were fixed in 1% paraformaldehyde for 1 hour. Cells from 2 mL of cell culture were fixed using a 30-minute incubation in 1% paraformaldehyde (final concentration) at room temperature. Formaldehyde-fixed samples were washed with 0.02 % SSC (Saline Sodium Citrate - Invitrogen) by gentle centrifugation (6,000 x G) for 2.5 minutes. After the wash, cell pellets were resuspended in 1 mL MAAM (4:1 V:V dilution of methanol to glacial acetic acid). Samples were kept at -20oC for up to 2 days before further processing. For in-situ probe hybridization, 150 µL of fixed sample was centrifuged and washed once in PBS to remove methanol and acetic acid. After the wash step, cells were incubated in 200 µL PBS with 350 u/µL of lysozyme solution (Epicentre ready-lyse) for 30 minutes at room temperature. Lysozyme concentration was optimized and other enzyme combinations were tested to achieve a protocol with maximal probe signal and minimal cell lysis (see Supplementary Figure S12) After 30 minutes cells were pelleted and washed with 500 µL PBS-tween (PBS with 0.1 % Tween 20). Cells were then re-suspended with 100 µL of probe binding buffer consisting of 5x SSC, 30% formamide, 9mM citric acid (pH 6.0). 0.1% Tween 20, 50 ug/ml heparin, and 10% low MW dextran sulfate42. Cell suspensions were placed in a 50oC shaker-incubator and allowed to pre-equilibrate for 1 hour. After 1 hour 50 µL of probes, (600 ng/µL) were added to each cell suspension, and samples were left to incubate overnight.  Following the overnight incubation samples were washed 5 times in pre-warmed (50oC) probe-wash solution (5 x SSC, 30% formamide, 9 mM citric acid pH 6.0, 0.1% Tween 20, and 50 ug/mL heparin).
Library was performed according to specifications of McNulty et al bacterial scRNAseq protocols (single cell 3’ v2 protocol, 10x Genomics). Briefly, Single cell partitioning, barcoding, and cDNA library generation was achieved using the 10X Genomics Chromium Controller with the Chromium Single Cell 3’ Reagents Kit (v2 chemistry) as described by 10X Genomics (https://support.10Xgenomics.com/single cell-gene-expression/index/doc/user-guide-chromium-single cell-3-reagent-kits-user-guide-v2-chemistry). The protocol was modified to achieve bacterial scRNA-seq. For GEM generation (10X microfluidic encapsulation), a master mix containing the following reagents (per rxn, not accounting for excess volume) was prepared: 33 µL of 4X ddPCR Multiplex Supermix (BioRad), 4 µL of custom primer (10 µM), 2.4 µL additive A (10X Genomics), 26.8 µL dH2O. All other reagents specified by 10X Genomics were omitted. Prepared cell samples were washed 3X in PBS and diluted to 1000 cells/µL before loading on the microfluidic chip (“Chip A Single Cell”) with a targeted cell recovery of 10,000 cells.

