title: Ly6C+_MHC2+_72h_rep1_L006


title: CGD_Ly6C+_MHC2-_72h_rep3_L005

status: Public on Feb 10 2024

type: SRA

city: Denver

first: Donna

middle: Leslie

last: Bratton

state: CO

address: 1400 Jackson St. Rm A540

department: Pediatrics

country: USA

institute: National Jewish Health

library_source: transcriptomic

data_processing:
FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17).
Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt.
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 assembly of the mouse genome using gene using gene annotations from Ensembl version 84.
Reads mapping to each gene of the Ensembl 84 annotation were counted with the featureCounts program from the Subread software package (v1.5.1).
Transcripts per million aligned fragments (TPM) were calculated from the gene counts using the sum of all bases covered by any transcript of a gene as its transcript length.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts and transcripts per million (TPM) assigned to each gene of the mouse Ensembl 84 annotation and sample, as tab-separated text tables: 1) output from subread featureCounts (2 subread_genecounts.txt* files), separated by sequencing run, 2) aggregated by adding different sequencing runs for each sample (counts and TPM)

molecule: total RNA

organism: Mus musculus

source_name: CGD 72h LyC6+ MHC2– rep3

growth_protocol: Parent animals were obtained from Jackson laboratories. Experimental mice were bred and housed in a specific pathogen free facility at National Jewish Health, Denver, CO, USA.

extract_protocol:
Peritoneal lavage was collected using 8mL buffer (HBSS w/o Ca2+ Mg2+,  20mM HEPES, 1mM EDTA). Total lavage cells were stained with antibodies for FACS and sorted to purify monocytes/macrophages of the indicated phenotype. Total RNA was extracted using the Qiagen RNeasy micro kit according to manufacturer's instructions.
A Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Mountain View, CA, USA) and Nextera XT (San Diego, CA, USA) kit were used. Briefly, library construction started from isolation of total RNA species, followed by SMARTer 1st strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. After that, the samples were taken to the Nextera XT protocol where the sample is simultaneously fragmented and tagged with adapters followed by a limited-cycle PCR that adds indexes. Once validated, the barcoded-pooled libraries were sequenced using 1×50bp chemistry on the HiSeq 2500 as routinely performed by the NJH Genomics Facility.

treatment_protocol: Mice were treated with intraperitoneal injection of 200ug Zymosan A (Sigma)

tag: strain

tag: tissue

value: Peritoneal Lavage

tag: genotype

tag: Sex

value: Male

tag: age

value: 8-12 weeks

tag: treatment

value: i.p. Zymosan

tag: time point

value: 72 hours

tag: cell type

value: MoMac Ly6C+ MHCII-


title: Ly6C+_MHC2+_72h_rep2_L007

source_name: WT 72h LyC6+ MHC2+ rep2

value: wildtype

value: MoMac Ly6C+ MHCII+


title: MU01CELL067

city: Bunkyo-ku

first: Naoaki

last: Mizuno

state: Tokyo

address: 1-5-45 Yushima

country: Japan

institute: Tokyo Medical and Dental University

description: omitted

library_source: transcriptomic single cell

data_processing:
Reads were adpter-trimmed by Trimmomatic and aligned onto mm10 by HISAT2 on a local Galaxy server.
Mapped reads are counted by featureCounbts on the Galaxy server based on the GTF file of Ensemble36 version-release.97.
Transcript integrity number (TIN) and Gene Body Coverage were analyzed by RSeQC to exclude low-quality samples.
The count was normalized by DESeq2 (version 1.36.0) and analyzed for differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: The  processed data file, raw_counts_B6N_E14.5_skin_PRJNA1056324.tsv, is a raw count matrix in tabuler/tsv format.

source_name: skin

growth_protocol: C57BL/6N wild type or Trp63 mutant embryos at E14.5 in surrogate ICR mothers.

extract_protocol:
The single cells were sorted by flowcytometry onto CDS Sorting Solution of SMART-Seq HT Kit (Takara Bio Inc., Shiga, Japan. Catalog No. Z4436N). The crude lysate were subjected to reverse transcriptions and cDNA amplifications.
cDNA library was constructed by SMART-Seq HT following the FACSAria sorting. cDNA library of Trp63 mutant embryos was screened by qPCR for enrichment of the target cell lineage. Illumina library was prepared by NexteraXT.

treatment_protocol: The skin of WT (C57BL/6N background) fetuses at E14.5 was soaked in dispase and separated into the epidermis and dermis. The single cells of the WT epidermis by treated with trypsin. The p63 knockout fetuses (C57BL/6N background) were directly digested with trypsin. Samples were stained with following antibodies: anti-mouse CD45 (clone 30-F11, eBioscience), TER119 (clone TER-119, eBioscience), anti-CD140a (clone APA5, Biolegend). The single cell of the PI-/CD45- /TER119-/CD140a- population was sorted by FACS aria II or III (BD).

value: skin

value: mutant fibroblast

value: Trp63 mutant


title: CGD_Ly6C+_MHC2-_72h_rep3_L004


title: MU01CELL066

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep3_L003


title: MU01CELL065

description: omitted


title: MU01CELL063

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep3_L002


title: CGD_Ly6C+_MHC2-_72h_rep3_L001


title: CGD_Ly6C+_MHC2-_72h_rep2_L004

source_name: CGD 72h LyC6+ MHC2– rep2


title: MU01CELL062

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep2_L005


title: MU01CELL061

description: omitted


title: MU01CELL060

description: omitted


title: MU01CELL058

description: omitted

value: unknown cell


title: CGD_Ly6C+_MHC2-_72h_rep2_L003


title: MU01CELL056

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep1_L005

source_name: CGD 72h LyC6+ MHC2– rep1


title: MU01CELL059

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep1_L004


title: MU01CELL057

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep1_L002


title: MU01CELL054

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep2_L001


title: CGD_Ly6C+_MHC2-_72h_rep1_L003


title: MU01CELL055

description: omitted


title: CGD_Ly6C+_MHC2-_72h_rep1_L001


title: MU01CELL053

description: omitted


title: MU01CELL050

description: omitted


title: MU01CELL052

description: omitted


title: MU01CELL049

description: omitted


title: Ly6C+_MHC2-_72h_rep3_L006

source_name: WT 72h LyC6+ MHC2– rep3


title: MU01CELL047

description: omitted


title: MU01CELL051

description: omitted


title: MU01CELL064

description: omitted


title: Ly6C+_MHC2-_72h_rep3_L005


title: MU01CELL048

description: omitted


title: Ly6C+_MHC2-_72h_rep3_L007


title: CGD_Ly6C-_MHC2+_72h_rep3_L005

source_name: CGD 72h LyC6– MHC2+ rep3

value: MoMac Ly6C- MHCII+


title: CGD_Ly6C+_MHC2-_72h_rep2_L002


title: Ly6C+_MHC2-_72h_rep2_L007

source_name: WT 72h LyC6+ MHC2– rep2


title: Ly6C+_MHC2-_72h_rep2_L006


title: MU01CELL041

description: omitted


title: Ly6C+_MHC2-_72h_rep2_L005


title: CGD_Ly6C-_MHC2+_72h_rep3_L003


title: MU01CELL045

description: omitted


title: Ly6C+_MHC2-_72h_rep1_L006

source_name: WT 72h LyC6+ MHC2– rep1


title: MU01CELL043

description: omitted


title: Ly6C+_MHC2-_72h_rep1_L007


title: Ly6C+_MHC2-_72h_rep1_L005


title: MU01CELL042

description: omitted


title: MU01CELL038

description: omitted


title: MU01CELL044

description: omitted


title: CGD_Ly6C-_MHC2+_72h_rep3_L004


title: CGD_Ly6C-_MHC2+_72h_rep2_L004

source_name: CGD 72h LyC6– MHC2+ rep2


title: MU01CELL037

description: omitted


title: CGD_Ly6C-_MHC2+_72h_rep3_L002


title: MU01CELL040

description: omitted


title: CGD_Ly6C-_MHC2+_72h_rep3_L001


title: MU01CELL035

description: omitted


title: MU01CELL039

description: omitted


title: CGD_Ly6C-_MHC2+_72h_rep2_L005


title: Sham _rep3

city: Changsha

first: Wei

last: Jiang

state: Hunan

address: Lushan Road (S), Yuelu District,Changsha, Hunan Province

department: College of Biology

country: China

institute: Hunan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: mm8
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: Hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three replicate of Cerebral Ischemia 1.5 h Reperfusion 24 h (IR24)

value: Hippocampus

value: Sham operation


title: MU01CELL046

description: omitted


title: MU01CELL036

description: omitted


title: MU01CELL034

description: omitted


title: CGD_Ly6C-_MHC2+_72h_rep2_L002


title: MU01CELL033

description: omitted


title: CGD_Ly6C-_MHC2+_72h_rep2_L001


title: CGD_Ly6C-_MHC2+_72h_rep1_L005

source_name: CGD 72h LyC6– MHC2+ rep1


title: CGD_Ly6C-_MHC2+_72h_rep1_L004


title: Ischemia 1.5 h Reperfusion 24 h (IR24) _rep3

value: focal middle cerebral artery occlusion (MCAO) 1.5 h reperfusion 24 h (IR24)


title: MU01CELL032

description: omitted


title: Ly6C-_MHC2+_72h_rep3_L006

source_name: WT 72h LyC6– MHC2+ rep3


title: CGD_Ly6C-_MHC2+_72h_rep1_L002


title: CGD_Ly6C-_MHC2+_72h_rep1_L003


title: CGD_Ly6C-_MHC2+_72h_rep2_L003


title: CGD_Ly6C-_MHC2+_72h_rep1_L001


title: MU01CELL031

description: omitted


title: MU01CELL029

description: omitted


title: Ly6C-_MHC2+_72h_rep3_L005


title: Sham _rep2


title: Ly6C-_MHC2+_72h_rep1_L006

source_name: WT 72h LyC6– MHC2+ rep1


title: MU01CELL028

description: omitted


title: Sham _rep1


title: Ly6C-_MHC2+_72h_rep1_L005


title: Ischemia 1.5 h Reperfusion 24 h (IR24) _rep2


title: Ly6C-_MHC2+_72h_rep2_L007

source_name: WT 72h LyC6– MHC2+ rep2


title: MU01CELL030

description: omitted


title: CGD_Ly6C-_MHC2-_72h_rep3_L003

source_name: CGD 72h LyC6– MHC2– rep3

value: MoMac Ly6C- MHCII-


title: Ly6C-_MHC2+_72h_rep2_L006

value: Peritoneal Lavage


title: CGD_Ly6C-_MHC2-_72h_rep3_L001

value: Male


title: Ischemia 1.5 h Reperfusion 24 h (IR24) _rep1


title: MU01CELL026

description: omitted


title: MU01CELL024

description: omitted


title: CGD_Ly6C-_MHC2-_72h_rep2_L003

source_name: CGD 72h LyC6– MHC2– rep2

value: 8-12 weeks


title: BC397_Tumor

city: Duarte

first: Peter

middle: P

last: Lee

state: CA

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

description: 10X genmonics Single Cell 5'

data_processing:
CellRanger (v3.0.2) was used to align sequence reads (raw data files) to human genome (GRCh38) and count the aligned transcripts for each cell (processed data files). More details about this procedure were available here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov. The processed data has been filtered, normalized, integrated, batch corrected, clustered, and visualized with Seurat R package.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Homo sapiens

source_name: Breast

extract_protocol:
Fresh tumour tissue specimens were obtained through surgical resection and immediately placed in tube containing cold HBSS (Life Technologies, Thermo Fisher Scientific). To prepare single-cell suspension, tissues were first minced into smaller pieces and a gentleMACS Dissociator (Miltenyi Biotec) was used for mechanical dissociation. Enzymatic treatment was then carried out using 0.2 Wunsch U/mL Liberase TM (Roche) and 10 U/mL DNase (MilliporeSigma) in RPMI for up to 1 hour, if necessary. In cases where red blood cells (RBCs) were present and needed to be removed, RBC lysis was performed using RBC Lysis Buffer (BioLegend).
Single-cell RNA sequencing was performed using the Chromium Single-Cell 5′ Chemistry Library, Gel Bead, Multiplex and Chip Kits (10x Genomics) according to the manufacturer’s protocol.

