title: BB2_HAB_G_ATAC

description:
glia_HAB-includes-blacklisted-regions_peaks.narrowPeak
glia_HAB.bw

value: HAB


title: BB1_VLPFC_G_ATAC

status: Public on Aug 25 2022

type: SRA

city: New York

first: Panos

last: Roussos

state: NY

address: 1470 madison ave

country: USA

institute: Icahn school of medicine at mount sinai

description:
glia_VLPFC-includes-blacklisted-regions_peaks.narrowPeak
glia_VLPFC.bw

library_source: genomic

data_processing:
The raw reads were trimmed with Trimmomatic and then mapped to the human reference genome GRCh38 analysis set reference genome with the pseudoautosomal region masked on chromosome Y with the STAR aligner.
To correct for allelic bias resulting from individual-specific genome variation, we ran STAR with enabled WASP module as we provide both ATAC-seq FASTQ file and WGS file of the corresponding individual.
This yielded for each sample a BAM file of mapped paired-end reads sorted by genomic coordinates. From these files, reads that mapped to multiple loci or to the mitochondrial genome were removed using samtools and duplicated reads were removed with PICARD. Quality control metrics were reported with phantompeakqualtools and Picard.
The samples from the same brain region and cell type were subsampled and merged.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01 and parameters "--shift -100 --extsize 200"
bigWig files were generated using the genomeCoverageBed from bedtools
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

molecule: genomic DNA

organism: Homo sapiens

source_name: Ventrolateral Prefrontal Cortex

extract_protocol:
ATAC-seq reactions were performed on Neuronal (NeuN+) and non-neuronal (NeuN-) nuclei isolated by FANS from 149 tissue dissections from 25 brain regions
Where available, 100,000 sorted nuclei were centrifuged at 500 × g for 10 min, 4°C. Pellets were resuspended in the transposase reaction mix and libraries were generated using an established protocol.

tag: group

value: non-neuron

tag: brain region

value: VLPFC

tag: tissue

value: Forebrain

tag: age of_death

tag: Sex

value: Female


title: BB1_VLPFC_N_ATAC

description:
neuron_VLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_VLPFC.bw

value: neuron


title: BB1_DLPFC_N_ATAC

description:
neuron_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_DLPFC.bw

source_name: Dorsolateral Prefrontal Cortex

value: DLPFC


title: BB1_NAC_G_ATAC

description:
glia_NAC-includes-blacklisted-regions_peaks.narrowPeak
glia_NAC.bw

source_name: Nucleus Accumbens

value: NAC

value: BasalGanglia


title: BB1_RMTG_G_ATAC

description:
glia_RMTG-includes-blacklisted-regions_peaks.narrowPeak
glia_RMTG.bw

source_name: Rostromedial Tegmental Nucl

value: RMTG

value: Midbrain


title: BB1_VTA_G_ATAC

description:
glia_VTA-includes-blacklisted-regions_peaks.narrowPeak
glia_VTA.bw

source_name: Ventral Tegmental Area

value: VTA


title: BB1_RMTG_N_ATAC

description:
neuron_RMTG-includes-blacklisted-regions_peaks.narrowPeak
neuron_RMTG.bw


title: BB1_PSC_G_ATAC

description:
glia_PSC-includes-blacklisted-regions_peaks.narrowPeak
glia_PSC.bw

source_name: Primary Somatosensory Cortex

value: PSC


title: BB1_CRBLM_G_ATAC

description:
glia_CRBLM-includes-blacklisted-regions_peaks.narrowPeak
glia_CRBLM.bw

source_name: Cerebellum

value: CRBLM

value: Hindbrain


title: BB1_AMY_N_ATAC

description:
neuron_AMY-includes-blacklisted-regions_peaks.narrowPeak
neuron_AMY.bw

source_name: Amygdaloid Complex

value: AMY


title: BB1_EC_N_ATAC

description:
neuron_EC-includes-blacklisted-regions_peaks.narrowPeak
neuron_EC.bw

value: EC


title: BB1_ACC_N_ATAC

description:
neuron_ACC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ACC.bw

source_name: Anterior Cingulate Cortex

value: ACC


title: BB1_ACC_G_ATAC

description:
glia_ACC-includes-blacklisted-regions_peaks.narrowPeak
glia_ACC.bw

value: non-neuron


title: BB1_PVPC_G_ATAC

description:
glia_PVPC-includes-blacklisted-regions_peaks.narrowPeak
glia_PVPC.bw

source_name: Posteroventral (Inferior) Parietal Cortex

value: PVPC


title: BB1_PSC_N_ATAC

description:
neuron_PSC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PSC.bw

value: Forebrain


title: BB1_EC_G_ATAC

description:
glia_EC-includes-blacklisted-regions_peaks.narrowPeak
glia_EC.bw

value: Female


title: BB1_DRN_G_ATAC

description:
glia_DRN-includes-blacklisted-regions_peaks.narrowPeak
glia_DRN.bw

source_name: Dorsal Raphe Nucleus

value: DRN


title: BB1_HIPP_G_ATAC

description:
glia_HIPP-includes-blacklisted-regions_peaks.narrowPeak
glia_HIPP.bw

source_name: Hippocampus

value: HIPP


title: BB1_INS_N_ATAC

description:
neuron_INS-includes-blacklisted-regions_peaks.narrowPeak
neuron_INS.bw

source_name: Insula

value: neuron

value: INS


title: BB1_PSTC_N_ATAC

description:
neuron_PSTC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PSTC.bw

source_name: Posterior Superior Temporal Cortex

value: PSTC


title: BB1_PSTC_G_ATAC

description:
glia_PSTC-includes-blacklisted-regions_peaks.narrowPeak
glia_PSTC.bw


title: BB1_OFC_G_ATAC

description:
glia_OFC-includes-blacklisted-regions_peaks.narrowPeak
glia_OFC.bw

source_name: Orbital Frontal Cortex

value: OFC


title: BB4_MDT_N_ATAC

description:
neuron_MDT-includes-blacklisted-regions_peaks.narrowPeak
neuron_MDT.bw

source_name: Mediodorsal Thalamus

value: MDT

value: Midbrain


title: BB4_MDT_G_ATAC

description:
glia_MDT-includes-blacklisted-regions_peaks.narrowPeak
glia_MDT.bw


title: BB6_NAC_G_ATAC

description:
glia_NAC-includes-blacklisted-regions_peaks.narrowPeak
glia_NAC.bw

value: NAC

value: BasalGanglia


title: BB5_PMC_G_ATAC

description:
glia_PMC-includes-blacklisted-regions_peaks.narrowPeak
glia_PMC.bw

source_name: Primary Motor Cortex

value: PMC

value: Male


title: BB6_ARC_N_ATAC

description:
neuron_ARC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ARC.bw

source_name: Arcuate Nucleus

value: ARC


title: BB4_INS_N_ATAC


title: BB6_ARC_G_ATAC

description:
glia_ARC-includes-blacklisted-regions_peaks.narrowPeak
glia_ARC.bw

value: non-neuron


title: BB5_PMC_N_ATAC

description:
neuron_PMC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PMC.bw


title: BB4_INS_G_ATAC

description:
glia_INS-includes-blacklisted-regions_peaks.narrowPeak
glia_INS.bw


title: BB6_ACC_N_ATAC

description:
neuron_ACC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ACC.bw

value: ACC


title: BB4_ARC_G_ATAC


title: BB5_PAC_G_ATAC

description:
glia_PAC-includes-blacklisted-regions_peaks.narrowPeak
glia_PAC.bw

source_name: Primary Auditory Cortex

value: PAC

value: Forebrain


title: BB5_MDT_N_ATAC


title: BB4_ACC_G_ATAC

description:
glia_ACC-includes-blacklisted-regions_peaks.narrowPeak
glia_ACC.bw

value: Female


title: BB5_EC_N_ATAC

description:
neuron_EC-includes-blacklisted-regions_peaks.narrowPeak
neuron_EC.bw

value: EC


title: BB5_PAC_N_ATAC

description:
neuron_PAC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PAC.bw

value: neuron


title: BB4_ARC_N_ATAC


title: BB4_ACC_N_ATAC


title: BB6_ACC_G_ATAC


title: BB5_EC_G_ATAC

description:
glia_EC-includes-blacklisted-regions_peaks.narrowPeak
glia_EC.bw


title: BB1_HIPP_N_ATAC

description:
neuron_HIPP-includes-blacklisted-regions_peaks.narrowPeak
neuron_HIPP.bw