value: Bacterial cells in suspension

value: Mid log phase


title: Moderate HS (35oC), TAP medium, T3a, Replicate A

value: Asynchronous single cells

value: CLiP mutant library


title: Deeper sequencing of B subtilis PCR scRNAseq replicate 1

description:
RNA hybridizing probes
10x Genomics

organism: Bacillus subtilis

value: Late log phase


title: Control 25oC, TAP medium, T1, Replicate B

value: vegatative


title: Control 25oC, TAP medium, T1, Replicate A


title: GeneBody_K27me3_KO

description: CUT&Tag DNA


title: E coli and B subtilis barnyard experiment

description:
RNA hybridizing probes
10x Genomics

organism:
Escherichia coli
Bacillus subtilis

value: BS 168 and Ec_MG1655


title: B subtilis PCR scRNAseq

description:
RNA hybridizing probes
10x Genomics


title: Control 25oC, TAP medium, T3b, Replicate B


title: KO1

status: Public on Feb 05 2023

first: juntao

last: chen

address: 180 Fenglin Road

institute: Zhongshan Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed using the Trimmomatic software. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.Meanwhile, Use the SortMeRNA software for ribosomal RNA reads removal.After discarded the rRNA reads, the remainly clean reads were mapped to the reference genome GRCh38.p12 using HISAT2 with default parameters. Unique reads with high mapping quality were retained
The m6A-enriched peaks in each m6A immunoprecipitation sample were identified by MeTDiff peak calling software with the corresponding input sample  serving as control. MeTDiff was run with options (‘FRAGMENT_LENGTH=200,PEAK_CUTOFF_PVALUE = 0.05, PEAK_CUTOFF_FDR = 0.05’) for peak detection. Called peaks were annotated by intersection with gene architecture using ChIPseeker
Differential analysis for m6A-Seq identifies differences in RNA methylome in a case-control study, The differential peak were detected by MeTDiff with parameter  (‘FRAGMENT_LENGTH = 200, PEAK_CUTOFF_PVALUE = 0.01,DIFF_PEAK_CUTOFF_FDR = 0.05, PEAK_CUTOFF_FDR = 0.05’), after which,differential peak were annotated by ChIPseeker
Assembly: GRCm38.p6
Supplementary files format and content: bigWig

source_name: kidney

extract_protocol:
Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol.
We utilized input and post m6A-IP positive fraction for library construction utilizing the Illumina TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego,  CA, USA) according to the manufacturer’s instructions.

value: kidney

value: m6A IP


title: KO2


title: KO3


title: WT2-input

value: WT

value: m6A input


title: WT1-input


title: WT3-input


title: WT1


title: WT2


title: Liver CC082 M

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Reads were aligned to the pooled transcriptomes (mm10) of the eight founder strains using bowtie v1.0.0 with parameters -q -p 8 -a --best --strata --sam -v 3 -m 100.
Aligned reads were input into the Genotype recontruction by RNA-Seq (GBRS) software which estimated total gene counts using the Expectation-Maximization for Allele Specific Expression (EMASE) software.
Filtered out genes for which > 50% of samples had no expression.
Assembly: mm10

source_name: Liver tissue

extract_protocol:
Hearts, livers, and kidneys were removed, flash frozen, and RNA was harvested using Trizol reagent. KAPA mRNA HyperPrep Kit (Roche) was used with total RNA for the construction of sequencing libraries.
Pooled libraries were sequenced on the NovaSeq 6000 platform (Illumina) using the S1 Reagent Kit v1, yielding 20-40M (target 30M) 1 x 1000bp single-end reads per sample.

tag: mouse

value: CC082 M

tag: Sex

value: male

value: liver


title: WT664

city: shanghai

first: george

last: yue

address: Room 4B, the 3rd Building, No. 401, Caobao Road, Xuhui District, Shanghai, China, 200233

institute: Genergy Bio-technology (Shanghai) Co., Ltd

description: 10x Genomics

data_processing:
Differentially expressed genes (DEG) analysis was conducted between WT and WAS-KO mice to identify significantly up- or downregulated genes. DEG analysis was done using the FindMarkers or FindAllMarkers functions with a minimum of 20% of the gene-expressing cells, adjusted P value < 0.05 in gene expression between each cluster, and | log2 FC | > 1. Functional annotation clustering was performed using TopGO software (http://www.bioconductor.org). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp) annotations were tested for enrichment, and a Benjamini–Hochberg-corrected p value < 0.05 was deemed significant.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
The separated single cells of spleen from WT or WAS-KO mcie, the gel beads with barcoded sequences and the oil droplets were put into the machine together. Thee gel beads precisely captured the target cells, then the target cells were lysed, thus releasing a large quantity of RNA and barcoded sequences for further reverse transcription.
Every cell and transcript were barcoded uniquely by using a unique molecular identifier (UMI). Next, libraries were established and sequenced from the cDNA and the 10 × barcodes were adopted to relate individual reads back to the individual partitions. The single cell 3’ protocol generating libraries were then sequenced using an Illumina HiSeq4000 or Novaseq sequencer. Transcripts were mapped to the mm10-3.0.0 reference genome.