value: Breast

value: Female

tag: cancer subtypes

value: ER+

value: treatment-naïve


title: Ly6C-_MHC2+_72h_rep1_L007

value: wildtype

value: i.p. Zymosan

value: 72 hours


title: MU01CELL027

description: omitted

value: skin

value: mutant fibroblast

value: Trp63 mutant


title: Ly6C-_MHC2+_72h_rep2_L005

value: MoMac Ly6C- MHCII+


title: BC419_Tumor

description: 10X genmonics Single Cell 5'

value: TNBC


title: BC401_Tumor

description: 10X genmonics Single Cell 5'


title: BC302_Tumor

description: 10X genmonics Single Cell 5'


title: BC428_Tumor

description: 10X genmonics Single Cell 5'


title: Ly6C-_MHC2+_72h_rep3_L007


title: CGD_Ly6C-_MHC2-_72h_rep3_L004


title: CGD_Ly6C-_MHC2-_72h_rep3_L005


title: BC258_Tumor

description: 10X genmonics Single Cell 5'

value: ER+ HER2+


title: CGD_Ly6C-_MHC2-_72h_rep1_L003

source_name: CGD 72h LyC6– MHC2– rep1

value: MoMac Ly6C- MHCII-


title: MU01CELL025

description: omitted

source_name: skin


title: BC394_Tumor

description: 10X genmonics Single Cell 5'


title: CGD_Ly6C-_MHC2-_72h_rep2_L002

value: Peritoneal Lavage


title: CGD_Ly6C-_MHC2-_72h_rep3_L002

value: Male


title: CGD_Ly6C-_MHC2-_72h_rep2_L005

value: 8-12 weeks


title: CGD_Ly6C-_MHC2-_72h_rep1_L004


title: Ly6C-_MHC2-_72h_rep3_L007

source_name: WT 72h LyC6– MHC2– rep3


title: CGD_Ly6C-_MHC2-_72h_rep2_L001


title: BC17086-35_Tumor

description: 10X genmonics Single Cell 5'

value: Breast


title: Ly6C-_MHC2-_72h_rep3_L006


title: MU01CELL023

description: omitted

value: unknown cell


title: Ly6C-_MHC2-_72h_rep2_L006

source_name: WT 72h LyC6– MHC2– rep2


title: MU01CELL019

description: omitted


title: BC17086-12_Tumor

description: 10X genmonics Single Cell 5'

value: Female

value: ER+


title: Ly6C-_MHC2-_72h_rep3_L005

value: wildtype


title: MU01CELL022

description: omitted


title: CGD_Ly6C-_MHC2-_72h_rep2_L004

value: i.p. Zymosan


title: CGD_Ly6C-_MHC2-_72h_rep1_L001

value: 72 hours


title: CGD_Ly6C-_MHC2-_72h_rep1_L002


title: Ly6C-_MHC2-_72h_rep2_L007


title: MU01CELL020

description: keratinocyte

value: skin

value: surface ectoderm remnant


title: BC17086-24_Tumor

description: 10X genmonics Single Cell 5'

value: treatment-naïve


title: Ly6C-_MHC2-_72h_rep1_L006

source_name: WT 72h LyC6– MHC2– rep1


title: MU01CELL018

description: omitted

value: mutant fibroblast

value: Trp63 mutant


title: HEK293_KO_Nascent

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the reference genome with Bowtie2. For linear RNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels. For circRNA annotation, CIRI2 and Find_circ were used, and backspliced read per million (BRPM) was used to calculate circRNA levels.
Assembly: hg19 (human), mm10 (mouse) and ASM294v2 (yeast)
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: HEK293 cells

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) followed by RNase R treatment or not according to the manufacturer’s instructions.

tag: cell line

value: HEK293 cells

value: ZC3H14 knockout


title: ZC3H14_iCLIP_R2

description: ZC3H14_iCLIP_crosslinked_nucleotide.txt.gz

value: WT


title: CGD_Ly6C+_MHC2+_18h_rep2_L001

source_name: CGD 18h LyC6+ MHC2+ rep2

value: Peritoneal Lavage

value: Male

value: 18 hours

value: MoMac Ly6C+ MHCII+


title: CGD_Ly6C+_MHC2+_18h_rep1_L001

source_name: CGD 18h LyC6+ MHC2+ rep1

value: 8-12 weeks


title: MU01CELL014

description: omitted

value: unknown cell


title: HEK293_KO


title: MU01CELL021

description: keratinocyte


title: Ly6C-_MHC2-_72h_rep2_L005

value: wildtype

value: MoMac Ly6C- MHCII-


title: MU01CELL017

description: omitted


title: BC17086-25_Tumor

description: 10X genmonics Single Cell 5'

value: Breast

value: Female

value: TNBC


title: Ly6C-_MHC2-_72h_rep1_L007

value: i.p. Zymosan

value: 72 hours


title: ZC3H14_iCLIP_R1


title: MU01CELL012

description: omitted

value: skin

value: Trp63 mutant


title: MU01CELL016

description: omitted

value: mutant fibroblast


title: HEK293_siZC3H14_polyA

value: HEK293 cells

value: WT


title: Ly6C-_MHC2-_72h_rep1_L005

value: Peritoneal Lavage

value: Male


title: Ly6C+_MHC2+_18h_rep2_L005

source_name: WT 18h LyC6+ MHC2+ rep2

value: 18 hours

value: MoMac Ly6C+ MHCII+


title: CGD_Ly6C+_MHC2+_18h_rep3_L001

source_name: CGD 18h LyC6+ MHC2+ rep3

value: 8-12 weeks


title: Ly6C+_MHC2+_18h_rep1_L007

source_name: WT 18h LyC6+ MHC2+ rep1

value: wildtype


title: Ly6C+_MHC2+_18h_rep3_L006

source_name: WT 18h LyC6+ MHC2+ rep3


title: MU01CELL013

description: omitted


title: Ly6C+_MHC2+_18h_rep3_L005


title: Ly6C+_MHC2+_18h_rep3_L007


title: CGD_Ly6C+_MHC2-_18h_rep3_L001

source_name: CGD 18h LyC6+ MHC2– rep3

value: MoMac Ly6C+ MHCII-


title: MU01CELL015

description: omitted


title: HEK293_WT


title: Ly6C+_MHC2+_18h_rep2_L007


title: CGD_Ly6C+_MHC2-_18h_rep2_L001

source_name: CGD 18h LyC6+ MHC2– rep2


title: HEK293_WT_Nascent


title: CGD_Ly6C-_MHC2-_72h_rep1_L005

value: MoMac Ly6C- MHCII-


title: Ly6C+_MHC2+_18h_rep2_L006


title: Ly6C+_MHC2+_18h_rep1_L006


title: MU01CELL011

description: omitted


title: Ly6C+_MHC2-_18h_rep3_L007

source_name: WT 18h LyC6+ MHC2– rep3


title: HEK293_siNC_polyA


title: GFP_Low

library_source: genomic

molecule: genomic DNA


title: Ly6C+_MHC2-_18h_rep3_L006


title: Ly6C+_MHC2+_18h_rep1_L005


title: HEK293_siZC3H14

description:
ZC3H14_KD_circRNA.txt.gz
ZC3H14_KD_mRNA.txt.gz


title: MU01CELL010

description: omitted


title: HEK293_siNC


title: MU01CELL007

description: omitted


title: MU01CELL009

description: omitted


title: CGD_Ly6C+_MHC2-_18h_rep1_L001

source_name: CGD 18h LyC6+ MHC2– rep1


title: MU01CELL008

description: omitted


title: MU01CELL005

description: omitted


title: Ly6C+_MHC2-_18h_rep2_L006

source_name: WT 18h LyC6+ MHC2– rep2


title: Ly6C+_MHC2-_18h_rep3_L005


title: Ly6C+_MHC2-_18h_rep1_L007

source_name: WT 18h LyC6+ MHC2– rep1


title: Ly6C+_MHC2-_18h_rep2_L007


title: MU01CELL004

description: omitted

source_name: skin

value: unknown cell


title: Ly6C+_MHC2-_18h_rep1_L005


title: GFP_High


title: Ly6C+_MHC2-_18h_rep2_L005


title: Ly6C+_MHC2-_18h_rep1_L006


title: CGD_Ly6C+_MHC2-_6h_rep3_L005

source_name: CGD 6h LyC6+ MHC2– rep3

value: 6 hours


title: PLC/PRF/5-CSTF2-KO-rep2

city: Shenzhen

first: Qiangnu

last: Zhang

state: None Selected

address: 1017 Dongmen Bei Lu, 518020Shenzhen, China

department: Department of General Surgery

institute: Shenzhen people's hospital

description: gene_expression_PLC CSTF2_KO.csv

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
clean data were mapped to the reference genome using STRA software (version 2.5.3a) with default parameters
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1)
Assembly: Hg18
Supplementary files format and content: Excel csv files include FPKM value for sampples

source_name: liver

growth_protocol: HUH7 and PLC/PRF/5 cells were cultured in DMEM medium containing 10% fetal bovine serum in a cell incubator at 5%CO2 and 37 ° C

extract_protocol:
TRIzol reagent was used to extract total RNA from cell samples
KCTM Stranded mRNA Library Prep Kit for Illumina® was used

value: liver

value: hepatocellular carcinoma cells

value: CSTF2 knockout


title: MU01CELL003

description: omitted

value: skin

value: Trp63 mutant


title: CGD_Ly6C+_MHC2-_6h_rep3_L004

value: i.p. Zymosan


title: GFP_Input

value: HEK293 cells

value: WT


title: PLC/PRF/5-CSTF2-KO-rep1

description: gene_expression_PLC CSTF2_KO.csv


title: CGD_Ly6C+_MHC2-_6h_rep3_L003

value: Peritoneal Lavage

value: Male


title: PLC/PRF/5-control-rep3

description: gene_expression_PLC CSTF2_KO.csv


title: CGD_Ly6C+_MHC2-_6h_rep3_L001


title: CGD_Ly6C+_MHC2-_6h_rep3_L002


title: MU01CELL002

description: omitted

value: mutant fibroblast


title: MU01CELL006

description: omitted


title: MU01CELL001

description: omitted


title: CGD_Ly6C+_MHC2-_6h_rep2_L005

source_name: CGD 6h LyC6+ MHC2– rep2

value: 8-12 weeks


title: WT01CELL024

description: keratinocyte

value: basal layer

value: wild type


title: PLC/PRF/5-control-rep2

description: gene_expression_PLC CSTF2_KO.csv


title: PLC/PRF/5-CSTF2-KO-rep3

description: gene_expression_PLC CSTF2_KO.csv


title: CGD_Ly6C+_MHC2-_6h_rep2_L004

value: MoMac Ly6C+ MHCII-


title: PLC/PRF/5-control-rep1

description: gene_expression_PLC CSTF2_KO.csv


title: CGD_Ly6C+_MHC2-_6h_rep2_L003


title: CGD_Ly6C+_MHC2-_6h_rep2_L002


title: WT01CELL023

description: keratinocyte


title: CGD_Ly6C+_MHC2-_6h_rep2_L001


title: HUH7-CSTF2-KO-rep3

description: gene_expression_HUH7 CSTF2_KO


title: CGD_Ly6C+_MHC2-_6h_rep1_L005

source_name: CGD 6h LyC6+ MHC2– rep1


title: CGD_Ly6C+_MHC2-_6h_rep1_L004


title: WT01CELL022

description: keratinocyte


title: WT01CELL021

description: keratinocyte


title: CGD_Ly6C+_MHC2-_6h_rep1_L003


title: HUH7-CSTF2-KO-rep2

description: gene_expression_HUH7 CSTF2_KO


title: CGD_Ly6C+_MHC2-_6h_rep1_L002


title: CGD_Ly6C+_MHC2-_6h_rep1_L001


title: Ly6C+_MHC2-_6h_rep3_L005

source_name: WT 6h LyC6+ MHC2– rep3

value: wildtype


title: HUH7-control-rep3

description: gene_expression_HUH7 CSTF2_KO


title: Ly6C+_MHC2-_6h_rep3_L004

value: 6 hours


title: HUH7-control-rep2

description: gene_expression_HUH7 CSTF2_KO

value: liver


title: Ly6C+_MHC2-_6h_rep3_L001


title: Ly6C+_MHC2-_6h_rep3_L002


title: Ly6C+_MHC2-_6h_rep3_L003


title: WT01CELL018

description: keratinocyte

value: intermediate layer


title: WT01CELL019

description: keratinocyte

value: K17 high


title: Ly6C+_MHC2-_6h_rep2_L004

source_name: WT 6h LyC6+ MHC2– rep2


title: Ly6C+_MHC2-_6h_rep2_L003


title: Ly6C+_MHC2-_6h_rep2_L002


title: WT01CELL016

description: keratinocyte

value: skin


title: HUH7-control-rep1

description: gene_expression_HUH7 CSTF2_KO

value: hepatocellular carcinoma cells


title: HEK293T, WT, RNAPII, Rnase I crosslinked footprinting

city: NYC

first: Kevin

last: Yang

state: New York

institute: New York University Medical Center

library_source: other

data_processing:
Sequencing adapters were first trimmed with CutAdapt (Martin, 2011) and then aligned to the hg19 reference genome using HISAT2 (Zhang et al., 2021).
Alignment files were converted to bigwig format with CPM normalization using bamCoverage from deepTools2 (Ramírez et al., 2016) for genome browser visualization with pyGenomeTracks (Lopez-Delisle et al., 2021).
For other analyses, alignment files were converted to bed format and annotated using Samtools and BEDtools (Danecek et al., 2021; Quinlan and Hall, 2010).
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: Rnase I crosslinked footprinting

molecule: other

growth_protocol: DMEM, 15% fetal bovine serum. Cells were cultured at 37C, 5% CO2.