value: HIPP


title: BB3_ACC_G_ATAC


title: BB1_INS_G_ATAC

value: INS


title: BB5_INS_N_ATAC

description:
neuron_INS-includes-blacklisted-regions_peaks.narrowPeak
neuron_INS.bw


title: human PBMCs, WT, RC group_1

status: Public on Sep 02 2022

city: Hangzhou

first: QIXIA

last: SHEN

state: Zhejiang

address: Qinchun Rd.79, Hangzhou

country: China

institute: The first affiliated hospital, Hangzhou, China

library_source: transcriptomic

data_processing:
sequence reads were aligned to the genome using HISAT2 first.
Then, Stringtie was used to assemble and quantify expressed genes and transcripts.
Then, differential expression analysis was performed by the ballgown package of R software.
Transcripts and genes statistically different between groups were identified by stattest using R 266 software.
Assembly: mm10
Supplementary files format and content: .csv files comparing the differentially expressed genes between two groups (Rm versus Rc group, Rc versus HC group, Rc versus Hc group, Rm versus Hc group)

molecule: total RNA

source_name: human PBMCs, WT, RC group

extract_protocol:
PBMCs were isolated from 5 to 10 ml peripheral blood of KTx recipients and healthy individuals by Ficoll–Hypaque density gradient centrifugation at diagnosis of FSGS and stored at −20°C for future use. The TRIzol Reagent (Invitrogen) and the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) were used for total RNA extraction. A NanoDropTM 2000 (Thermo Scientific, Waltham, MA) spectrophotometer was used for a purity check, followed by agarose gel electrophoresis for degradation and contamination.  216 monitoring. A total amount of DNA of >700 ng or RNA >1 mg  217 was at least required for library preparation and sequencing.
For RNA extracted, the first and second strand cDNA and NEBNext Adaptor hybridization were performed, successively. Then, the AMPure XP system (Beckman Coulter, Beverly, USA) was used for fragment purification. A cBot Cluster Generation System using a HiSeq 2500 PE Cluster Kit (Illumina) was used for cluster generation.
The library sequencing was performed by the Illumina. Hiseq 2500 platform (Illumina Inc., San Diego, CA, USA). Paired-end reads of 125 bp/150 bp were generated for RNA sequencing.

value: whole blood

tag: cell type

value: peripheral blood mononuclear cells

tag: genotype

value: WT

tag: disease state

value: FSGS with recurrence


title: BB5_ARC_N_ATAC

value: Midbrain


title: BB1_OFC_N_ATAC

description:
neuron_OFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_OFC.bw

value: OFC


title: BB3_ACC_N_ATAC

value: Male


title: BB5_INS_G_ATAC


title: BB5_ARC_G_ATAC

value: ARC


title: BB6_ITC_N_ATAC

description:
neuron_ITC-includes-blacklisted-regions_peaks.narrowPeak
neuron_ITC.bw

source_name: Inferior Temporal Cortex

value: ITC


title: BB5_MDT_G_ATAC

description:
glia_MDT-includes-blacklisted-regions_peaks.narrowPeak
glia_MDT.bw

value: non-neuron

value: MDT


title: BB6_HIPP_N_ATAC

value: Forebrain


title: BB6_HIPP_G_ATAC

description:
glia_HIPP-includes-blacklisted-regions_peaks.narrowPeak
glia_HIPP.bw

value: Female


title: BB4_ITC_N_ATAC


title: BB6_HAB_N_ATAC

description:
neuron_HAB-includes-blacklisted-regions_peaks.narrowPeak
neuron_HAB.bw

source_name: Habenula

value: HAB


title: BB5_ACC_N_ATAC

value: neuron

value: ACC


title: BB4_ITC_G_ATAC

description:
glia_ITC-includes-blacklisted-regions_peaks.narrowPeak
glia_ITC.bw


title: BB6_HAB_G_ATAC

description:
glia_HAB-includes-blacklisted-regions_peaks.narrowPeak
glia_HAB.bw


title: BB6_GP_G_ATAC

description:
glia_GP-includes-blacklisted-regions_peaks.narrowPeak
glia_GP.bw

source_name: Globus Pallidus

value: GP

value: BasalGanglia


title: BB4_HIPP_G_ATAC

value: HIPP


title: BB4_HAB_G_ATAC


title: BB4_DLPFC_N_ATAC

description:
neuron_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_DLPFC.bw

source_name: Dorsolateral Prefrontal Cortex

value: DLPFC


title: BB6_CN_N_ATAC

description:
neuron_CN-includes-blacklisted-regions_peaks.narrowPeak
neuron_CN.bw

source_name: Caudate Nucleus

value: CN


title: BB4_DLPFC_G_ATAC

description:
glia_DLPFC-includes-blacklisted-regions_peaks.narrowPeak
glia_DLPFC.bw


title: BB5_HIPP_N_ATAC


title: BB4_GP_G_ATAC


title: BB6_CN_G_ATAC

description:
glia_CN-includes-blacklisted-regions_peaks.narrowPeak
glia_CN.bw


title: BB6_DRN_G_ATAC

description:
glia_DRN-includes-blacklisted-regions_peaks.narrowPeak
glia_DRN.bw

value: DRN

value: Midbrain


title: BB5_PSTC_N_ATAC

description:
neuron_PSTC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PSTC.bw

value: PSTC

value: Male


title: BB4_DRN_G_ATAC


title: BB5_PSTC_G_ATAC

description:
glia_PSTC-includes-blacklisted-regions_peaks.narrowPeak
glia_PSTC.bw


title: BB4_CN_G_ATAC


title: BB4_CN_N_ATAC


title: BB5_HAB_G_ATAC


title: BB6_PSTC_G_ATAC


title: BB6_PSTC_N_ATAC


title: BB4_NAC_G_ATAC

description:
glia_NAC-includes-blacklisted-regions_peaks.narrowPeak
glia_NAC.bw

source_name: Nucleus Accumbens

value: NAC


title: BB4_NAC_N_ATAC

description:
neuron_NAC-includes-blacklisted-regions_peaks.narrowPeak
neuron_NAC.bw


title: BB6_NAC_N_ATAC


title: BB4_PSTC_N_ATAC


title: BB4_PSTC_G_ATAC

value: non-neuron


title: BB3_PSTC_G_ATAC


title: BB5_DLPFC_N_ATAC


title: BB6_DRN_N_ATAC

description:
neuron_DRN-includes-blacklisted-regions_peaks.narrowPeak
neuron_DRN.bw


title: BB5_DLPFC_G_ATAC


title: BB6_PVPC_G_ATAC

description:
glia_PVPC-includes-blacklisted-regions_peaks.narrowPeak
glia_PVPC.bw

source_name: Posteroventral (Inferior) Parietal Cortex

value: PVPC


title: BB6_AMY_G_ATAC

description:
glia_AMY-includes-blacklisted-regions_peaks.narrowPeak
glia_AMY.bw

source_name: Amygdaloid Complex

value: AMY

value: Forebrain


title: BB4_AMY_G_ATAC

value: Female


title: BB5_CN_G_ATAC


title: BB5_DRN_N_ATAC

source_name: Dorsal Raphe Nucleus

value: neuron


title: BB4_AMY_N_ATAC

description:
neuron_AMY-includes-blacklisted-regions_peaks.narrowPeak
neuron_AMY.bw


title: BB5_CN_N_ATAC


title: BB6_ITC_G_ATAC

value: ITC


title: BB4_PVPC_N_ATAC

description:
neuron_PVPC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PVPC.bw


title: BB5_DRN_G_ATAC


title: BB6_OFC_N_ATAC

description:
neuron_OFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_OFC.bw

value: OFC


title: BB4_PVPC_G_ATAC


title: BB6_OFC_G_ATAC

description:
glia_OFC-includes-blacklisted-regions_peaks.narrowPeak
glia_OFC.bw


title: BB4_OFC_G_ATAC


title: BB4_OFC_N_ATAC


title: BB5_GP_G_ATAC

description:
glia_GP-includes-blacklisted-regions_peaks.narrowPeak
glia_GP.bw

value: GP

value: BasalGanglia


title: BB6_CRBLM_N_ATAC

description:
neuron_CRBLM-includes-blacklisted-regions_peaks.narrowPeak
neuron_CRBLM.bw