tag: mouse model

value: Wiskott-Aldrich Syndrome

value: spleen cells

value: spleen

tag: age

value: 6-8 weeks old


title: WAS660

description: 10x Genomics


title: KO3-input


title: KO2-input


title: WT3


title: Liver CC080 M

value: CC080 M


title: Liver CC082 F

value: CC082 F

value: female


title: Liver CC080 F

value: CC080 F


title: Liver CC079 M

value: CC079 M


title: Liver CC078 M

value: CC078 M


title: Liver CC081 M

value: CC081 M


title: Liver CC079 F

value: CC079 F


title: Liver CC078 F

value: CC078 F


title: Liver CC075 F

value: CC075 F


title: Liver CC072 F

value: CC072 F


title: Liver CC072 M

value: CC072 M

value: male


title: Liver CC071 M

value: CC071 M

value: liver


title: KO1-input

value: kidney

value: m6A input


title: Liver CC071 F

value: CC071 F


title: Liver CC062 M

value: CC062 M


title: Liver CC059 M

value: CC059 M


title: Liver CC061 M

value: CC061 M


title: Liver CC059 F

value: CC059 F

value: female


title: Liver CC058 M

value: CC058 M


title: Liver CC081 F

value: CC081 F


title: Liver CC060 M

value: CC060 M


title: Liver CC060 F

value: CC060 F


title: Liver CC057 M

value: CC057 M


title: Liver CC062 F

value: CC062 F


title: Liver CC058 F

value: CC058 F


title: Liver CC061 F

value: CC061 F


title: Liver CC051 M

value: CC051 M

value: male

value: liver


title: Liver CC057 F

value: CC057 F


title: Liver CC053 M

value: CC053 M


title: Liver CC053 F

value: CC053 F


title: Liver CC055 F

value: CC055 F


title: Liver CC055 M

value: CC055 M


title: Liver CC075 M

value: CC075 M


title: Liver CC051 F

value: CC051 F

value: female


title: Liver CC045 M

value: CC045 M


title: Liver CC043 M

value: CC043 M


title: Liver CC043 F

value: CC043 F


title: Liver CC044 F

value: CC044 F


title: Liver CC046 F

value: CC046 F


title: Liver CC049 M

value: CC049 M


title: Liver CC049 F

value: CC049 F


title: Liver CC045 F

value: CC045 F


title: Liver CC046 M

value: CC046 M

value: male

value: liver


title: Liver CC044 M

value: CC044 M


title: Liver CC042 M

value: CC042 M


title: Liver CC042 F

value: CC042 F


title: Liver CC041 M

value: CC041 M


title: Liver CC041 F

value: CC041 F


title: Liver CC040 M

value: CC040 M


title: Liver CC040 F

value: CC040 F

value: female


title: Liver CC032 M

value: CC032 M


title: Liver CC037 M

value: CC037 M


title: Liver CC035 M

value: CC035 M


title: Liver CC038 F

value: CC038 F


title: Liver CC036 M

value: CC036 M


title: Liver CC035 F

value: CC035 F


title: Liver CC033 F

value: CC033 F


title: Liver CC036 F

value: CC036 F


title: Liver CC037 F

value: CC037 F

value: liver


title: Liver CC039 F

value: CC039 F


title: Liver CC032 F

value: CC032 F


title: Liver CC038 M

value: CC038 M

value: male


title: Liver CC033 M

value: CC033 M


title: Liver CC027 F

value: CC027 F


title: Liver CC029 M

value: CC029 M


title: Liver CC030 F

value: CC030 F

value: female


title: Liver CC030 M

value: CC030 M


title: Liver CC031 M

value: CC031 M


title: Liver CC031 F

value: CC031 F


title: Liver CC026 M

value: CC026 M


title: Liver CC029 F

value: CC029 F


title: Liver CC026 F

value: CC026 F


title: Liver CC027 M

value: CC027 M


title: Liver CC039 M

value: CC039 M

value: liver


title: Liver CC025 F

value: CC025 F


title: Liver CC025 M

value: CC025 M


title: Liver CC024 F

value: CC024 F


title: Liver CC024 M

value: CC024 M

value: male


title: Liver CC023 M

value: CC023 M


title: Liver CC023 F

value: CC023 F


title: Liver CC021 M

value: CC021 M