extract_protocol:
Starting with 40E6 cells, nuclear fractionation was done as described in POINT (Sousa-Luis et al., 2021) with HLB+N and HLB+NS buffers. Then, nuclei were resuspended in NUN1 and NUN2 with 3% Empigen (Sigma) and the chromatin was washed with PBS and treated with 50ul TURBO DNase (ThermoFisher), 100ul 10x digestion buffer (100mM Tris-HCl pH 7.5, 25mM MgCl2, 1mM CaCl2), and 10ul Rnasin (Promega) in a volume of 1mL for 15 minutes at 37 °C. Next, Pol II is immunoprecipitated with Rpb1 CTD (4H8) mouse mAB (#2629; Cell Signaling) conjugated to Dynabeads M-280 sheep anti-mouse IgG (ThermoFisher) for 1 hour at 4 °C. Isolated transcription complexes are washed with cold NET-2 buffer with 1% Empigen 5 times before being treated with 100ul cleavage buffer (40mM Tris-HCl pH 7.5, 100mM NaCl, 10mM MgCl2), 2.5ul rSAP (NEB), and 1ul RNasin for 10 minutes at 37 °C, shaking. Magnetic beads were then washed with cold NET-2 with 1% Empigen an additional 5 times before being treated with 50ul cleavage buffer, 2.5uM human TFIIS, and 1ul RNasin for 30 minutes at 37 °C, shaking. Trizol (ThermoFisher) and the Direct-zol RNA microprep (Zymo) was used to purify RNA from the magnetic beads. mNETseq was done essentially as described (Nojima et al., 2015), using Rpb1 CTD (4H8) mouse mAB conjugated to Dynabeads M-280 sheep anti-mouse IgG (ThermoFisher). For crosslinked pol II RNA footprinting, mNET-seq was modified in the following ways. Prior to the experiment, cells were treated with 100uM 4-thiouridine (Sigma) for 12 hours. Immediately before collection, media was removed and cells were crosslinked at >310nm at .15J/cm^2, similar to PAR-CLIP (Hafner et al., 2010). Transcription complexes were then isolated and treated with Rnase I (ThermoFisher) in NET-2 buffer for 5 minutes at 37C, washed with NET-2, and digested with proteinase K (ThermoFisher) in elution buffer (50mM Tris-HCl pH 7.5, 10mM EDTA, 1% SDS) for 90 minutes at 55C before collection in Trizol. Purified RNA was treated with polynucleotide kinase (NEB) to prepare 5’ and 3’ ends for library construction as described for LORAX-seq.
RNA was prepared for sequencing with the NEBNext Small RNA library Prep kit (NEB).

value: Human embryonic kidney


title: Ly6C+_MHC2-_6h_rep2_L001

value: i.p. Zymosan


title: HUH7-CSTF2-KO-rep1

description: gene_expression_HUH7 CSTF2_KO

value: CSTF2 knockout


title: WT01CELL014

description: keratinocyte


title: Ly6C+_MHC2-_6h_rep1_L005

source_name: WT 6h LyC6+ MHC2– rep1

value: Peritoneal Lavage


title: Ly6C+_MHC2-_6h_rep1_L003

value: Male


title: HEK293T, TFIIS KO, RNAPII, LORAXseq (2)

data_processing:
Sequencing adapters were first trimmed with CutAdapt (Martin, 2011) and then aligned to the hg19 reference genome using HISAT2 (Zhang et al., 2021).
Alignment files were converted to bigwig format with CPM normalization using bamCoverage from deepTools2 (Ramírez et al., 2016) for genome browser visualization with pyGenomeTracks (Lopez-Delisle et al., 2021).
For other analyses, alignment files were converted to bed format and annotated using Samtools and BEDtools (Danecek et al., 2021; Quinlan and Hall, 2010).
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: LORAXseq

value: TFIIS KO


title: WT01CELL020

description: keratinocyte

value: K8, K20 high


title: Ly6C+_MHC2-_6h_rep1_L004

value: 8-12 weeks


title: HEK293T, WT, RNAPII, LORAXseq (2)

value: WT


title: Ly6C+_MHC2-_6h_rep1_L002

value: MoMac Ly6C+ MHCII-


title: Ly6C+_MHC2-_6h_rep1_L001

value: wildtype


title: WT01CELL013

description: keratinocyte

value: basal layer

value: wild type


title: RNA_OGDpKD_rep1

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Aligned using STAR
Counts generated with featureCounts and GENCODE vM12
Assembly: mm10
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: HT22 cells

extract_protocol:
Total RNA was extracted with Bio-Rad Aurum Kit
RNA-seq libraries were prepared with Illumina TruSeq RNA Library Prep Kit v2
Libraries were sequenced at single-end 75 nt

value: HT22 cells

value: Immortalized Hippocampal Neuronal Cell Line

value: Oxygen-Glucose Deprivation (OGD)


title: Ly6C+_MHC2-_6h_rep2_L005

value: 6 hours


title: RNA_prmt5KD_rep1

value: Untreated


title: WT01CELL017

description: keratinocyte

value: skin


title: HEK293T, TFIIS KO, RNAPII, Rnase I crosslinked footprinting

value: Human embryonic kidney


title: HEK293T, WT, RNAPII, mNETseq

data_processing:
Sequencing adapters were first trimmed with CutAdapt (Martin, 2011) and then aligned to the hg19 reference genome using HISAT2 (Zhang et al., 2021).
Alignment files were converted to bigwig format with CPM normalization using bamCoverage from deepTools2 (Ramírez et al., 2016) for genome browser visualization with pyGenomeTracks (Lopez-Delisle et al., 2021).
For other analyses, alignment files were converted to bed format and annotated using Samtools and BEDtools (Danecek et al., 2021; Quinlan and Hall, 2010).
Assembly: hg19
Supplementary files format and content: bedgraph
Library strategy: LORAX and mNETseq

extract_protocol:
Starting with 40E6 cells, nuclear fractionation was done as described in POINT (Sousa-Luis et al., 2021) with HLB+N and HLB+NS buffers. Then, nuclei were resuspended in NUN1 and NUN2 with 3% Empigen (Sigma) and the chromatin was washed with PBS and treated with 50ul TURBO DNase (ThermoFisher), 100ul 10x digestion buffer (100mM Tris-HCl pH 7.5, 25mM MgCl2, 1mM CaCl2), and 10ul Rnasin (Promega) in a volume of 1mL for 15 minutes at 37 °C. Next, Pol II is immunoprecipitated with Rpb1 CTD (4H8) mouse mAB (#2629; Cell Signaling) conjugated to Dynabeads M-280 sheep anti-mouse IgG (ThermoFisher) for 1 hour at 4 °C. Isolated transcription complexes are washed with cold NET-2 buffer with 1% Empigen 5 times before being treated with 100ul cleavage buffer (40mM Tris-HCl pH 7.5, 100mM NaCl, 10mM MgCl2), 2.5ul rSAP (NEB), and 1ul RNasin for 10 minutes at 37 °C, shaking. Magnetic beads were then washed with cold NET-2 with 1% Empigen an additional 5 times before being treated with 50ul cleavage buffer, 2.5uM human TFIIS, and 1ul RNasin for 30 minutes at 37 °C, shaking. Trizol (ThermoFisher) and the Direct-zol RNA microprep (Zymo) was used to purify RNA from the magnetic beads. mNETseq was done essentially as described (Nojima et al., 2015).
RNA was prepared for sequencing with the NEBNext Small RNA library Prep kit (NEB).


title: RNA_OGDpKD_rep2


title: WT01CELL011

description: keratinocyte

value: K17 high


title: HEK293T, WT, RNAPII, LORAXseq


title: RNA_OGDcon_rep2


title: RNA_OGDcon_rep1


title: WT01CELL010

description: keratinocyte


title: HEK293T, TFIIS KO, RNAPII, LORAXseq


title: RNA_NGcon_rep2


title: WT01CELL015

description: keratinocyte


title: MBC2, replicate 2, spatial transcriptomics

city: New York

first: SIYU

last: HE

state: NY

institute: Columbia University

description:
10x Genomics
P4B_MBC

data_processing:
10x genomics pipeline
Supplementary files format and content: h5ad files and zip file for spatial information

source_name: primary breast cancer

extract_protocol: Visium Spatial Gene Expression slides prepared by the Molecular Cytology Core at MSKCC were permeabilized at 37°C for 6 minutes and polyadenylated mRNA was captured by oligos bound to the slides. Reverse transcription, second strand synthesis, cDNA amplification, and library preparation proceeded using the Visium Spatial Gene Expression Slide & Reagent Kit (10X Genomics PN 1000184) according to the manufacturer’s protocol. After evaluation by real-time PCR, cDNA amplification included 13-14 cycles; sequencing libraries were prepared with 15 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/120 run using the NovaSeq 6000 SP Reagent Kit (200 cycles) (Illumina). An average of 228 million paired reads was generated per sample.

value: mixed -whole tissue

value: primary breast cancer

value: 52 year-old


title: RNA_NGcon_rep1


title: MBC2, replicate 1, spatial transcriptomics

description:
10x Genomics
P4A_MBC


title: WT01CELL009

description: keratinocyte


title: RP_dCas13_AUG_target_biol_rep_2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: S205 Bioscience Bldg. 2-1 Hirosawa

department: Cluster for Pioneering Research

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38 gencode 32
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribo-Seq

source_name: HEK293 Flp-In T-Rex

growth_protocol: Approximately 4 × 10^6 HEK293 Flp-In T-Rex with EGFP integrants were cultured in DMEM containing high glucose and GlutaMAX supplement, supplemented with 10% fetal bovine serum at 37°C with 5% CO2

extract_protocol:
Following FACS, in the cell harvest cycloheximide (100 μg/ml) was added to PBS, trypsin solution, and DMEM to stop ribosomal movement along mRNAs
For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification. RNA-Seq was performed by TruSeq Stranded Total RNA Library Prep Gold (Illumina).

treatment_protocol: Cells were co-transfected with the Cas13 variant expressing plasmid (8 μg) and the gRNA expressing plasmid (12 μg) using TransIT-293 (Mirus). Cells were then incubated for 48 h. To induce EGFP expression cells were treated with tetracycline (1 μg/ml) for 24 h prior to FACS.