source_name: Cerebellum

value: CRBLM

value: Hindbrain


title: BB6_VTA_G_ATAC

description:
glia_VTA-includes-blacklisted-regions_peaks.narrowPeak
glia_VTA.bw

source_name: Ventral Tegmental Area

value: VTA


title: BB5_NAC_G_ATAC


title: BB4_CRBLM_G_ATAC

description:
glia_CRBLM-includes-blacklisted-regions_peaks.narrowPeak
glia_CRBLM.bw


title: BB4_VTA_N_ATAC

description:
neuron_VTA-includes-blacklisted-regions_peaks.narrowPeak
neuron_VTA.bw

value: Midbrain


title: BB6_CRBLM_G_ATAC


title: BB6_AMY_N_ATAC


title: BB3_CRBLM_N_ATAC


title: BB6_PVPC_N_ATAC


title: BB3_CRBLM_G_ATAC


title: BB6_VLPFC_G_ATAC

description:
glia_VLPFC-includes-blacklisted-regions_peaks.narrowPeak
glia_VLPFC.bw

source_name: Ventrolateral Prefrontal Cortex

value: VLPFC


title: BB6_VLPFC_N_ATAC

description:
neuron_VLPFC-includes-blacklisted-regions_peaks.narrowPeak
neuron_VLPFC.bw


title: BB6_RMTG_G_ATAC

description:
glia_RMTG-includes-blacklisted-regions_peaks.narrowPeak
glia_RMTG.bw

source_name: Rostromedial Tegmental Nucl

value: RMTG


title: BB5_PVPC_N_ATAC

value: Male


title: BB4_RMTG_G_ATAC

value: non-neuron


title: BB4_VLPFC_G_ATAC


title: BB5_PVPC_G_ATAC

value: PVPC


title: BB4_VLPFC_N_ATAC


title: BB5_OFC_N_ATAC

source_name: Orbital Frontal Cortex


title: BB6_PVC_N_ATAC

description:
neuron_PVC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PVC.bw

source_name: Primary Visual Cortex

value: PVC


title: BB6_PVC_G_ATAC

description:
glia_PVC-includes-blacklisted-regions_peaks.narrowPeak
glia_PVC.bw

value: Forebrain


title: BB3_VLPFC_G_ATAC


title: BB5_NAC_N_ATAC

description:
neuron_NAC-includes-blacklisted-regions_peaks.narrowPeak
neuron_NAC.bw

value: NAC


title: BB6_PSC_G_ATAC

description:
glia_PSC-includes-blacklisted-regions_peaks.narrowPeak
glia_PSC.bw

source_name: Primary Somatosensory Cortex

value: PSC

value: Female


title: BB4_PVC_N_ATAC

value: neuron


title: BB5_CRBLM_G_ATAC


title: BB5_VTA_N_ATAC


title: BB6_PMC_N_ATAC

description:
neuron_PMC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PMC.bw

source_name: Primary Motor Cortex

value: PMC


title: BB6_PMC_G_ATAC

description:
glia_PMC-includes-blacklisted-regions_peaks.narrowPeak
glia_PMC.bw


title: BB5_OFC_G_ATAC

value: OFC


title: BB4_PVC_G_ATAC


title: BB6_RMTG_N_ATAC

description:
neuron_RMTG-includes-blacklisted-regions_peaks.narrowPeak
neuron_RMTG.bw


title: BB5_VTA_G_ATAC


title: BB6_PAC_G_ATAC

description:
glia_PAC-includes-blacklisted-regions_peaks.narrowPeak
glia_PAC.bw

source_name: Primary Auditory Cortex

value: PAC


title: BB6_PAC_N_ATAC

description:
neuron_PAC-includes-blacklisted-regions_peaks.narrowPeak
neuron_PAC.bw


title: BB5_VLPFC_G_ATAC


title: BB4_PMC_G_ATAC


title: BB4_PMC_N_ATAC


title: BB5_RMTG_N_ATAC


title: BB5_CRBLM_N_ATAC

value: CRBLM

value: Hindbrain


title: BB6_EC_N_ATAC

description:
neuron_EC-includes-blacklisted-regions_peaks.narrowPeak
neuron_EC.bw

value: EC


title: BB5_RMTG_G_ATAC

value: Midbrain


title: BB4_PAC_N_ATAC


title: BB6_MDT_G_ATAC

description:
glia_MDT-includes-blacklisted-regions_peaks.narrowPeak
glia_MDT.bw

source_name: Mediodorsal Thalamus

value: MDT


title: BB6_MDT_N_ATAC

description:
neuron_MDT-includes-blacklisted-regions_peaks.narrowPeak
neuron_MDT.bw


title: BB6_EC_G_ATAC

description:
glia_EC-includes-blacklisted-regions_peaks.narrowPeak
glia_EC.bw


title: BB4_PAC_G_ATAC


title: BB5_PVC_N_ATAC

value: Male


title: BB4_EC_G_ATAC

value: non-neuron


title: BB6_DLPFC_N_RNA

data_processing:
Each set of pair-end reads was processed by Trimmomatic to remove low-quality base pairs and sequence adapters. Reads were subsequently aligned to the human reference genome GRCh38 using STAR.
To correct for allelic bias resulting from individual-specific genome variation, we ran STAR with the enabled WASP module as we provide both RNA-seq FASTQ file and Whole Genome sequencing (WGS) file of the corresponding individual. The BAM files that were generated contain the mapped paired-end reads, including those spanning splice junctions.
Following read alignment, expression quantification was performed at the transcript isoform level using RSEM and then summarized at the gene level. Gene quantifications correspond to GENCODE.
We employed the proActiv package to determine the promoter-isoform expression. Briefly, we first identified the uniquely identified promoter-isoform, which exclude the isoform that is a single-exon or uses an internal intron (first intron edge of current isoform overlapped with non-first intron edge of other isoforms). We assign the isoform-transcript id as the promoter-isoform, when a promoter-isoform corresponding to multiple isoforms, we randomly choose one. Then we quantified the promoter-isform expression by estimating the junction reads aligned to the first intron.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample
Supplementary files format and content: tab-delimited text files include Transcripts Per Kilobase Million(TPM) values for each Sample
Supplementary files format and content: tab-delimited text files include promoter-isoform raw count values for each Sample

extract_protocol:
RNA was isolated from Neuronal (NeuN+) and non-neuronal (NeuN-) nuclei with FACS soring from 149 tissue dissections from 25 brain regions
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-seq kit v2 following manufacturer's protocols.