title: Liver CC021 F

value: CC021 F

value: female


title: Liver CC019 F

value: CC019 F


title: Liver CC017 M

value: CC017 M


title: Liver CC017 F

value: CC017 F


title: Liver CC015 F

value: CC015 F


title: Liver CC015 M

value: CC015 M


title: Liver CC011 M

value: CC011 M


title: Liver CC019 M

value: CC019 M

value: liver


title: Liver CC012 F

value: CC012 F


title: Liver CC013 M

value: CC013 M


title: Liver CC011 F

value: CC011 F


title: Liver CC010 F

value: CC010 F


title: Liver CC010 M

value: CC010 M

value: male


title: Liver CC012 M

value: CC012 M


title: Liver CC008 M

value: CC008 M


title: Liver CC009 F

value: CC009 F

value: female


title: Liver CC009 M

value: CC009 M


title: Liver CC007 M

value: CC007 M


title: Liver CC006 M

value: CC006 M


title: Liver CC005 M

value: CC005 M


title: Liver CC005 F

value: CC005 F


title: Liver CC007 F

value: CC007 F


title: Liver CC006 F

value: CC006 F

value: liver


title: Liver CC016 M

value: CC016 M


title: Liver CC016 F

value: CC016 F


title: Liver CC013 F

value: CC013 F


title: Liver CC004 F

value: CC004 F


title: Liver CC003 M

value: CC003 M

value: male


title: Liver CC002 F

value: CC002 F


title: Kidney CC082 M

source_name: Kidney tissue

value: CC082 M

value: kidney


title: Kidney CC080 F

value: CC080 F

value: female


title: Kidney CC082 F

value: CC082 F


title: Kidney CC081 F

value: CC081 F


title: Liver CC008 F

value: CC008 F


title: Liver CC002 M

value: CC002 M


title: Liver CC003 F

value: CC003 F


title: Liver CC001 M

value: CC001 M

value: liver


title: Liver CC001 F

value: CC001 F


title: Kidney CC079 M

value: CC079 M


title: Kidney CC075 F

value: CC075 F


title: Kidney CC072 M

value: CC072 M


title: Kidney CC081 M

value: CC081 M

value: male


title: Kidney CC080 M

value: CC080 M


title: Kidney CC078 M

value: CC078 M

value: kidney


title: Kidney CC079 F

value: CC079 F

value: female


title: Kidney CC078 F

value: CC078 F


title: Kidney CC072 F

value: CC072 F


title: Kidney CC062 M

value: CC062 M


title: Liver CC004 M

value: CC004 M


title: Kidney CC071 F

value: CC071 F


title: Kidney CC061 M

value: CC061 M


title: Kidney CC061 F

value: CC061 F


title: Kidney CC060 M

value: CC060 M


title: Kidney CC059 M

value: CC059 M


title: Kidney CC060 F

value: CC060 F


title: Kidney CC075 M

value: CC075 M


title: Kidney CC053 M

value: CC053 M

value: male


title: Kidney CC059 F

value: CC059 F


title: Kidney CC058 M

value: CC058 M

value: kidney


title: Kidney CC057 F

value: CC057 F

value: female


title: Kidney CC053 F

value: CC053 F


title: Kidney CC058 F

value: CC058 F


title: Kidney CC071 M

value: CC071 M


title: Kidney CC055 F

value: CC055 F


title: Kidney CC051 F

value: CC051 F


title: Kidney CC051 M

value: CC051 M


title: Kidney CC062 F

value: CC062 F


title: Kidney CC044 M

value: CC044 M


title: Kidney CC055 M

value: CC055 M


title: Kidney CC045 M

value: CC045 M


title: Kidney CC046 M

value: CC046 M


title: Kidney CC049 M

value: CC049 M

value: male


title: Kidney CC044 F

value: CC044 F


title: Kidney CC042 M

value: CC042 M

value: kidney


title: Kidney CC045 F

value: CC045 F

value: female


title: Kidney CC042 F

value: CC042 F


title: Kidney CC043 F

value: CC043 F


title: Kidney CC043 M

value: CC043 M


title: Kidney CC041 M

value: CC041 M


title: Kidney CC041 F

value: CC041 F


title: Kidney CC040 F

value: CC040 F


title: Kidney CC040 M

value: CC040 M


title: Kidney CC057 M

value: CC057 M


title: Kidney CC039 M

value: CC039 M