value: HEK293 Flp-In T-Rex

value: tetracycline

value: plasmid transfection (dCas13 + target  gRNA expressing plasmid)


title: RP_dCas13_AUG_target_biol_rep_1


title: HEK293T, TFIIS KO, RNAPII, mNETseq

value: TFIIS KO


title: RP_dCas13_control_biol_rep_1

value: plasmid transfection (dCas13 + control gRNA expressing plasmid)


title: WT01CELL008

description: keratinocyte

value: basal layer

value: wild type


title: RP_dCas13_control_biol_rep_2


title: RP_Cas13_AUG_target_biol_rep_2

value: plasmid transfection (Cas13 + target  gRNA expressing plasmid)


title: WT01CELL007

description: keratinocyte


title: MBC1, replicate 2, spatial transcriptomics

description:
10x Genomics
P3B_MBC

value: 71 year-old


title: WT01CELL012

description: keratinocyte


title: RNA_prmt5KD_rep2

value: HT22 cells

value: Immortalized Hippocampal Neuronal Cell Line


title: WT01CELL005

description: keratinocyte

value: skin


title: RP_Cas13_AUG_target_biol_rep_1


title: WT01CELL006

description: keratinocyte

value: intermediate layer


title: TNBC, replicate 2, spatial transcriptomics

description:
10x Genomics
P2B_TNBC

value: 84 year-old


title: RP_Cas13_control_biol_rep_2

value: plasmid transfection (Cas13 + control gRNA expressing plasmid)


title: RP_Cas13_control_biol_rep_1


title: RNASeq_dCas13_control_biol_rep_2

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Library sorting based on sample barcode sequence with custom script
Random barcode triming with custom script
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: hg38 gencode 32
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts


title: ER+, replicate 2, spatial transcriptomics

description:
10x Genomics
P1B_ER

value: mixed -whole tissue

value: primary breast cancer

value: 70 year-old


title: RNASeq_dCas13_AUG_target_biol_rep_2

value: HEK293 Flp-In T-Rex

value: tetracycline

value: plasmid transfection (dCas13 +target  gRNA expressing plasmid)


title: MBC1, replicate 1, spatial transcriptomics

description:
10x Genomics
P3A_MBC


title: TNBC, replicate 1, spatial transcriptomics

description:
10x Genomics
P2A_TNBC


title: WT01CELL004

description: keratinocyte


title: ER+, replicate 1, spatial transcriptomics

description:
10x Genomics
P1A_ER


title: RNASeq_Cas13_AUG_target_biol_rep_2


title: RNASeq_dCas13_control_biol_rep_1

value: plasmid transfection (dCas13 + control gRNA expressing plasmid)


title: WT01CELL002

description: keratinocyte

value: basal layer


title: RNASeq_Cas13_control_biol_rep_2


title: WT01CELL001

description: keratinocyte

value: wild type


title: RNASeq_Cas13_AUG_target_biol_rep_1

value: plasmid transfection (Cas13 + target  gRNA expressing plasmid)


title: RNASeq_dCas13_AUG_target_biol_rep_1

value: plasmid transfection (dCas13 + target  gRNA expressing plasmid)


title: RNASeq_Cas13_control_biol_rep_1


title: Total RNA (mRNA) from arsenite-treated WT cells [TWT4]

status: Public on Feb 09 2024

city: Aarhus

first: Ulf

middle: Andersson

last: Vang Ørom

address: Universitetsbyen 81

country: Denmark

institute: Aarhus University

data_processing:
Adapters were trimmed with Bbduk.
Reads were aligned using STAR.
Reads were counted with bedtools multicov.
Assembly: hg19
Supplementary files format and content: *.txt files include raw counts.
Supplementary files format and content: SG_enrichment.xlsx includes expression level in rpm and log2FC of WT/SG for both WT and NAT10 KO.

source_name: HeLa

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s medium (DMEM; Gibco, #41966-029) supplemented with 10% Fetal Bovine Serum (FBS; Gibco) and 1% Penicillin/Streptomycin (P/S; Gibco) at 37°C with 5% CO2 until 90% confluency.

extract_protocol:
As described in Khong et al., 2017 (PMID 29129640).
DNBSEQ stranded mRNA library.

treatment_protocol: Cells were treated with 500µM Arsenite for 30' to induce stress granules.

value: HeLa

value: WT

value: Arsenite


title: Total RNA (mRNA) from arsenite-treated WT cells [TWT3]


title: Total RNA (mRNA) from arsenite-treated WT cells [TWT2]


title: Total RNA (mRNA) from arsenite-treated WT cells [TWT1]


title: Total RNA (mRNA) from arsenite-treated NAT10 KO cells [TNT3]

value: NAT10 KO


title: Total RNA (mRNA) from arsenite-treated NAT10 KO cells [TNT2]


title: Total RNA (mRNA) from arsenite-treated NAT10 KO cells [TNT4]


title: Total RNA (mRNA) from arsenite-treated NAT10 KO cells [TNT1]


title: WT stress granule [SGWT4]

description:
SGWT4
Stress granule


title: WT stress granule [SGWT3]

description:
SGWT3
Stress granule


title: WT stress granule [SGWT2]

description:
SGWT2
Stress granule


title: NAT10 KO stress granule [SGNT4]

description:
SGNT4
Stress granule


title: NAT10 KO stress granule [SGNT3]

description:
SGNT3
Stress granule


title: NAT10 KO stress granule [SGNT2]

description:
SGNT2
Stress granule


title: NAT10 KO stress granule [SGNT1]

description:
SGNT1
Stress granule


title: T3-3

city: Philadelphia

first: Duancheng

last: Guo

state: PA

address: 333 Cottman AVE

institute: Fox Chase Cancer Center

description: Gene expression data from T3-3 sample use RNA-seq analysis.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence use fastp software, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.2.1.
FPKM were calculated using StringTie software version 2.1.4, and readcount number were calculated using featureCounts software version 2.0.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Medulloblastoma cells from Patched 1 deficient mice

growth_protocol: Medulloblastoma cells were suspended in NB-B22 culture medium (Neurobasal, 1 mmol/L sodium pyruvate, 2 mmol/L L-glutamine, B22 supplement, and 1% penicillin/streptomycin,all from Invitrogen)

extract_protocol:
tumor cells were dissociated enzymatically by papain for 30 mins and then harvested by centrifugation.Total RNA was extracted from tumor cells treated with T3 or PBS. Strand-specific mRNA-seq libraries for the Illumina platform were generated and sequenced
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: In vitro experiments, 200nM T3 was added to the culture medium. Without T3 treatment as PBS group

value: MB tumor cells were treated by T3

value: primary Medulloblastoma cells

value: ptch-/-


title: PBS3

description: Gene expression data from PBS3 sample use RNA-seq analysis.

value: MB tumor cells were treated by PBS


title: PBS2

description: Gene expression data from PBS2 sample use RNA-seq analysis.


title: T3-2

description: Gene expression data from T3-2 sample use RNA-seq analysis.


title: T3-1

description: Gene expression data from T3-1 sample use RNA-seq analysis.


title: WT stress granule [SGWT1]

description:
SGWT1
Stress granule


title: WT01CELL003

description: keratinocyte

value: skin


title: PBS1

description: Gene expression data from PBS1 sample use RNA-seq analysis.


title: TH17 under glutamine-free condition, biological rep3

type: RNA

city: Taoyaun

first: Chung-Ying

last: Tsai

address: No. 5, Fuxing St., Guishan Dist.

department: Kidney Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital

description: Gene expression data from TH17 cells cultured without glutamine

hyb_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol

scan_protocol: Standard Applied Biosystems protocol

data_processing: Normalize with SST-RMA by Applied Biosystems Transcriptome Analysis Console Ver 4.0

label: biotin

source_name: Naïve CD4+ T cells culture in TH17 skewing condition without glutamine

growth_protocol: Naive T cells were purified as a CD4+CD25-CD62L+CD44- population using a FACS Melody sorter prior to stimulation with anti-CD3 /CD28 antibodies in a 24-well plate (5 and 2 mg/well, respectively; Biolegend) for 3 days. TH17-skewing conditions consisted of IMDM media supplemented with 10% FBS, 20 ng/ml IL-6 and IL-23, 1.25 ng/ml TGFb, and 10 ug/ml neutralizing antibodies against IFNg, IL-4, and IL-12 (Biolegend).

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

treatment_protocol: Naive T cells were cultured in TH17-skewing medium in the presence or absence of glutamine for 3 days. Polarized cells were lysed in the Trizol solution (GibcoBRL).

value: CD4+ T cells

value: no glutamine


title: TH17 under glutamine-free condition, biological rep2

label_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol


title: Control TH17, biological rep3

description: Gene expression data from TH17 cells cultured with glutamine

source_name: Naïve CD4+ T cells culture in TH17 skewing condition with glutamine

value: glutamine


title: TH17 under glutamine-free condition, biological rep1


title: Control TH17, biological rep2


title: PBMC from HC1092 at timepoint malaria, during uncomplicated malaria

type: genomic

city: Cleveland

first: Emily

middle: Rae

last: Hannon

state: Ohio

address: 10900 Euclid Ave

department: The Center for Global Health and Diseases

institute: Case Western Reserve University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the iScan System using standard recommended Illumina scanner setting

data_processing: Funnorm, filter probes with detection P>0.001, BMIQ probe type adjustment, filter cross-reactive probes

label: Cy5 and Cy3

source_name: PBMC

label_protocol: Standard Illumina protocol

extract_protocol: Qiagen allprep mini kit was used following manufacturer protocols

value: PBMC

value: M


title: NIT-1 cells, culture medium, 24h, biological rep 2

city: Dali

first: Yahao

last: MOU

address: No. 22, Wanhua Road

institute: Dali University

hyb_protocol: none provided

scan_protocol: none provided

data_processing: The transcriptome expression profile was detected on the Clariom D mouse microarray from Affymetrix GeneChip by Shanghai Baygene Biotechnology Co., Ltd..

label_protocol: none provided

growth_protocol: NIT-1 cells were cultured in an incubator with saturated humidity, 37 ℃, and 5% CO2. The culture medium was 1640 medium with 10% fetal bovine serum. 100 Units/mL penicillin and 100 μg/mL streptomycin were routinely added to the culture medium.

extract_protocol: Total RNA was extracted by using RNA simple total RNA kit.

treatment_protocol: NIT-1 cells were inoculated in 6-well plates for 24h and treated with 0 μmol/L and 4 μmol/L CdSO4 for 24h.

value: Pancreas, Islet of Langerhans

value: beta cell

value: culture medium


title: PBMC from HC1020 at timepoint baseline, before uncomplicated malaria

value: F


title: PBMC from HC1020 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: Control TH17, biological rep1


title: PBMC from HC1157 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1181 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1014 at timepoint malaria, during uncomplicated malaria


title: PBMC from HC1014 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1157 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1034 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1092 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1014 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1074 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1034 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1157 at timepoint malaria, during uncomplicated malaria


title: PBMC from HC1034 at timepoint malaria, during uncomplicated malaria


title: PBMC from HC1115 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1074 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: NIT-1 cells, 4 μmol/L CdSO4, 24h, biological rep 3


title: PBMC from HC1181 at timepoint malaria, during uncomplicated malaria


title: NIT-1 cells, culture medium, 24h, biological rep 3


title: PBMC from HC1092 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1115 at timepoint malaria, during uncomplicated malaria


title: PBMC from HC1115 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1181 at timepoint baseline, before uncomplicated malaria


title: Light-0h-GMUCT-1

city: Shanghai

first: Pengfei

last: Xu

state: Shanghai

address: 800 Dongchuan

institute: Shanghai Jiao Tong University

description: uncapped and cleaved transcripts

data_processing:
GMUCT reads were trimmed to remove the adapter sequences using cutadapt with default parameter
RNA-Seq reads (150-nucleotide paired-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Tomato genome (SL4.0) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Tomato protein-coding genes using STAR as above.
The gene expression leves of protein coding genes were normalized by RPM.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
Assembly: Slycopersicum_691_SL4.0.fa
Supplementary files format and content: txt files, count
Library strategy: GMUCT

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: 25℃ 12h light/ 12-h dark, and leaves were harvest at  4 weeks of age

extract_protocol:
Leaf tissue was ground with a mortar and pestle. RNA was extracted with a RNA isolation kit (Bioer Technology, Cat. BSC65S1).
RNA-seq libraries were prepared with paired-end and 150 nt ; GMUCT was prepared with Single-end and 50 nt

treatment_protocol: 25℃ 12h light/ 12-h dark

value: Leaf

value: HeinZ 1706


title: Light-4h-GMUCT-3

description: uncapped and cleaved transcripts


title: PBMC from HC1020 at timepoint malaria, during uncomplicated malaria


title: PBMC from HC1074 at timepoint malaria, during uncomplicated malaria


title: Dark-4h-GMUCT-3

description: uncapped and cleaved transcripts


title: Dark-8h-GMUCT-3

description: uncapped and cleaved transcripts


title: Dark-4h-GMUCT-2

description: uncapped and cleaved transcripts


title: NIT-1 cells, 4 μmol/L CdSO4, 24h, biological rep 2


title: Dark-0h-GMUCT-3

description: uncapped and cleaved transcripts


title: NIT-1 cells, 4 μmol/L CdSO4, 24h, biological rep 1


title: Dark-0h-GMUCT-2

description: uncapped and cleaved transcripts


title: Light-4h-mRNA-3

data_processing:
GMUCT reads were trimmed to remove the adapter sequences using cutadapt with default parameter
RNA-Seq reads (150-nucleotide paired-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Tomato genome (SL4.0) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Tomato protein-coding genes using STAR as above.
The gene expression leves of protein coding genes were normalized by RPM.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
Assembly: Slycopersicum_691_SL4.0.fa
Supplementary files format and content: txt files, count

molecule: polyA RNA


title: Light-4h-mRNA-2


title: Light-0h-mRNA-2


title: Dark-4h-mRNA-3


title: Dark-4h-mRNA-1


title: Dark-0h-mRNA-2


title: Light-8h-mRNA-2


title: Dark-8h-mRNA-1


title: Light-8h-GMUCT-3

description: uncapped and cleaved transcripts


title: Light-8h-GMUCT-2

description: uncapped and cleaved transcripts


title: Amplicon sequencing of Off-target sites of treated samples

city: Freiburg

first: Kay

middle: Ole

last: Chmielewski

address: Breisacherstr. 115

department: Institute for transfusion medicine and gene therapy

country: Germany

institute: University clininics Freiburg

data_processing:
Paired-end reads were analyzed using the command line version of CRISPResso2 and the mutation frequency was calculated from the allele frequency table
Assembly: hg38
Supplementary files format and content: Allele frequency table, text file

source_name: T-cells/HSPCs/IPSCs

growth_protocol: CD34+ cells were cultured in CellGenix GMP SCGM (CellGenix, Freiburg, Germany, Cat# 20802-0500) supplemented with recombinant human cytokines SCF (300 ng/ml), Flt3-L (300 ng/ml), IL-3 (60 ng/ml; all ImmunoTools, Friesoythe, Germany, Cat# 11343327, 11343307, 11340037), TPO (100 ng/ml; PeproTech, Hamburg, Germany, Cat# 300-18) as previously described. After nucleofection (see section below), IL-3 was removed from the medium and HSPCs cultured at 37°C with 5% CO2 until harvested for downstream analyses. The PAP iPSC line was reprogramed from a patient harboring compound heterozygous mutations in exon 3 (A17G) and exon 7 (G196R). The iPSCs were cultured on matrigel (Corning, Bedford, USA, Cat# 354277) or laminin 521 LN (Biolamina, Sundbyberg, Sweden, Cat# LN521) coated plates under feeder-free conditions using mTesRTM1 Basal Medium (StemCell Technologies, Bothell, WA, USA, Cat# 85850) supplemented with mTesR TM1 supplement (StemCell Technologies, Bothell, WA, USA, Cat# 85852) at 37°C with 5% CO2.