value: DLPFC


title: BB6_DLPFC_G_RNA


title: BB5_PVC_G_ATAC

value: PVC


title: BB5_VLPFC_N_ATAC

value: VLPFC

value: Forebrain


title: BB5_ITC_G_RNA

source_name: Inferior Temporal Cortex

value: ITC


title: BB5_ITC_N_RNA


title: BB3_EC_G_RNA


title: BB3_EC_N_RNA


title: BB3_PVPC_G_RNA

value: PVPC


title: BB2_DRN_G_RNA

value: DRN


title: BB6_INS_N_RNA

source_name: Insula

value: neuron

value: INS

value: Female


title: BB2_CRBLM_N_RNA

value: CRBLM


title: BB5_PSC_G_RNA

value: PSC


title: BB2_PVC_N_RNA


title: BB2_DRN_N_RNA


title: BB2_PAC_G_RNA

value: PAC


title: BB2_RMTG_G_RNA

value: RMTG

value: Midbrain


title: BB2_ITC_N_RNA

value: Male


title: BB2_ITC_G_RNA

value: non-neuron


title: BB2_CN_N_RNA

source_name: Caudate Nucleus

value: CN

value: BasalGanglia


title: BB4_EC_N_ATAC

value: EC


title: BB2_GP_N_RNA

source_name: Globus Pallidus

value: GP


title: BB2_VTA_G_RNA

value: VTA


title: BB2_PAC_N_RNA

value: Forebrain


title: BB2_CN_G_RNA


title: BB2_VTA_N_RNA


title: BB3_PVPC_N_RNA

source_name: Posteroventral (Inferior) Parietal Cortex

value: PVPC


title: BB2_PSC_N_RNA

value: neuron


title: BB2_PSC_G_RNA


title: BB6_INS_G_RNA

value: INS


title: BB2_CRBLM_G_RNA

value: Hindbrain


title: BB2_GP_G_RNA


title: BB5_PSC_N_RNA


title: BB2_MDT_N_RNA

value: MDT


title: BB2_OFC_N_RNA

value: OFC


title: BB2_PSTC_N_RNA

source_name: Posterior Superior Temporal Cortex

value: PSTC


title: BB2_DLPFC_N_RNA

source_name: Dorsolateral Prefrontal Cortex

value: DLPFC


title: BB2_MDT_G_RNA

value: Midbrain


title: BB2_DLPFC_G_RNA

value: Male


title: BB2_PVC_G_RNA

value: non-neuron

value: PVC


title: BB2_EC_N_RNA


title: BB2_NAC_N_RNA

source_name: Nucleus Accumbens

value: NAC

value: BasalGanglia


title: BB2_INS_G_RNA


title: BB2_HAB_N_RNA

source_name: Habenula

value: HAB


title: BB2_HAB_G_RNA


title: BB2_NAC_G_RNA


title: BB2_AMY_G_RNA

source_name: Amygdaloid Complex

value: AMY


title: BB2_AMY_N_RNA

value: Forebrain


title: BB2_VLPFC_N_RNA

source_name: Ventrolateral Prefrontal Cortex

value: VLPFC


title: BB2_VLPFC_G_RNA


title: BB2_PVPC_N_RNA

value: neuron

value: PVPC


title: BB2_PSTC_G_RNA


title: BB2_HIPP_N_RNA

source_name: Hippocampus

value: HIPP


title: BB2_ARC_N_RNA

source_name: Arcuate Nucleus

value: ARC


title: BB2_ARC_G_RNA


title: BB2_HIPP_G_RNA


title: BB1_CN_N_RNA

value: CN

value: Female


title: BB1_PAC_N_RNA

value: PAC


title: BB2_OFC_G_RNA

source_name: Orbital Frontal Cortex

value: OFC


title: BB2_INS_N_RNA

value: INS

value: Male


title: BB1_CN_G_RNA

value: non-neuron


title: BB1_ITC_N_RNA

value: ITC


title: BB1_PVC_N_RNA

source_name: Primary Visual Cortex

value: PVC


title: BB1_PMC_G_RNA

source_name: Primary Motor Cortex

value: PMC


title: BB1_PVC_G_RNA


title: BB1_PMC_N_RNA


title: BB1_ITC_G_RNA


title: BB1_DLPFC_N_RNA

value: DLPFC


title: BB2_EC_G_RNA

value: EC

value: Forebrain


title: BB2_PVPC_G_RNA


title: BB1_HAB_G_RNA

value: HAB

value: Midbrain


title: BB1_VLPFC_N_RNA

value: neuron

value: VLPFC


title: BB1_DLPFC_G_RNA


title: BB1_VLPFC_G_RNA


title: BB1_CRBLM_N_RNA

source_name: Cerebellum

value: CRBLM

value: Hindbrain


title: BB1_ARC_G_RNA

value: ARC

value: Female


title: BB1_RMTG_N_RNA

source_name: Rostromedial Tegmental Nucl

value: RMTG


title: BB1_VTA_G_RNA

source_name: Ventral Tegmental Area

value: VTA


title: BB1_AMY_N_RNA

value: AMY


title: BB1_PVPC_N_RNA

value: PVPC


title: BB1_PSC_N_RNA

source_name: Primary Somatosensory Cortex

value: PSC


title: BB1_PSC_G_RNA

value: non-neuron


title: BB1_ACC_N_RNA

source_name: Anterior Cingulate Cortex

value: ACC


title: BB1_EC_N_RNA

value: EC


title: BB1_EC_G_RNA

value: Forebrain


title: BB1_ACC_G_RNA


title: BB1_HIPP_G_RNA

value: HIPP


title: BB1_HIPP_N_RNA


title: BB1_INS_N_RNA

source_name: Insula

value: INS


title: BB1_PSTC_G_RNA

source_name: Posterior Superior Temporal Cortex

value: PSTC


title: BB1_PSTC_N_RNA

value: neuron


title: BB4_MDT_N_RNA

source_name: Mediodorsal Thalamus

value: MDT

value: Midbrain


title: BB3_MDT_N_RNA

value: Male


title: BB1_INS_G_RNA

value: Female


title: BB1_AMY_G_RNA


title: BB5_PMC_N_RNA

value: PMC


title: BB6_ARC_N_RNA

value: ARC


title: BB3_MDT_G_RNA


title: BB5_PMC_G_RNA


title: BB3_INS_G_RNA


title: BB4_INS_N_RNA


title: BB4_MDT_G_RNA


title: BB3_INS_N_RNA


title: BB6_ACC_N_RNA


title: BB1_OFC_G_RNA

value: OFC


title: BB5_PAC_N_RNA

source_name: Primary Auditory Cortex

value: PAC


title: BB6_ACC_G_RNA


title: BB4_ARC_N_RNA


title: BB1_OFC_N_RNA


title: BB4_ACC_G_RNA


title: BB5_EC_N_RNA


title: BB5_PAC_G_RNA


title: BB4_ACC_N_RNA


title: BB4_ARC_G_RNA


title: BB1_RMTG_G_RNA

value: RMTG


title: BB5_MDT_N_RNA


title: BB5_MDT_G_RNA

value: non-neuron


title: BB5_OFC_G_RNA


title: BB5_INS_N_RNA


title: BB6_ARC_G_RNA


title: BB4_INS_G_RNA


title: BB3_ACC_G_RNA

value: ACC


title: BB3_ACC_N_RNA


title: BB6_ITC_N_RNA

source_name: Inferior Temporal Cortex

value: ITC


title: BB5_ARC_G_RNA


title: BB5_INS_G_RNA

value: Forebrain


title: BB5_ARC_N_RNA


title: BB6_ITC_G_RNA


title: BB6_HIPP_G_RNA

value: HIPP


title: BB4_ITC_N_RNA


title: BB4_ITC_G_RNA


title: BB3_HIPP_N_RNA


title: BB3_ITC_G_RNA


title: BB4_HAB_N_RNA

source_name: Habenula

value: HAB


title: BB4_HAB_G_RNA


title: BB5_ACC_G_RNA


title: BB3_HIPP_G_RNA


title: BB6_GP_G_RNA

source_name: Globus Pallidus

value: GP

value: BasalGanglia


title: BB3_HAB_N_RNA

value: neuron


title: BB4_HIPP_N_RNA

source_name: Hippocampus


title: BB6_GP_N_RNA


title: BB4_HIPP_G_RNA


title: BB3_GP_N_RNA


title: BB3_HAB_G_RNA

value: Midbrain


title: BB4_GP_N_RNA


title: BB6_CN_G_RNA

source_name: Caudate Nucleus

value: CN


title: BB4_GP_G_RNA

value: Female


title: BB3_GP_G_RNA

value: Male


title: BB6_CN_N_RNA


title: BB5_ACC_N_RNA


title: BB6_DRN_G_RNA

source_name: Dorsal Raphe Nucleus

value: DRN


title: BB4_DLPFC_N_RNA

source_name: Dorsolateral Prefrontal Cortex

value: DLPFC


title: BB5_HIPP_G_RNA


title: BB6_DRN_N_RNA