extract_protocol:
DNeasy Blood & Tissue Kit was used to extract DNA
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina was used for library preperation
Amplicon sequencing

treatment_protocol: To form RNPs, 19 pmol of Cas12a Ultra (IDT, Coralville, USA, Cat# 10001272) or wild-type Cas12a proteins (IDT, Coralville, USA, gift from IDT) and 95 pmol of indicated gRNA were complexed in a ratio of 1:5 before incubation for 10 min at room temperature (RT)

value: T-cells/HSPCs/IPSCs

value: CPF1 Ultra


title: Light-8h-GMUCT-1

description: uncapped and cleaved transcripts


title: Dark-4h-mRNA-2


title: Light-0h-GMUCT-3

description: uncapped and cleaved transcripts


title: Amplicon sequencing of CSF2RB ON-target and OFF-target sites of treated samples


title: Light-4h-GMUCT-1

description: uncapped and cleaved transcripts


title: Light-4h-GMUCT-2

description: uncapped and cleaved transcripts


title: WT KDS1 + MMC rep3 - INPUT

city: Ann Arbor

first: Yulduz

last: Rakibova

state: MI

address: 1150 W Medical center drive

department: Biological Chemistry

institute: University of Michigan

data_processing:
For IPOD, INPUT and ChIP-seq: ipod singularity container version 2.7.2 was used (available at https://github.com/freddolino-lab/ipod). Peak calling was done with version 2.8.1
Assembly: We obtained an initial genome reference sequence for KDS1 by sequencing high molecular weight genomic DNA purified from the strain. Raw reads are available at SRA########. Initial assembly was performed on the Nanopore reads using NECAT (version 0.0.1 20200803), resulting in two contigs which clearly correspond to the two V. cholerae chromosomes. The assembly was then polished using pilon (version 1.24) using default arguments, with all available reads from INPUT samples (aligned using bowtie2) as the short read inputs. Manual finishing was performed using a set of iterative rounds of breseq (version 0.37.0) runs to identify remaining discrepancies between the Illumina short read data and the in-progress assembly and resolving them by applying differences with gdtools. We then manually assigned the starting position of each chromosome to match those of commonly used El Tor reference genomes.  Annotation of the newly obtained assembly was performed using prokka (version 1.14.5) with arguments --genus Vibrio --species cholerae --accver 2, using a draft genome obtained from the ***** as a reference for potential proteins. We then assigned VC numbers to all identifiable genes matching the reference El Tor strain (EMBL reference sequences AE003852.1 and AE003853.1 for chromosomes 1 and 2, respectively). Annotated genes from the El Tor reference were aligned to those of our prokka-annotated KDS1 assembly, using nucmer (v. 3.1) with default settings. We further required that for each potential match, the starting and ending positions of the reference El Tor version and the KDS1 version in the identified features differed by no more than 20 nucleotides.
Supplementary files format and content: Files with suffix _IPOD_rzchipsub_rep*.bedgraph are four-column bedgraph files with the first column representing the reference genome, second – start coordinate in 5nt increments and third – end coordinate in 5nt increments, and the fourth column represents the occupancy robust z-score of quantified total protein occupancy with RNA ChIP-seq subtracted. The robust z-scores are given for each 5 nucleotides on the genome. The rep* represents the replicate number for the sample
Supplementary files format and content: Files with suffix _IPOD_vs_inp_rzlograt_rep*.bedgraph are four column bedgraph files with the first column representing the reference genome, second -- start coordinate in 5nt increments and third – end coordinate in 5nt increments, and the fourth column represents the robust z-score of quantified total protein occupancy. The robust z-scores are given for each 5 nucleotides on the genome. The rep* represents the replicate number for the sample
Supplementary files format and content: Files with suffix _CHIP_vs_inp_rzlograt_rep*.bedgraph are four column bedgraph files with the first column representing the reference genome, second – start coordinate in 5nt increments and third – end coordinate in 5nt increments, and the fourth column represents the robust z-score of quantified RNA polymerase ChIP-seq. The robust z-scores are given for each 5 nucleotides on the genome. The rep* represents the replicate number for the sample
Supplementary files format and content: EPODs: file KDS1_IPOD_rzchipsub_mean_epods_strict.bedgraph represents called strict EPODs by the IPOD pipeline and represents the extended protein occupancy regions based on protein occupancy with RNA polymerase ChIP-seq subtracted in each of the conditions (IPOD-HR). The file is a bedgraph file where the first column is the reference genome chromosome, second – start and third – end coordinates on the genome in 5 nucleotide intervals, and fourth – 1 or 0 for whether the position is an EPOD (1) or not (0)
Supplementary files format and content: inverted EPODs (nEPODs): file KDS1_IPOD_vs_inp_rzlograt_mean_inverted_epods_strict.bedgraph represents called strict inverted EPODs by the IPOD pipeline and represents the extended negative protein occupancy regions based on total protein occupancy negative scores in each of the conditions (IPOD). The file is a bedgraph files where the first column is the reference genome chromosome, second – start and third -- end coordinates on the genome in 5 nucleotide intervals, and fourth – 1 or 0 for whether the position is an inverted EPOD (i.e. nEPOD; 1) or not (0)
Supplementary files format and content: KDS1_IPOD_vs_inp_rzlograt_inverted_strict_merged_epods.narrowpeak and KDS1_IPOD_rzchipsub_strict_merged_epods.narrowpeak are narrowpeak files where the columns represent: col 1 – reference genome chromosome, col 2 – start and col 3 – end coordinates of merged EPODs from each replicate of IPOD-HR samples. The files are generated from IPOD pipeline, see https://github.com/freddolino-lab/ipod for details.
Supplementary files format and content: Peak calls: files with suffix _idr_passed.narrowpeak are called peak files generated from our IPOD pipeline, see  https://github.com/freddolino-lab/ipod for details.
Library strategy: IPOD-HR which include ChIP-seq and IPOD

organism: Vibrio cholerae

growth_protocol: All standard overnight bacterial cultures were grown from a single colony in 2 mL volume with aeration at 37C in standard LB Miller liquid growth medium, supplemented with streptomycin (100 µg/mL). For cultures requiring mitomycin C treatment, an overnight culture grown in standard conditions was diluted to an OD600 of 0.003 into 140 mL of pre-warmed LB Miller liquid medium supplemented with mitomycin C to a final concentration of 20 ng/mL. Cultures were grown to a final OD600 of 0.3.

extract_protocol:
IPOD sample preparation. IPOD samples were collected as previously described (Freddolino PL et al, PLoS Biology, 2022) with minor modifications. Overnight cultures were diluted to a starting OD600 of approximately 0.003 in a final volume of 140 mL of LB medium in a 1 L flask. The diluted cultures were grown at 37C with shaking at 250 RPM until a final OD600 of 0.3. 28.9 mL of culture was collected at each time point and mixed with 300 μL 1 M sodium phosphate buffer (pH 7.4) and 810 μL formaldehyde (37%, fresh) in a 50 mL conical tube, then allowed to crosslink for 5 minutes shaking at room temperature (notably, unlike in Freddolino PL et al, no rifampicin was added prior to crosslinking). After 5 minutes, the crosslinking reactions were quenched with 6 mL of 2M glycine and returned to the room temperature shaker. After 10 minutes of shaking, tubes were placed in ice for 10 minutes and then pelleted at 7,000x g at 4C for 4 minutes. Pellets were washed twice with 10 mL of ice-cold phosphate-buffered saline and the final cell pellets were snap-frozen in a dry ice-ethanol slurry and stored at -80C. Cell lysis, digestion, and lysate clarification. The original IPOD-HR protocol is from ref. (Freddolino PL et al, PLoS Biology, 2022); below we summarize the procedures applied here. Frozen cell pellets were resuspended in 600 μL of 1X IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) with 1x protease inhibitors tablet (Roche Complete Mini, EDTA free, Roche Diagnostics GmbH, Mannheim, Germany) and 1.5 μL lysozyme (ThermoScientific, REF90082, 50 mg/mL) incubated for 15 minutes at 30C with gentle shaking and then placed on ice. Resuspended cells were sonicated with a Branson sonicator at 25% power with three bursts of 10s ON and 10s OFF while in an ice water bath. Sonicated cells were then digested with 6μL RNaseA (SIG 10109169001, Sigma-Aldrich/Roche, 10mg/mL), 5.4 μL  of 100mM MnCl2, 4.5 μL of 100mM CaCl2, 9 μL of DNase I, RNAse-free (ThermoScientific, #89836, 1U/μL) and incubated on ice for 30 minutes, after which reactions were quenched with 50 μL 500mM EDTA (pH 8.0); we aimed to obtain fragment sizes of about 150 bp. 400 μL of 1x IPOD lysis buffer without protease inhibitors and lysozyme was added to the digested mixture and vortexed. The mixture was clarified by centrifugation for 10 minutes at 15,700 x g at 4C and transferred to new tubes. The clarified lysate was partitioned into three different tubes: 50 μL for INPUT (for baseline reference), 400 μL for IPOD (for total protein occupancy), and the rest for CHIP (for RNA polymerase occupancy). 450 μL of ChIP elution buffer (50mM Tris (pH 8.0), 10mM EDTA, 1% SDS) was added to the INPUT sample and kept on ice until reverse cross-linking step (mentioned in the next step). Cell lysis, digestion, and lysate clarification. The original IPOD-HR protocol is from ref. (Freddolino PL et al, PLoS Biology, 2022); below we summarize the procedures applied here. Frozen cell pellets were resuspended in 600 μL of 1X IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) with 1x protease inhibitors tablet (Roche Complete Mini, EDTA free, Roche Diagnostics GmbH, Mannheim, Germany) and 1.5 μL lysozyme (ThermoScientific, REF90082, 50 mg/mL) incubated for 15 minutes at 30C with gentle shaking and then placed on ice. Resuspended cells were sonicated with a Branson sonicator at 25% power with three bursts of 10s ON and 10s OFF while in an ice water bath. Sonicated cells were then digested with 6μL RNaseA (SIG 10109169001, Sigma-Aldrich/Roche, 10mg/mL), 5.4 μL  of 100mM MnCl2, 4.5 μL of 100mM CaCl2, 9 μL of DNase I, RNAse-free (ThermoScientific, #89836, 1U/μL) and incubated on ice for 30 minutes, after which reactions were quenched with 50 μL 500mM EDTA (pH 8.0); we aimed to obtain fragment sizes of about 150 bp. 400 μL of 1x IPOD lysis buffer without protease inhibitors and lysozyme was added to the digested mixture and vortexed. The mixture was clarified by centrifugation for 10 minutes at 15,700 x g at 4C and transferred to new tubes. The clarified lysate was partitioned into three different tubes: 50 μL for INPUT (for baseline reference), 400 μL for IPOD (for total protein occupancy), and the rest for CHIP (for RNA polymerase occupancy). 450 μL of ChIP elution buffer (50mM Tris (pH 8.0), 10mM EDTA, 1% SDS) was added to the INPUT sample and kept on ice until reverse cross-linking step (mentioned in the next step). Interphase extraction and nucleic acid purification. 400 μL of 100 mM Tris Base and 800 μL of 25:24:1 phenol:chloroform:isoamyl alcohol (Sigma Aldrich, #77617) was added to the 400 μL of clarified lysate kept for the IPOD-HR sample, vortexed for 10s, and then incubated for 10 minutes at room temperature. To obtain a separation of the organic and aqueous layers and formation of the white interphase disc, which is enriched in protein-DNA complexes, the mixture was spun for 2 minutes at 21,130 x g at room temperature. The aqueous and organic layers around the interphase were removed while minimizing disturbance of the interphase disc. The extracted disc was washed once in 350 μL TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 μL 100 mM Tris base, and 700 μL 24:1 chloroform:isoamyl alcohol. The layers were again separated by spinning for 2 minutes at 21,130 x g at room temperature. After removal of liquid around the interphase disc, a  final wash of 700 μL TE and 700 μL 24:1 chloroform:isoamyl alcohol was applied. After vortexing and spinning the final wash as before, as much of the liquid around the white disc as possible was removed and discarded. The interphase disc was resuspended in 500 μL of ChIP elution buffer and vortexed. The resuspended interphase of IPOD sample and INPUT sample (kept on ice from above step) were incubated at 65C overnight to reverse-crosslink (6-16 hours). RNA Polymerase Chromatin Immunoprecipitation. The rest of the clarified lysate (about 500 μL) was mixed with 1 volume of 2x immunoprecipitation (IP) buffer (200mM Tris (pH 8.0), 600mM NaCl, 4% Triton X-100) and incubated with 10μg of anti-E. coli RNA polymerase antibody (NeoClone WP023, NeoClone, Madison, WI, Lot: 2019G15-002) overnight with rocking at 4C. After overnight incubation, 50 μL of protein G beads (New England Biolabs (NEB), S1430S) per sample was equilibrated in 1x IP buffer. 50 μL of equilibrated protein G beads was added to each antibody-lysate mixture and then incubated with rocking 2 hours at 4C. After incubation, the beads were washed once in 1mL of the following buffers: IP wash buffer A, IP wash buffer B, IP wash buffer C, 1x IP buffer, and 1x TE.  1x wash buffer A (100mM Tris, pH 8.0; 250mM LiCl; 2% Triton X-100; 1mM EDTA) 1x wash buffer B (10mM Tris, pH 8.0; 500mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1mM EDTA) 1x wash buffer C (10mM Tris, pH 8.0; 500mM NaCl; 1% Triton X-100; 1mM EDTA) After the wash steps, beads with the immunoprecipitated material were resuspended in 500 μL of ChIP elution buffer by rocking for 5 minutes; the samples were then incubated for 30 minutes at 65C with vortexing every 5 minutes. The beads were then separated and discarded to retain only the eluted immunoprecipitated sample. The samples were then left to reverse-crosslink overnight (6-16 hours) at 65C. DNA extraction post reverse cross-linking. The DNA from INPUT, IPOD, and ChIP samples were isolated and purified following identical steps. After overnight incubation to reverse the formaldehyde crosslinks, each sample was incubated with 10 μL of RNAse A (Roche Diagnostics GmbH, #SIG10109169001, 10mg/mL) for 2 hours at 37C. Then we followed by adding 10 μL Proteinase K (ThermoScientific, #EO0491, 20mg/mL) and incubating for 2 hours at 50 oC. The DNA of each sample was isolated by phenol-chloroform extraction using one volume of 25:24:1 phenol:chloroform:isoamyl alcohol, then re-extracted with one volume of 24:1 chloroform:isoamyl alcohol. At the last stage the samples went into DNA LoBind tubes. The isolated DNA was then precipitated by adding 1/25th volume of 5M NaCl as a precipitating salt, 1/300th volume of GlycoBlue (Invitrogen, #AM9515, 15mg/mL) as a co-precipitant, and two volumes of ice cold 1:1 isopropanol:ethanol. The DNA was precipitated at 4C for one hour and at -20C for more than 1 hour or overnight.  Chilled samples were then centrifuged for 15 minutes at 16,100 x g at 4C to pellet the DNA. All the liquid was then removed without disturbing the DNA pellet. Pellets were then washed in freshly diluted 95% ethanol, vortexed and then centrifuged for 5 minutes at 16,100 x g at 4C. Finally, the liquid was removed, and the remaining ethanol was left to evaporate for 30 minutes or less. The following volumes of TEe (10 mM Tris, pH 8.0; 0.1 mM EDTA) were added to resuspend the DNA from the three sample types: 200 μL for INPUT pellets, 50 μL for IPOD, and 30 μL for ChIP. All samples were quantified with QuantiFluor dsDNA System (Promega, #2670) using a BioTek Synergy plate reader. Input samples were assessed for fragment sizes on 2% agarose gel electrophoresis.
Illumina library preparation for IPOD-HR. The purified and quantified DNA from INPUT, IPOD, and RNA Polymerase ChIP samples were then prepared for Illumina sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (#7645S/L) with NEBNext® Multiplex Oligos for Illumina® Unique Dual Index UMI Adaptors DNA Set 1 (#E7395S) or NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (#E7600S) and Dual Index Primers Set 2 (#E7780S). Omega Biotek Mag-Bind DNA purification or Axygen purification beads were used for all SPRI bead cleanup steps. The bead purification at the post-adaptor ligation stage was modified as follows: 1.8x volume of DNA purification beads and 0.7x isopropanol were added instead of the normal 0.9x volume of beads.  Each sample prepared for sequencing was quantified and assessed for fragment size and for the presence of any adaptor present on 2% agarose gel electrophoresis. The samples were pooled into libraries, which were sequenced on a NextSeq 550 instrument at the Michigan Advanced Genomics Core.

value: wild type

tag: media

value: LB + Mitomycin C

tag: time of_harvest

value: logarithmic phase


title: Δihfa KDS1 rep2 - ChIP

value: {delta}ihfA

value: LB

tag: chip antibody

value: anti-RNA polymerase antibody (NeoClone WP023)


title: Dark-8h-GMUCT-2

description: uncapped and cleaved transcripts


title: Δhns KDS1 rep2 - ChIP


title: Dark-4h-GMUCT-1

description: uncapped and cleaved transcripts


title: Light-8h-mRNA-3


title: Dark-0h-GMUCT-1

description: uncapped and cleaved transcripts


title: Light-4h-mRNA-1


title: Light-0h-mRNA-3


title: NIT-1 cells, culture medium, 24h, biological rep 1


title: Light-0h-mRNA-1


title: Dark-8h-mRNA-3


title: Light-8h-mRNA-1


title: ΔtsrAΔhns KDS1 rep4 - RNA-seq

data_processing:
Illumina Truseq adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA) were removed with with cutadapt (version 4.1 with Python 3.8.6)
Low quality reads were trimmed with Trimmomatic (version 0.39) using this command: trimmomatic PE -threads 24 -phred33 -validatePairs TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:14
The surviving reads from adapter removal and trimming (described above) were quantified and pseudoaligned with kallisto (version 0.48.0). Arguments for indexing: -k 21 –make-unique Arguments for quantitation: -t 4 -b 200 –rf-stranded –bias
The quantified and pseudoaligned reads were subjected to differential expression calling using sleuth R package (version 0.30.1) using Sleuth response error measurement (full) model where we fitted our model by condition ~ batch parameter where condition refers to each genotype: wild type, ΔtsrAΔhns, ΔtsrA, Δhns, and ΔihfA.
Assembly: We obtained an initial genome reference sequence for KDS1 by sequencing high molecular weight genomic DNA purified from the strain. Raw reads are available at SRA########. Initial assembly was performed on the Nanopore reads using NECAT (version 0.0.1 20200803), resulting in two contigs which clearly correspond to the two V. cholerae chromosomes. The assembly was then polished using pilon (version 1.24) using default arguments, with all available reads from INPUT samples (aligned using bowtie2) as the short read inputs. Manual finishing was performed using a set of iterative rounds of breseq (version 0.37.0) runs to identify remaining discrepancies between the Illumina short read data and the in-progress assembly and resolving them by applying differences with gdtools. We then manually assigned the starting position of each chromosome to match those of commonly used El Tor reference genomes.  Annotation of the newly obtained assembly was performed using prokka (version 1.14.5) with arguments --genus Vibrio --species cholerae --accver 2, using a draft genome obtained from the ***** as a reference for potential proteins. We then assigned VC numbers to all identifiable genes matching the reference El Tor strain (EMBL reference sequences AE003852.1 and AE003853.1 for chromosomes 1 and 2, respectively). Annotated genes from the El Tor reference were aligned to those of our prokka-annotated KDS1 assembly, using nucmer (v. 3.1) with default settings. We further required that for each potential match, the starting and ending positions of the reference El Tor version and the KDS1 version in the identified features differed by no more than 20 nucleotides.
Supplementary files format and content: Files that end with _abundance.h5 files are used by the differential expression calling with Sleuth R package (version 0.30.1). Files that end with _abundance.tsv are 5 column .tsv files (see column headers for descriptions) that show the abundances of transcripts for each annotated gene in the assembled transcriptome in the directory.
Supplementary files format and content: Files that end with _parameter_sleuth_results.tsv represent the sleuth tables from the differential expression calling using the Sleuth R package (version 0.30.1)
Supplementary files format and content: Files that end with _sleuth_obj are sleuth R objects that can be utilized to obtain the full sleuth results table

extract_protocol:
RNA isolation. Bacterial strains of interest were grown to an OD600 of 0.3 in 4 mL culture tubes and mixed 1:1 with ice-cold methanol in a 15 mL falcon tube, under culture conditions equivalent to the IPOD experiments described above. Methanol-treated samples were pelleted at 7,000 x g at 4C, and the resulting pellets were washed in ice-cold phosphate-buffered saline. The washed pellets were resuspended in 200 µL TRI Reagent (Millipore/Sigma) and incubated for 5 minutes at room temperature. The samples were mixed with 40 µL chloroform, vortexed, and incubated for 10 minutes at room temperature. The chloroform-treated samples were then centrifuged at 12,000 x g for 10 min at 4C. Following centrifugation, the upper (aqueous) phase was collected, promptly mixed with 110 µL 2-propanol and 11 µL pH 6.2 3M sodium acetate, and mixed vigorously. The samples were centrifuged at 12,000 x g for 15 min at 4C, and the pellets were washed twice with 500 µL of 75% ethanol. The washed pellets were incubated uncapped at 65C for 3 minutes to evaporate any residual ethanol and resuspended in 20 µL of diethyl dicarbonate (DEPC) treated water.
rRNA depletion and RNA-sequencing library preparation. Purified RNA was subjected to Baseline-ZERO™ DNase digestion in a 100 μL reaction of 20 μL of purified RNA, 5 μL Baseline-ZERO™ DNAse enzyme (LGC Biosearch Technologies, Pt# E0110-D1, 1 U/μL), 10 μL 10X Baseline-ZERO™ DNase Reaction Buffer, 2 μL RNase Inhibitor, Murine (NEB, #M0314S/L) and nuclease-free water at 37C for 30 minutes. The RNA was purified with Zymo RNA clean and concentrate kit and eluted with nuclease-free water. The quality of purified RNA was assessed on a 2% agarose gel with guanidine thiocyanate and quantified with a NanoDrop spectrophotometer. Purified RNA was depleted of ribosomal RNA (rRNA) using a NEBNext® rRNA Depletion Kit (Bacteria) (NEB, #E7850L/X) and library preparation was done using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB, #E7760S/L), according to the manufacturer’s instructions. The libraries were assessed for quality with agarose gel electrophoresis and quantified with a Promega Quantifluor High Sensitivity dsDNA kit.