title: BB6_HIPP_N_RNA


title: BB4_CN_N_RNA


title: BB6_HAB_N_RNA


title: BB5_HIPP_N_RNA


title: BB4_CN_G_RNA


title: BB3_DLPFC_N_RNA


title: BB3_DLPFC_G_RNA


title: BB5_HAB_G_RNA


title: BB4_DLPFC_G_RNA


title: BB5_PSTC_G_RNA

value: PSTC


title: BB5_HAB_N_RNA


title: BB6_PSTC_N_RNA


title: BB6_PSTC_G_RNA


title: BB4_DRN_G_RNA


title: BB5_PSTC_N_RNA


title: BB3_DRN_G_RNA


title: BB3_DRN_N_RNA


title: BB6_NAC_N_RNA

source_name: Nucleus Accumbens

value: NAC


title: BB4_NAC_N_RNA


title: BB4_NAC_G_RNA

value: non-neuron


title: BB5_GP_G_RNA


title: BB4_PSTC_G_RNA


title: BB3_PSTC_N_RNA


title: BB4_PSTC_N_RNA


title: BB6_AMY_N_RNA

source_name: Amygdaloid Complex

value: AMY


title: BB5_DLPFC_G_RNA


title: BB5_CN_N_RNA


title: BB5_DLPFC_N_RNA


title: BB6_AMY_G_RNA


title: BB6_PVPC_G_RNA

source_name: Posteroventral (Inferior) Parietal Cortex

value: PVPC


title: BB3_NAC_N_RNA


title: BB4_AMY_N_RNA

value: Forebrain


title: BB6_PVPC_N_RNA


title: BB5_CN_G_RNA


title: BB3_NAC_G_RNA


title: BB4_AMY_G_RNA


title: BB6_OFC_N_RNA

source_name: Orbital Frontal Cortex

value: OFC


title: BB5_DRN_N_RNA


title: BB3_AMY_N_RNA


title: BB3_AMY_G_RNA


title: BB3_CN_G_RNA


title: BB4_PVPC_G_RNA


title: BB6_OFC_G_RNA


title: BB5_DRN_G_RNA


title: BB3_CN_N_RNA


title: BB4_OFC_N_RNA


title: BB6_VTA_N_RNA

source_name: Ventral Tegmental Area

value: VTA


title: BB5_NAC_N_RNA


title: BB6_VTA_G_RNA


title: BB4_OFC_G_RNA


title: BB5_NAC_G_RNA


title: BB4_CRBLM_N_RNA

source_name: Cerebellum

value: CRBLM

value: Hindbrain


title: BB3_PSC_N_RNA

source_name: Primary Somatosensory Cortex

value: neuron

value: PSC


title: BB3_PSC_G_RNA


title: BB3_OFC_N_RNA


title: BB4_VTA_G_RNA

value: Midbrain


title: BB3_CRBLM_N_RNA


title: BB6_VLPFC_N_RNA

source_name: Ventrolateral Prefrontal Cortex

value: VLPFC

value: Female


title: BB4_VTA_N_RNA


title: BB3_CRBLM_G_RNA

value: Male


title: BB5_AMY_N_RNA


title: BB6_VLPFC_G_RNA


title: BB5_AMY_G_RNA


title: BB6_RMTG_N_RNA

source_name: Rostromedial Tegmental Nucl

value: RMTG


title: BB6_RMTG_G_RNA


title: BB5_PVPC_G_RNA


title: BB4_RMTG_N_RNA


title: BB4_VLPFC_G_RNA


title: BB4_VLPFC_N_RNA


title: BB5_PVPC_N_RNA


title: BB6_CRBLM_N_RNA


title: BB6_CRBLM_G_RNA


title: BB4_RMTG_G_RNA


title: BB6_PVC_N_RNA

source_name: Primary Visual Cortex

value: PVC


title: BB3_VLPFC_N_RNA


title: BB5_OFC_N_RNA


title: BB3_VLPFC_G_RNA


title: BB6_PSC_G_RNA


title: BB6_PSC_N_RNA


title: BB6_PVC_G_RNA


title: BB3_RMTG_G_RNA


title: BB3_RMTG_N_RNA


title: BB4_PVC_G_RNA


title: BB3_OFC_G_RNA


title: BB5_CRBLM_G_RNA


title: BB4_PVC_N_RNA


title: BB5_VTA_N_RNA


title: BB5_VTA_G_RNA


title: BB3_PVC_N_RNA


title: BB6_PMC_G_RNA

source_name: Primary Motor Cortex

value: PMC


title: BB3_PVC_G_RNA

value: non-neuron


title: BB5_VLPFC_G_RNA


title: BB5_VLPFC_N_RNA


title: BB6_PMC_N_RNA


title: BB4_PMC_N_RNA


title: BB5_RMTG_N_RNA


title: BB4_PMC_G_RNA


title: BB6_PAC_G_RNA

source_name: Primary Auditory Cortex

value: PAC


title: BB6_PAC_N_RNA


title: BB4_PAC_N_RNA


title: BB6_EC_G_RNA

value: EC


title: BB5_RMTG_G_RNA


title: BB6_EC_N_RNA

value: Forebrain


title: BB4_EC_N_RNA


title: BB6_MDT_G_RNA

source_name: Mediodorsal Thalamus

value: MDT


title: BB4_EC_G_RNA


title: BB3_PAC_N_RNA


title: BB6_MDT_N_RNA


title: BB5_PVC_N_RNA


title: BB5_CRBLM_N_RNA


title: BB3_PAC_G_RNA


title: BB3_ARC_G_RNA

source_name: Arcuate Nucleus

value: ARC


title: mESC_NEB_GLORI-

status: Public on Aug 06 2022

city: BeiJing

first: Kai

last: Li

address: Yi He Yuan Street No.5

department: School of Life Science

institute: Peking University

description: wildtype mESC cells with NEB #E7300 without GLORI treatment

data_processing:
Adapters and low-quality bases were trimmed with trim_galore (version 0.6.6). PCR duplications was removed with Seqkit. UMI were removed with FASTX-Toolkit (version 0.0.13).
Clean reads were firstly mapped to the genome with STAR and then transcriptome with bowtie. Pileup was performed using samtools API pysam. Customized scripts were used to call m6A sites from samples.
To make the analysis pipeline easy to implement, we developed GLORI-tools, a computational pipeline that quantifies the A rate of each A site and follows multiple filters for false positives. The code of the GLORI-tools is available in the following GitHub repositories: https://github.com/liucongcas/GLORI-tools.
Assembly: GRCh38/GRCm38
Supplementary files format and content: Sequencing data from parallel untreated RNA-seq samples was used to assess gene expression level. Adapters and low-quality bases were trimmed with trim_galore (version 0.6.6). PCR duplications was removed with Seqkit. UMI were removed with FASTX-Toolkit (version 0.0.13).  The cleaned reads were firstly mapped to the genome with STAR then the transcriptome with bowtie. Uniquely mapped reads were merged and sorted for calculating the expression level of genes. For each gene, reads coverage and gene length was calculated using featureCounts (version 2.0.3), and then RPKM value was calculated with a custom script. Genes with RPKM <1 were excluded from downstream analysis.

molecule: polyA RNA

organism: Mus musculus

source_name: mESC

growth_protocol: HEK293T, MEF, HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
mRNA was purified by oligo (dT) beads. 100-200 ng of mRNA was used for GLORI treatment and construction of sequencing libraries.
RNA libraries were prepared using modified eCLIP library construction, NEBNext Small RNA library kits (NEB) and SMARTer Stranded Total RNA-Seq kits (v3) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Transfection was performed by Lipofectamin RNAiMAX for siRNA when HeLa cells were grown to 50% confluence.
For heat shock, MEF cells were grown to 80% confluence in the 6-cm plastic dishes, placed in a 42°C water bath for 1 h, and then recover for 6 h at 37°C. For hypoxia treatment, HeLa cells were grown to 80% confluence, carried out in Hypoxia Hood which maintained at 37°C, 5% CO2, 1% oxygen for 24 h.