treatment_protocol: (see growth protocol)


title: Dark-8h-mRNA-2


title: Amplicon sequencing of CSF2RB ON-target and OFF-target  sites of untreated samples

description: used as untreated control

value: Untreated


title: Amplicon sequencing of Off-target sites of untreated samples

description: used as untreated control


title: Amplicon sequencing of ON-target sites of untreated samples

description: used as untreated control


title: Dark-0h-mRNA-3


title: Dark-0h-mRNA-1


title: ΔtsrAΔhns KDS1 rep1 - RNA-seq


title: Amplicon sequencing of ON-target sites of treated samples


title: WT KDS1 + MMC rep3 - ChIP


title: WT KDS1 + MMC rep3 - IPOD


title: Δhns KDS1 rep2 - RNA-seq


title: Δhns KDS1 rep1 - RNA-seq


title: Δihfa KDS1 rep2 - IPOD


title: Δihfa KDS1 rep2 - INPUT


title: Δhns KDS1 rep2 - IPOD


title: Δhns KDS1 rep2 - INPUT


title: ΔihfA KDS1 rep3 - RNA-seq


title: WT KDS1 rep3 - RNA-seq


title: ΔihfA KDS1 rep2 - RNA-seq


title: ΔihfA KDS1 rep1 - RNA-seq


title: ΔtsrAΔhns KDS1 rep3 - RNA-seq


title: ΔtsrA KDS1 rep2 - RNA-seq


title: ΔtsrA KDS1 rep3 - RNA-seq


title: ΔtsrA KDS1 rep1 - RNA-seq


title: ΔtsrA KDS1 rep4 - RNA-seq


title: WT KDS1 rep1 - RNA-seq


title: Δhns KDS1 rep4 - RNA-seq


title: Whole sac-fry, Medium choline, Family B, Sire 2, 14-days post-hatch

city: Birmingham

first: Peggy

last: Biga

state: Alabama

address: 902 14th Street South

department: Biology

institute: University of Alabama at Birmingham

data_processing:
Trimmed sequence reads were mapped to GCF_013265735.2_USDA_OmykA_1.1/GCF_013265735.2_USDA_OmykA_1.1_rna.fna.gz using Salmon (v0.14.1) (default parameters for paired end)
Read count extraction and normalization were performed using DESeq2.
Assembly: OmykA_1.1
Supplementary files format and content: Excel worksheet file includes normalized counts for each sample at different comparisons used in the manuscript.

organism: Oncorhynchus mykiss

source_name: Whole organism

extract_protocol:
RNA was harvested using Rneasy Minikit (Qiagen).
RNA libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's instructions.

value: Whole organism

value: NCCCWA breeding program

value: ARS-Fp/Fc-R

value: Medium Choline

tag: time

value: 14-days post-hatch


title: Δhns KDS1 rep3 - RNA-seq


title: ΔtsrAΔhns KDS1 rep2 - RNA-seq


title: WT KDS1 rep2 - RNA-seq


title: Whole sac-fry, Low choline, Family E, Sire 2, 14-days post-hatch

value: Low Choline


title: ΔtsrAΔhns KDS1 rep1 - ChIP


title: ΔtsrAΔhns KDS1 rep3 - ChIP


title: Whole sac-fry, Low choline, Family E, Sire 1, 14-days post-hatch


title: Whole sac-fry, Medium choline, Family A, Sire 2, 14-days post-hatch


title: Whole sac-fry, High choline, Family A, Sire 2, 14-days post-hatch

value: High Choline


title: Whole sac-fry, Low choline, Family A, Sire 2, 14-days post-hatch


title: ΔtsrAΔhns KDS1 rep2 - INPUT


title: Whole sac-fry, High choline, Family E, Sire 2, 14-days post-hatch


title: WT KDS1 rep4- RNA-seq


title: Whole sac-fry, Medium choline, Family E, Sire 1, 14-days post-hatch


title: ΔtsrAΔhns KDS1 rep1 - INPUT


title: Whole sac-fry, Medium choline, Family E, Sire 2, 14-days post-hatch


title: ΔtsrAΔhns KDS1 rep3 - IPOD


title: ΔtsrAΔhns KDS1 rep2 - IPOD


title: ΔtsrA KDS1 rep3 - ChIP


title: ΔtsrAΔhns KDS1 rep1 - IPOD


title: ΔtsrAΔhns KDS1 rep2 - ChIP


title: Whole sac-fry, Low choline, Family B, Sire 1, 14-days post-hatch


title: Whole sac-fry, Medium choline, Family B, Sire 1, 14-days post-hatch


title: ΔtsrA KDS1 rep2 - ChIP


title: Whole sac-fry, High choline, Family A, Sire 1, 14-days post-hatch


title: Whole sac-fry, High choline, Family E, Sire 1, 14-days post-hatch


title: ΔtsrA KDS1 rep1 - ChIP


title: Whole sac-fry, Medium choline, Family A, Sire 1, 14-days post-hatch


title: ΔtsrA KDS1 rep2 - INPUT


title: ΔtsrA KDS1 rep3 - INPUT


title: Whole sac-fry, Low choline, Family A, Sire 1, 14-days post-hatch


title: ΔtsrA KDS1 rep1 - INPUT


title: Whole sac-fry, Low choline, Family B, Sire 2, 14-days post-hatch


title: ΔtsrAΔhns KDS1 rep3 - INPUT


title: ΔtsrA KDS1 rep3 - IPOD


title: ΔtsrA KDS1 rep1 - IPOD


title: Whole sac-fry, Low choline, Family E, Sire 1, 0-days post-hatch

value: 0-days post-hatch


title: ΔtsrA KDS1 rep2 - IPOD


title: ΔvctA KDS1 rep2 - ChIP

value: {delta}vctA


title: Whole sac-fry, High choline, Family B, Sire 1, 14-days post-hatch


title: Whole sac-fry, High choline, Family B, Sire 2, 14-days post-hatch


title: Whole sac-fry, Medium choline, Family B, Sire 2, 0-days post-hatch


title: ΔvctA KDS1 rep1 - ChIP


title: Whole sac-fry, High choline, Family A, Sire 2, 0-days post-hatch


title: ΔvctA KDS1 rep2 - INPUT


title: Whole sac-fry, Low choline, Family A, Sire 2, 0-days post-hatch


title: ΔvctA KDS1 rep1 - INPUT


title: Whole sac-fry, Medium choline, Family A, Sire 2, 0-days post-hatch


title: ΔvctA KDS1 rep2 - IPOD


title: Whole sac-fry, High choline, Family E, Sire 2, 0-days post-hatch


title: ΔvctA KDS1 rep1 - IPOD


title: Whole sac-fry, Medium choline, Family E, Sire 2, 0-days post-hatch


title: Whole sac-fry, Low choline, Family E, Sire 2, 0-days post-hatch


title: Whole sac-fry, Medium choline, Family E, Sire 1, 0-days post-hatch


title: WT KDS1 rep4 - ChIP


title: Whole sac-fry, High choline, Family B, Sire 2, 0-days post-hatch


title: Whole sac-fry, High choline, Family E, Sire 1, 0-days post-hatch


title: WT KDS1 rep4 - INPUT


title: Whole sac-fry, Low choline, Family B, Sire 1, 0-days post-hatch


title: WT KDS1 rep3 - INPUT


title: WT KDS1 rep2 - ChIP


title: Whole sac-fry, Medium choline, Family B, Sire 1, 0-days post-hatch


title: WT KDS1 rep1 - INPUT


title: Whole sac-fry, Medium choline, Family A, Sire 1, 0-days post-hatch


title: WT KDS1 rep3 - IPOD


title: Whole sac-fry, Low choline, Family A, Sire 1, 0-days post-hatch


title: CLL-08, 6 months of ibrutinib (6m), migrated cells

city: Barcelona

first: Daniel

last: Medina

address: Centre Cellex, 115-117 Natzaret

department: Experimental Hematology

country: Spain

institute: Vall d'Hebron Institute of Oncology (VHIO)

description: Migrated_cells_analysis_limma_logcpm_counts

data_processing:
RNA-seq reads were mapped against human reference genome (GRCh38) using STAR software version 2.7.8a with ENCODE parameters
Annotated genes were quantified with RSEM version 1.3.02 with default parameters, using the annotation version GENCODE v41
Differential expression analysis was performed using limma v3.54.2 R package
Counts were normalized with TMM25 and transformed with the ‘voom’ function into logCPM.
To account for repeated measures on the same individual before and after treatment, the limma duplicateCorrelation function was used. Each linear model was fitted with the voom-transformed counts and contrasts were extracted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample.

source_name: Peripheral blood mononuclear cells

extract_protocol:
AllPrep DNA/RNA Micro kit (QIAGEN)
One paired-end library was prepared using the SMARTseq2 protocol

treatment_protocol: Initial B cell isolation kit (Stem cell) and migration towards CXCL12 (Peprotech).

value: Peripheral blood mononuclear cells

value: Ibrutinib


title: WT KDS1 rep4 - IPOD

value: wild type


title: Whole sac-fry, High choline, Family A, Sire 1, 0-days post-hatch


title: Whole sac-fry, High choline, Family B, Sire 1, 0-days post-hatch


title: CLL-08, before treatment (BT), migrated cells

value: Baseline


title: Whole sac-fry, Low choline, Family B, Sire 2, 0-days post-hatch


title: CLL-02, before treatment (BT), migrated cells


title: CLL-06, before treatment (BT), migrated cells


title: CME_R3

city: Beaucouzé

first: Matthieu

last: Gaucher

address: 42 rue Georges Morel

department: SPE

country: France

institute: INRAE

data_processing:
The sequenced reads (ranging from 23 to 44.6 million read pairs per sample) were mapped on the reference transcriptional units from GDDH13 v1.1 using Salmon software (Patro et al., 2017)
Identification of differentially expressed genes (DEGs) was performed with DESeq2, including a Benjamini–Hochberg procedure to control the false discovery rate (FDR) (Love et al., 2014)
Assembly: GDDH13 v1.1
Supplementary files format and content: tab-delimited file include raw counts values for each sample, logCPM and log2ratios of the CME/FB comparison

organism: Malus domestica

source_name: leaf

growth_protocol: Plants were grown in individual pots (8 x 5.5 x 7 cm) under greenhouse conditions (natural photoperiod supplemented with artificial light if needed, 17°C night and 20–23°C day)

extract_protocol:
RNA was harvested using NucleoSpin RNA Plant (Macherey Nagel)
Libraries were generated using the Illumina mRNA Stranded protocol

treatment_protocol: CME and FB were sprayed to runoff on entire plants with a spray gun. Plants received two treatments four days apart, and sampling for RNAseq analysis occurred 3 days after the second treatment

value: leaf

value: Golden delicious

value: formulated cutin monomer extract


title: CLL-06, 6 months of ibrutinib (6m), migrated cells


title: WT KDS1 rep3 - ChIP

value: LB

value: anti-RNA polymerase antibody (NeoClone WP023)

value: logarithmic phase


title: CME_R2


title: CLL-11, 6 months of ibrutinib (6m), migrated cells


title: CME_R1


title: FB_R3

value: formulation blank


title: CLL-11, before treatment (BT), migrated cells


title: CLL-03, 6 months of ibrutinib, migrated cells


title: FB_R2


title: CLL-09, 6 months of ibrutinib, migrated cells


title: CLL-03, before treatment (BT), migrated cells


title: 91_ASCL1_r4_D5PRNBSA

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutch Cancer Research

data_processing:
Peak calls for ASCL1, H3K4me1, H3K4me3 and H3K27ac from CUT&RUN data at different timepoints were performed using SEACR (v1.3)
Assembly: hg38
Supplementary files format and content: bed files
Library strategy: CUT&RUN

growth_protocol: C4-2B cells were maintained in Advanced DMEM/F12 medium supplemented with 1X serum-free B27, 10 ng/mL recombinant human basic FGF (bFGF), 10 ng/mL recombinant human EGF, 100 U/mL penicillin and 100 μg/mL streptomycin, and 4 mmol/L GlutaMAX in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cut-and-Run_extract_protocol.rtf PMID 25827087
Libraries were prepared using the AutoCUT&RUN protocol (https://www.protocols.io/view/autocut-run-genome-wide-profiling-of-chromatin-pro-6qpvre6zblmk/v1)

value: Prostate cancer cells

value: ASCL1 (Abcam, #ab74065)


title: 90_IgGr_r3_D14PRNBSA

value: Rabbit IgG (EpiCypher, 13-0042)


title: 89_IgGr_r2_D14PRNBSA


title: CLL-07, before treatment (BT), migrated cells


title: FB_R1


title: CLL-05, 6 months of ibrutinib (6m), migrated cells


title: 87_H3K27ac_r3_D14PRNBSA

value: H3K27ac (EMD, MABE647)


title: CLL-09, before treatment (BT), migrated cells


title: 88_IgGr_1_D14PRNBSA


title: CLL-10, 6 months of ibrutinib (6m)


title: CLL-07, 6 months of ibrutinib, migrated cells


title: 84_H3K4me1_r3_D14PRNBSA

value: H3K4me1 (Abcam, #ab8895)


title: CLL-10, before treatment (BT), migrated cells


title: CLL-01, 6 months of ibrutinib (6m), migrated cells


title: 83_H3K4me1_r2_D14PRNBSA


title: 85_H3K27ac_r1_D14PRNBSA


title: CLL-01, before treatment (BT), migrated cells


title: 82_H3K4me1_r1_D14PRNBSA


title: CLL-05, before treatment (BT), migrated cells


title: 92_ASCL1_r4_D14PRNBSA


title: CLL-04, 6 months of ibrutinib, migrated cells


title: 79_H3K4me3_r1_D14PRNBSA


title: CLL-12, before treatment (BT), migrated cells


title: CLL-04, before treatment (BT), migrated cells


title: CLL-12, 6 months of ibrutinib (6m), migrated cells


title: 81_H3K4me3_r3_D14PRNBSA


title: 78_ASCL1_r3_D14PRNBSA


title: 76_ASCL1_r1_D14PRNBSA


title: 86_H3K27ac_r2_D14PRNBSA


title: Breast tumor Emseq Replicate 2

city: Ipswich

first: Bo

last: Yan

state: MA

address: County Road

institute: New England Biolabs

data_processing:
illumina adapter sequence was trimmed trim_galore
reads were mapped to human genome using bowtie2
C to T transition was extracted using samtools mpileup
regional methylation was calculated using custom scripts based on the C to T transition rate
SNP was identified using gatk
Assembly: hg38
Supplementary files format and content: custom format with regional methylation level
Library strategy: EM-seq

source_name: Breast tumor

extract_protocol:
genomic DNA isolated from the GM12878 cell line by Coriell Institute
RIMSseq with or without exome Target enrichment

value: Breast tumor


title: Breast tumor RIMSseq TES Replicate 3

data_processing:
illumina adapter sequence was trimmed trim_galore
reads were mapped to human genome using bowtie2
C to T transition was extracted using samtools mpileup
regional methylation was calculated using custom scripts based on the C to T transition rate
SNP was identified using gatk
Assembly: hg38
Supplementary files format and content: custom format with regional methylation level
Library strategy: RIMS-seq


title: 75_IgGr_r3_D8PRNBSA


title: 77_ASCL1_r2_D14PRNBSA


title: Breast tumor Emseq Replicate 1


title: Breast tumor RIMSseq TES Replicate 2


title: 74_IgGr_r2_D8PRNBSA


title: 73_IgGr_1_D8PRNBSA


title: 72_H3K27ac_r3_D8PRNBSA


title: Light-0h-GMUCT-2

description: uncapped and cleaved transcripts

value: Leaf

value: HeinZ 1706


title: Breast tumor RIMSseq TES Replicate 1


title: 69_H3K4me1_r3_D8PRNBSA


title: 71_H3K27ac_r2_D8PRNBSA


title: 70_H3K27ac_r1_D8PRNBSA


title: Leaf, shr2, rep2, scRNAseq

city: Irapuato

first: Carlos

last: Ortiz-Ramírez

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León.

department: UGA

country: Mexico

institute: Cinvestav

data_processing:
Raw scRNAseq data was analyzed by Cell Ranger 5.0.1 (10x Genomics) to generate gene-cell matrices. Gene reads were aligned to Setaria viridis 2.1 reference genome. Cell-type analysis and clustering were performed using Seurat v4.3.0
Assembly: Setaria viridis 2.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Setaria viridis

source_name: Leaf middle section

extract_protocol:
Leaf segments were sectioned in ∼3-mm fragments using a scalpel. Fragments were placed in a small petri dish and weighted to calculate protoplast yield. Protoplasting solution was added immediately after weighting, which consisted of 1.25% (w/v) Cellulase R-10, 2% (w/v) Cellulase RS, 0.4% (w/v) macerozyme R10, and 0.2% (w/v) pectolyase Y23. Tissue digestion was carried out with gentle shaking at room temperature for 1 hour and 40 minutes. The cell suspension was then filtered using a 40 μm nylon filter and cells were then centrifuged at 200 rcf for 5 min. Cells were resuspended in pre-filtered (0.22 µm) washing buffer (0.4 M mannitol, 0.02 M MES, 0.02 M KCl, 0.01 M CaCl2, 0.015 mM BSA). Cells were then re-suspended at a concentration of 2000-3000 cells/μL and loaded into a Single Cell A chip (10× Genomics).
Approximately 10,000 cells were loaded per replicate. Three independent replicates per genotype were performed. Chips were loaded on a Chromium Controller (10x Genomics) to generate single-cell GEMs. Single-cell libraries were then prepared using the Chromium Single Cell 3´ library kit, following manufacturer instructions. The quality of resulting DNA libraries was assessed with an Agilent TapeStation system.

value: Leaf middle section

tag: developmental stage

value: 4 week old plants


title: Leaf, shr2, rep1, scRNAseq


title: Dark-8h-GMUCT-1

description: uncapped and cleaved transcripts


title: 80_H3K4me3_r2_D14PRNBSA


title: 67_H3K4me1_r1_D8PRNBSA


title: Leaf, rep3, scRNAseq

value: wild type


title: 64_H3K4me3_r1_D8PRNBSA


title: Leaf, rep2, scRNAseq


title: 65_H3K4me3_r2_D8PRNBSA


title: 63_ASCL1_r3_D8PRNBSA


title: 66_H3K4me3_r3_D8PRNBSA


title: Leaf, rep1, scRNAseq


title: PBMC from HC1181 at timepoint recovery, ~6 weeks after uncomplicated malaria

data_processing:
adapter trimming with trimmomatic 0.39, NexteraPE adapter sequences (parameters -LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:70)
alignment of trimmed reads with STAR 2.7.0e with a GENCODE generated index (parameters- –runThreadN 8 –genomeDir /home/erh90/indexes/20220131_STAR/ –readFilesCommand zcat –readFilesIn pe_forward.fq.gz pe_reverse.fq.gz –outSAMtype BAM SortedByCoordinate –outFileNamePrefix Sample
raw gene counts were calculated with HTSeq 0.13.5 (parameters- -s reverse -r pos -t exon -i gene_id -f bam)
Assembly: hg38
Supplementary files format and content: tab-delimited text file of raw counts per gene for each sample

extract_protocol:
Qiagen allprep mini kit was used following manufacturer protocols
Libraries were constructed with stranded mRNA (Poly-A) preparation with Nextera transposon adapters on a NovaSeq platform at the Cleveland Clinic Genomics Core

value: PBMC


title: Static_siTNIK2

city: Houston

first: Tu N

last: Tran

state: Texas

address: 6670 Bertner Ave,

department: Cardiovascular

institute: Houston Methodist Research Institute

data_processing:
We used Cuffdiff for differentially expressed gene (DEG) analysis, to estimate the significance of differential expression and calculate p value from transcript abundance data.
Assembly: hg38
Supplementary files format and content: FPKM of each sample

source_name: Human Aorta

growth_protocol: HAEC were maintained in ECM supplemented with 5% fetal bovine serum (FBS), Endothelial cell growth  supplements (ECGS), and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Library construction, and sequencing using a BGISEQ-500

treatment_protocol: HAECs were transfected with siControl or siTNIK for 48 hours; Disturbed flow or Laminar flow were applied for 24 hours using cone plate system.

value: Human Aorta

value: Primary cell

value: Human Aortic Endothelial Cells (HAEC)

value: siTNIK transfection


title: 61_ASCL1_r1_D8PRNBSA


title: 62_ASCL1_r2_D8PRNBSA


title: 59_IgGr_r2_D5PRNBSA


title: 58_IgGr_1_D5PRNBSA


title: Static_siTNIK1


title: 60_IgGr_r3_D5PRNBSA


title: PBMC from HC1181 at timepoint malaria, during uncomplicated malaria


title: 68_H3K4me1_r2_D8PRNBSA


title: 55_H3K27ac_r1_D5PRNBSA


title: PBMC from HC1181 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1157 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: Static_siCtrl2

value: siControl transfection


title: Static_siCtrl1


title: 53_H3K4me1_r2_D5PRNBSA

value: Prostate cancer cells


title: PBMC from HC1157 at timepoint malaria, during uncomplicated malaria


title: 51_H3K4me3_r3_D5PRNBSA


title: 50_H3K4me3_r2_D5PRNBSA


title: PBMC from HC1157 at timepoint baseline, before uncomplicated malaria


title: 49_H3K4me3_r1_D5PRNBSA


title: 48_ASCL1_r3_D5PRNBSA

value: ASCL1 (Abcam, #ab74065)


title: 47_ASCL1_r2_D5PRNBSA


title: 46_ASCL1_r1_D5PRNBSA


title: PBMC from HC1115 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: PBMC from HC1115 at timepoint malaria, during uncomplicated malaria


title: 57_H3K27ac_r3_D5PRNBSA


title: PBMC from HC1115 at timepoint baseline, before uncomplicated malaria


title: 43_IgGr_1_D4PRNBSA

value: Rabbit IgG (EpiCypher, 13-0042)


title: 44_IgGr_r2_D4PRNBSA


title: 42_H3K27ac_r3_D4PRNBSA

value: H3K27ac (EMD, MABE647)


title: 41_H3K27ac_r2_D4PRNBSA


title: 56_H3K27ac_r2_D5PRNBSA


title: PBMC from HC1092 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: 54_H3K4me1_r3_D5PRNBSA

value: H3K4me1 (Abcam, #ab8895)


title: 52_H3K4me1_r1_D5PRNBSA


title: 40_H3K27ac_r1_D4PRNBSA


title: 39_H3K4me1_r3_D4PRNBSA


title: PBMC from HC1092 at timepoint malaria, during uncomplicated malaria


title: PBMC from HC1092 at timepoint baseline, before uncomplicated malaria


title: PBMC from HC1074 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: 38_H3K4me1_r2_D4PRNBSA


title: 37_H3K4me1_r1_D4PRNBSA


title: 34_H3K4me3_r1_D4PRNBSA


title: PBMC from HC1074 at timepoint malaria, during uncomplicated malaria


title: 33_ASCL1_r3_D4PRNBSA


title: 32_ASCL1_r2_D4PRNBSA


title: PBMC from HC1074 at timepoint baseline, before uncomplicated malaria


title: 45_IgGr_r3_D4PRNBSA


title: 30_IgGr_r3_D3PRNBSA


title: 31_ASCL1_r1_D4PRNBSA


title: 29_IgGr_r2_D3PRNBSA


title: PBMC from HC1034 at timepoint malaria, during uncomplicated malaria


title: 27_H3K27ac_r3_D3PRNBSA


title: 26_H3K27ac_r2_D3PRNBSA


title: PBMC from HC1034 at timepoint baseline, before uncomplicated malaria


title: 24_H3K4me1_r3_D3PRNBSA


title: 28_IgGr_1_D3PRNBSA


title: 25_H3K27ac_r1_D3PRNBSA


title: 23_H3K4me1_r2_D3PRNBSA


title: PBMC from HC1020 at timepoint malaria, during uncomplicated malaria


title: 22_H3K4me1_r1_D3PRNBSA


title: 21_H3K4me3_r3_D3PRNBSA


title: PBMC from HC1020 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: 35_H3K4me3_r2_D4PRNBSA


title: PBMC from HC1020 at timepoint baseline, before uncomplicated malaria


title: 20_H3K4me3_r2_D3PRNBSA


title: 36_H3K4me3_r3_D4PRNBSA


title: 19_H3K4me3_r1_D3PRNBSA


title: 18_ASCL1_r3_D3PRNBSA


title: PBMC from HC1014 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: 17_ASCL1_r2_D3PRNBSA


title: PBMC from HC1034 at timepoint recovery, ~6 weeks after uncomplicated malaria


title: 16_ASCL1_r1_D3PRNBSA


title: PBMC from HC1014 at timepoint malaria, during uncomplicated malaria


title: HE_scRNAseq

first: Yijie

last: Huang

address: 上海市徐汇区淮海西路241号

department: Cardiology

institute: Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using Cell Ranger v3.0.0 (10x Genomics).
Assembly: mm10
Supplementary files format and content: Cell Ranger output

source_name: duodenum tissues

extract_protocol:
Tissues were cut into 0.5mm3 pieces, and digested in HBSS containing 0.2% collagenase type II in 37°C with a shaking speed of 50rpm for about 40min. The digested suspension was subsequently filtered through a 40-µm cell strainer and washed with pre-warmed Dulbecco's Modified Eagle’s Medium (DMEM)/F-12 50/50 supplemented with 10% fetal calf serum (FCS), 100U/ml penicillin, and 100U/ml streptomycin, and centrifuged at 300 x g for 5min.
Library was performed according to the manufacturer’s instructions  (single cell 3’ v3 protocol, 10x Genomics).

value: duodenum tissues

value: Lkb1 Heterozygous


title: 14_IgGr_r2_D2PRNBSA


title: PBMC from HC1014 at timepoint baseline, before uncomplicated malaria


title: 13_IgGr_1_D2PRNBSA


title: 15_IgGr_r3_D2PRNBSA