tag: cell line

value: mESC

value: Mouse embryonic stem cells

value: WT

tag: treatment

value: GLORI-

tag: time

value: Day 0


title: mESC_NEB_GLORI+_rep1

description: wildtype mESC cells with NEB #E7300 with GLORI treatment

value: GLORI+


title: MEF_heatshock+_GLORI-

description: heatshock treated MEF cells without GLORI treatment

source_name: MEF

value: MEF

value: mouse embryo fibroblast cells

value: heatshock+, GLORI-


title: MEF_heatshock+_GLORI+_rep2

description: heatshock treated MEF cells with GLORI treatment

value: heatshock+, GLORI+


title: MEF_heatshock+_GLORI+_rep1


title: MEF_heatshock-_GLORI-

description: wildtype MEF cells without GLORI treatment

value: heatshock-, GLORI-


title: MEF_heatshock-_GLORI+_rep2

description: wildtype MEF cells with GLORI treatment

value: heatshock-, GLORI+


title: MEF_heatshock-_GLORI+_rep1

description: wildtype MEF cells with GLORI treatment


title: HEK293T_STM2457+_GLORI-_rep2

description: STM2457+ treated HEK293T cells without GLORI treatment

value: human embryonic kidney 293 cells

value: METTL3 inhibition

value: STM2457+, GLORI-


title: BB4_PAC_G_RNA

value: non-neuron

value: PAC

value: Forebrain

value: Female


title: HEK293T_STM2457+_GLORI-_rep1


title: HEK293T_STM2457+_GLORI+_rep1

description: STM2457+ treated HEK293T cells with GLORI treatment

value: STM2457+, GLORI+


title: HeLa_STM2457+_GLORI-_rep1

description: STM2457+ treated HeLa cells without GLORI treatment

source_name: HeLa

value: HeLa

value: human adenocarcinoma epithelial cells


title: HEK293T_STM2457+_GLORI+_rep2

value: Day 0


title: HeLa_STM2457+_GLORI+_rep2

description: STM2457+ treated HeLa cells with GLORI treatment


title: HeLa_siNC-YTHDF2_GLORI-_rep1

description: control knockdown HeLa cells  for siYTHDF2 without GLORI treatment

value: Control knockdown

value: sicontrol, GLORI-


title: HeLa_siNC-YTHDF2_GLORI+_rep1

description: control knockdown HeLa cells for siYTHDF2 with GLORI treatment

value: sicontrol, GLORI+


title: HeLa_STM2457+_GLORI-_rep2


title: HeLa_siNC-YTHDF2_GLORI-_rep2


title: HeLa_STM2457+_GLORI+_rep1


title: HeLa_siNC-YTHDF2_GLORI+_rep2

description: control knockdown HeLa cells  for siYTHDF2 with GLORI treatment


title: HeLa_siYTHDF2_GLORI-_rep1

description: YTHDF2 knockdown HeLa cells without GLORI treatment

value: YTHDF2 knockdown

value: siYTHDF2, GLORI-


title: HeLa_siYTHDF2_GLORI+_rep1

description: YTHDF2 knockdown HeLa cells with GLORI treatment

value: siYTHDF2, GLORI+


title: BB5_PVC_G_RNA

value: PVC

value: Male


title: HeLa_siNC-writer_GLORI-_rep2

description: control knockdown HeLa cells without GLORI treatment


title: mESC_NEB_GLORI+_rep2

value: mESC

value: Mouse embryonic stem cells

value: WT

value: GLORI+


title: HeLa_siNC-writer_GLORI-_rep1


title: HeLa_siNC-writer_GLORI+_rep2

description: control knockdown HeLa cells with GLORI treatment


title: HeLa_siNC-writer_GLORI+_rep1


title: HeLa_siWTAP_GLORI-_rep2

description: WTAP knockdown HeLa cells without GLORI treatment

value: WTAP knockdown


title: HeLa_siWTAP_GLORI+_rep2

description: WTAP knockdown HeLa cells with GLORI treatment


title: HeLa_siWTAP_GLORI-_rep1


title: HeLa_siWTAP_GLORI+_rep1


title: HeLa_siMETTL14_GLORI-_rep2

description: METTL14 knockdown HeLa cells without GLORI treatment

value: METTL14 knockdown


title: HeLa_siMETTL14_GLORI+_rep2

description: METTL14 knockdown HeLa cells with GLORI treatment

value: HeLa


title: HeLa_siMETTL14_GLORI-_rep1

value: human adenocarcinoma epithelial cells


title: HeLa_siMETTL14_GLORI+_rep1

value: Day 0


title: HeLa_siMETTL3_GLORI-_rep1

description: METTL3 knockdown HeLa cells without GLORI treatment

value: METTL3 knockdown


title: HeLa_siYTHDF2_GLORI-_rep2


title: HeLa_siMETTL3_GLORI+_rep2

description: METTL3 knockdown HeLa cells with GLORI treatment


title: HeLa_siMETTL3_GLORI+_rep1


title: HEK293T_Takara_GLORI-

description: wildtype HEK293T cells with Takara 634487 without GLORI treatment

value: human embryonic kidney 293 cells

value: GLORI-


title: HEK293T_Takara_GLORI+_rep2

description: wildtype HEK293T cells with Takara 634487 with GLORI treatment


title: HeLa_siMETTL3_GLORI-_rep2


title: HEK293T_Takara_GLORI+_rep1


title: HeLa_hypoxia+_GLORI-

description: hypoxia treated  HeLa cells without GLORI treatment

value: hypoxia+, GLORI-


title: HEK293T_IVT_GLORI-

description: IVT RNA derived from HEK293T cells without GLORI treatment


title: HeLa_siYTHDF2_GLORI+_rep2

value: YTHDF2 knockdown


title: HeLa_hypoxia+_GLORI+_rep2

description: hypoxia treated  HeLa cells with GLORI treatment

value: hypoxia+, GLORI+


title: HeLa_hypoxia-_GLORI-

description: wildtype HeLa cells without GLORI treatment

value: hypoxia-, GLORI-


title: HEK293T_IVT_GLORI+_rep1

description: IVT RNA derived from HEK293T cells with GLORI treatment


title: HeLa_hypoxia-_GLORI+_rep2

description: wildtype HeLa cells with GLORI treatment

value: hypoxia-, GLORI+


title: HEK293T_IVT_GLORI+_rep2


title: HeLa_hypoxia-_GLORI+_rep1


title: HEK293T_FTO+_GLORI+_rep1

description: FTO treated HEK293T cells with GLORI treatment

value: FTO+, GLORI+


title: HEK293T_GLORI-

description: wildtype HEK293T cells without GLORI treatment


title: HEK293T_FTO+_GLORI+_rep2


title: HEK293T_GLORI+_rep2

description: wildtype HEK293T cells with GLORI treatment


title: HEK293T_GLORI+_rep1


title: Salmonella typhimurium ATCC 14028s, pH 5.0, rep1

city: Jinan

first: wei

middle: wei

last: wang

address: No. 6699 Qingdao Road, Huaiyin District, Jinan City, Shandong Province

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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: https://www.ncbi.nlm.nih.gov/genome/?term=Bacteria++Salmonella+typhimurium
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Salmonella enterica subsp. enterica serovar Typhimurium

source_name: Salmonella typhimurium

growth_protocol: Salmonella typhimurium ATCC 14028s was grown to OD600 = 0.4  in Vogel and Bonner E medium with a final concentration of 0.4% glucose at 37 °C

extract_protocol:
3 mL bacterial cells were obtained by centrifugation (3000 rpm, 5 min) and freezing treatment in liquid nitrogen. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Half of the culture was treated with acid stress at pH 5.0 for 2 h and the remaining bacteria were further cultured. For acid stress experiments, the bacteria was cultured under acidic condition (pH 5.0, 10 mM L-lysine).

value: Salmonella typhimurium

value: ATCC 14028s

value: Salmonella typhimurium strain

value: wild type

value: Acid treatment (pH 5.0)


title: Salmonella typhimurium ATCC 14028s, pH 5.0, rep2


title: Salmonella typhimurium ATCC 14028s, pH 7.0, rep3

value: Control (pH 7.0)


title: Salmonella typhimurium ATCC 14028s, pH 7.0, rep2


title: Salmonella typhimurium ATCC 14028s, pH 7.0, rep1


title: H3K4me3_2

status: Public on Aug 02 2022

city: San Francisco

first: David

last: Wu

state: California

address: 35 Medical Center Way

institute: UCSF

description:
H3K4me3 CUT&Tag of iPSC WTC cells, rep 2
H3K4me3_CT.bw

data_processing:
Library strategy: CUT&Tag
RNA-Seq: Quality assessment using fastqc (0.11.8)
RNA-Seq: Adapter and quality trimming using bbduk (38.36)
RNA-Seq: Pseudoalignment and gene expression quantification using kallisto (0.45)
Perturb-Seq: pre-processing, alignment, and gene quantification using cellranger (3.1.0)
CUT&Tag: Quality and adaptor trimming with fastp (0.13)
CUT&Tag: Genome alignment using bowtie2 (2.2.5) with these parameters: --local–very-sensitive-local–no-unal–no-mixed–no-discordant–phred33 -I 10 -X 700
CUT&Tag: bigwig generation using deeptools bamCoverage (3.4.0)
PLAC-Seq: Quality and adaptor trimming with fastp (0.13)
PLAC-Seq: Genome alignment using BWA-MEM (0.7.17)
PLAC-Seq: Chromatin interacting calling using MAPS
Genome_build: GRCh37.74
Supplementary_files_format_and_content: Counts matrix for RNA-Seq and Perturb-Seq; bigwig traces for CUT&Tag data; bedpe interaction files for PLAC-Seq data; Perturb-Seq Seurat object.

source_name: iPSC WTC

growth_protocol: Essential 8 medium.

extract_protocol:
RNA-Seq: RNA extracted by Zymo Direct-zol RNA miniprep columns; Perturb-Seq: 10x Genomics Chromium 3' Assay v3; CUT&Tag: DNA fragments were isolated using protein A-Tn5 transposase fusion proteins targeted to H3K4me3 antibodies (Millipore 04-745), following protocol in Kaya-Okur et al., 2019; PLAC-Seq: cross-linked cells were treated with MboI, followed by proximity ligation and ChIP using H3K4me3 antibody (Millipore 04-745), see Fang et al., 2016.
RNA-Seq: NEBNext Stranded Directional RNA with polyA-selection or rRNA depletion; Perturb-Seq: 10x Genomics Chromium 3' Assay v3; CUT&Tag: See Kaya-Okur et al., 2019; PLAC-Seq: See Fang et al., 2016.
RNA-Seq: SE50; Perturb-Seq: PE100; CUT&Tag: PE50; PLAC-Seq: PE150.

treatment_protocol: Dual SMAD-inhibition neural induction medium.

value: iPSC WTC

tag: antibody

tag: library type

value: CUT&Tag


title: H3K4me3_1

description:
H3K4me3 CUT&Tag of iPSC WTC cells, rep 1
H3K4me3_CT.bw


title: PLAC_Seq_1

description:
PLAC-Seq of iPSC WTC cells, rep 1
PLAC_Seq.bedpe

data_processing:
Library strategy: PLAC-seq
RNA-Seq: Quality assessment using fastqc (0.11.8)
RNA-Seq: Adapter and quality trimming using bbduk (38.36)
RNA-Seq: Pseudoalignment and gene expression quantification using kallisto (0.45)
Perturb-Seq: pre-processing, alignment, and gene quantification using cellranger (3.1.0)
CUT&Tag: Quality and adaptor trimming with fastp (0.13)
CUT&Tag: Genome alignment using bowtie2 (2.2.5) with these parameters: --local–very-sensitive-local–no-unal–no-mixed–no-discordant–phred33 -I 10 -X 700
CUT&Tag: bigwig generation using deeptools bamCoverage (3.4.0)
PLAC-Seq: Quality and adaptor trimming with fastp (0.13)
PLAC-Seq: Genome alignment using BWA-MEM (0.7.17)
PLAC-Seq: Chromatin interacting calling using MAPS
Genome_build: GRCh37.74
Supplementary_files_format_and_content: Counts matrix for RNA-Seq and Perturb-Seq; bigwig traces for CUT&Tag data; bedpe interaction files for PLAC-Seq data; Perturb-Seq Seurat object.

value: PLAC-Seq


title: PLAC_Seq_2

description:
PLAC-Seq of iPSC WTC cells, rep 2
PLAC_Seq.bedpe


title: HeLa_hypoxia+_GLORI+_rep1

description: hypoxia treated HeLa cells with GLORI treatment

value: HeLa

value: human adenocarcinoma epithelial cells

value: WT

value: Day 0


title: D0_Total_Rep1

description: RNA-Seq of iPSCs on D0 of neural induction, Rep1

data_processing:
RNA-Seq: Quality assessment using fastqc (0.11.8)
RNA-Seq: Adapter and quality trimming using bbduk (38.36)
RNA-Seq: Pseudoalignment and gene expression quantification using kallisto (0.45)
Perturb-Seq: pre-processing, alignment, and gene quantification using cellranger (3.1.0)
Genome_build: GRCh37.74
Supplementary_files_format_and_content: Counts matrix

growth_protocol: Essential 8 medium

extract_protocol:
RNA-Seq: RNA extracted by Zymo Direct-zol RNA miniprep columns; Perturb-Seq: 10x Genomics Chromium 3' Assay v3
RNA-Seq: NEBNext Stranded Directional RNA with polyA-selection or rRNA depletion; Perturb-Seq: 10x Genomics Chromium 3' Assay v3

treatment_protocol: Dual SMAD-inhibition neural induction medium

tag: condition

value: Total

value: Gene Expression


title: D8_Total_Rep2

description: RNA-Seq of iPSCs on D8 of neural induction, Rep2


title: D0_Total_Rep2

description: RNA-Seq of iPSCs on D0 of neural induction, Rep2


title: D6_polyA_Rep1

description: RNA-Seq of iPSCs on D6 of neural induction, Rep1

value: polyA


title: D10_polyA_Rep2

description: RNA-Seq of iPSCs on D10 of neural induction, Rep2


title: D4_polyA_Rep1

description: RNA-Seq of iPSCs on D4 of neural induction, Rep1


title: D10_polyA_Rep1

description: RNA-Seq of iPSCs on D10 of neural induction, Rep1


title: D11_polyA_Rep1

description: RNA-Seq of iPSCs on D11 of neural induction, Rep1


title: D8_polyA_Rep2


title: D6_polyA_Rep2

description: RNA-Seq of iPSCs on D6 of neural induction, Rep2


title: D8_Total_Rep1

description: RNA-Seq of iPSCs on D8 of neural induction, Rep1


title: D8_polyA_Rep1


title: D4_polyA_Rep2

description: RNA-Seq of iPSCs on D4 of neural induction, Rep2


title: D0_polyA_Rep2


title: D10_Total_Rep2


title: Salmonella typhimurium ATCC 14028s, pH 5.0, rep3


title: D11_polyA_Rep2

description: RNA-Seq of iPSCs on D11 of neural induction, Rep2


title: D0_polyA_Rep1


title: perturbseq_grna_4-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 4, Lane 2, sgRNA capture
sgrna_counts.mtx.gz

data_processing:
Library strategy: Perturb-Seq
RNA-Seq: Quality assessment using fastqc (0.11.8)
RNA-Seq: Adapter and quality trimming using bbduk (38.36)
RNA-Seq: Pseudoalignment and gene expression quantification using kallisto (0.45)
Perturb-Seq: pre-processing, alignment, and gene quantification using cellranger (3.1.0)
CUT&Tag: Quality and adaptor trimming with fastp (0.13)
CUT&Tag: Genome alignment using bowtie2 (2.2.5) with these parameters: --local–very-sensitive-local–no-unal–no-mixed–no-discordant–phred33 -I 10 -X 700
CUT&Tag: bigwig generation using deeptools bamCoverage (3.4.0)
PLAC-Seq: Quality and adaptor trimming with fastp (0.13)
PLAC-Seq: Genome alignment using BWA-MEM (0.7.17)
PLAC-Seq: Chromatin interacting calling using MAPS
Genome_build: GRCh37.74
Supplementary_files_format_and_content: Counts matrix for RNA-Seq and Perturb-Seq; bigwig traces for CUT&Tag data; bedpe interaction files for PLAC-Seq data; Perturb-Seq Seurat object.

value: CRISPR gRNA Capture


title: perturbseq_grna_5-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 5, Lane 1, sgRNA capture
sgrna_counts.mtx.gz


title: perturbseq_grna_6-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 6, Lane 1, sgRNA capture
sgrna_counts.mtx.gz


title: perturbseq_grna_2-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 2, Lane 2, sgRNA capture
sgrna_counts.mtx.gz


title: perturbseq_grna_2-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 2, Lane 1, sgRNA capture
sgrna_counts.mtx.gz


title: D10_Total_Rep1


title: perturbseq_grna_4-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 4, Lane 1, sgRNA capture
sgrna_counts.mtx.gz


title: perturbseq_grna_1-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 1, Lane 1, sgRNA capture
sgrna_counts.mtx.gz


title: perturbseq_grna_1-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 1, Lane 2, sgRNA capture
sgrna_counts.mtx.gz


title: perturbseq_gene_4-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 4, Lane 2, gene expression
perturbseq_counts.mtx.gz


title: perturbseq_gene_6-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 6, Lane 1, gene expression
perturbseq_counts.mtx.gz


title: perturbseq_gene_2-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 2, Lane 1, gene expression
perturbseq_counts.mtx.gz


title: perturbseq_gene_5-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 5, Lane 1, gene expression
perturbseq_counts.mtx.gz


title: perturbseq_gene_1-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 1, Lane 2, gene expression
perturbseq_counts.mtx.gz


title: perturbseq_gene_4-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 4, Lane 1, gene expression
perturbseq_counts.mtx.gz


title: V+T_P8_rep3

status: Public on Aug 01 2022

city: Athens

first: He

last: Fu

state: GA

address: 120 Cedar St

department: Microbiology

institute: University of Georgia

description:
P8_V_VT_3
P8_T_VT_3
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx

data_processing:
FASTX toolkit was used to retain reads with a minimum quality score of 28 over 70% of read length
rRNA reads were filtered using SortMeRNA (30) and a custom-curated rRNA database
The remaining mRNA reads were mapped to the respective genomes using STAR (2.6.1c-foss-2016b) and counted using HTSeq
Genes with zero reads mapping in all samples were removed from further analysis. Counts were converted to transcripts per million (TPM)
Supplementary files format and content: Matrix table with raw gene counts for every gene of each bacterium in different conditions

organism:
Vibrio hepatarius
Thalassospira sp. HF15

source_name: bacterial cells

growth_protocol: All bacteria were grown on marine basel medium supplemented with 1.25 mM ectoine.

extract_protocol:
RNA was extracted from filters using the ZymoBIOMICS RNA Miniprep Kit (Zymo Research), treated with Turbo DNase (Invitrogen, Waltham, MA, USA), and cleaned using RNA Clean & Concentrator (Zymo Research). Ribosomal rRNA was removed using the NEBNext® rRNA Depletion Kit (NEB, Ipswich, MA, USA).
Stranded RNA-seq libraries were prepared and sequenced using an Illumina NextSeq 500 SE75 High Output flow cell at the Georgia Genomics and Bioinformatics Core (University of Georgia). Mono-culture samples of three bacterial species were pooled together for RNA-seq library prep and sequencing run.

tag: time point


title: V+T_P8_rep2

description:
P8_V_VT_2
P8_T_VT_2
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: perturbseq_grna_3-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 3, Lane 2, sgRNA capture
sgrna_counts.mtx.gz


title: V+T_P8_reP8

description:
P8_V_VT_4
P8_T_VT_4
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: V+T_P8_rep1

description:
P8_V_VT_1
P8_T_VT_1
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: V+T_P4_rep3

description:
Vib70_duet_VT_3
Tha_duet_VT_3
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx

tag: v. hepatarius strain

value: Vibrio hepatarius HF70


title: perturbseq_grna_3-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 3, Lane 1, sgRNA capture
sgrna_counts.mtx.gz


title: V+T_P4_rep4

description:
Vib70_duet_VT_4
Tha_duet_VT_4
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: V+T_P4_rep1

description:
Vib70_duet_VT_1
Tha_duet_VT_1
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: V+T_P4_rep2

description:
Vib70_duet_VT_2
Tha_duet_VT_2
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: perturbseq_gene_3-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 3, Lane 2, gene expression
perturbseq_counts.mtx.gz


title: R+V_P8_rep3

description:
P8_R_RV_3
P8_V_RV_3
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx

organism:
Vibrio hepatarius
Ruegeria pomeroyi DSS-3


title: R+V_P4_rep4

description:
Rpom_duet_RV_4
Vib70_duet_RV_4
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx


title: R+V_P8_rep2

description:
P8_R_RV_2
P8_V_RV_2
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx


title: R+V_P4_rep2

description:
Rpom_duet_RV_2
Vib70_duet_RV_2
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx


title: R+V_P4_rep1

description:
Rpom_duet_RV_1
Vib70_duet_RV_1
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx


title: R+T+V_P8_reP8

description:
P8_R_RVT_4
P8_V_RVT_4
P8_T_RVT_4
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx

organism:
Vibrio hepatarius
Ruegeria pomeroyi DSS-3
Thalassospira sp. HF15


title: perturbseq_gene_1-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 1, Lane 1, gene expression
perturbseq_counts.mtx.gz


title: R+V_P8_rep1

description:
P8_R_RV_1
P8_V_RV_1
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx


title: perturbseq_gene_3-1

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 3, Lane 1, gene expression
perturbseq_counts.mtx.gz


title: perturbseq_gene_2-2

description:
Perturb-Seq of iPSCs on D8 of neural induction, Batch 2, Lane 2, gene expression
perturbseq_counts.mtx.gz


title: R+T+V_P8_rep1

description:
P8_R_RVT_1
P8_V_RVT_1
P8_T_RVT_1
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: R+T+V_P8_rep2

description:
P8_R_RVT_2
P8_V_RVT_2
P8_T_RVT_2
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: R+V_P4_rep3

description:
Rpom_duet_RV_3
Vib70_duet_RV_3
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P8 rep3

description:
P8_R_solo_3
P8_V_solo_3
P8_T_solo_3
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: R+T+V_P8_rep3

description:
P8_R_RVT_3
P8_V_RVT_3
P8_T_RVT_3
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P8 rep4

description:
P8_R_solo_4
P8_V_solo_4
P8_T_solo_4
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P8 rep2

description:
P8_R_solo_2
P8_V_solo_2
P8_T_solo_2
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P8 rep1

description:
P8_R_solo_1
P8_V_solo_1
P8_T_solo_1
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: R+T+V_P4_rep4

description:
Rp_trio_RVT_4
Vib70_trio_RVT_4
Tha_trio_RVT_4
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: R+T+V_P4_rep3

description:
Rp_trio_RVT_3
Vib70_trio_RVT_3
Tha_trio_RVT_3
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: R+T+V_P4_rep2

description:
Rp_trio_RVT_2
Vib70_trio_RVT_2
Tha_trio_RVT_2
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P4 rep4

description:
Rpom_solo_4
Vib70_solo_4
Tha_solo_4
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: R+V_P8_reP8

description:
P8_R_RV_4
P8_V_RV_4
P8_Rpom_RV_RT_RVT.xlsx
P8_Vib_RV_TV_RVT.xlsx


title: R+T+V_P4_rep1

description:
Rp_trio_RVT_1
Vib70_trio_RVT_1
Tha_trio_RVT_1
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P4 rep3

description:
Rpom_solo_3
Vib70_solo_3
Tha_solo_3
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P4 rep2

description:
Rpom_solo_2
Vib70_solo_2
Tha_solo_2
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: pooled monoculture (Rpom_Vib70_Tha15) P4 rep1

description:
Rpom_solo_1
Vib70_solo_1
Tha_solo_1
P4_Rpom_RT_RV_RVT.xlsx
P4_Vib_V_RV_VT_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: Sample 3 H3K4me3 CUT&RUN

first: Bjorn

middle: FC

last: Kafsack

address: 1300 York Avenue

department: Microbiology & Immunology

institute: Weill Cornell Medicine

data_processing:
Reads in sequenced libraries were checked for quality with FASTQC v0.11.9, adapter and quality-trimmed with trimmomatic v0.39
Properly paired reads were aligned against P.falciparum 3D7 genome v51 with bwa v.0.7.17 and sorted by name using samtools v1.13
Differential genome-wide enrichment between relative to matched isotype controls  was calculated using macs2 v2.2.7.1 to generate poisson-based FDR and fold-enrichment tracks and significant peaks
Peak annotation and visualization were carried out in R using GenomicRanges v1.44.0, Gviz v1.36.1, and ChIPpeakAnno v3.26.2 packages from Bioconductor using P.falciparum 3D7 genome annotation v51 from PlasmoDB
Assembly: Plasmodium falciparum 3D7 v51 from PlasmoDB
Supplementary files format and content: bedgraph
Library strategy: Cut&Run

organism: Plasmodium falciparum

source_name: early Schizonts

growth_protocol: synchronous early schizonts

extract_protocol:
1e7 parasites were used per sample for cut & run
Libraries were prepared according to Illumina's instructions accompanying the KAPA library preparation kit (KK8230) and sequenced at PE75 on a NextSeq500 machine

value: early Schizonts

tag: strain

value: NF54 pfpeg4-tdTomato

tag: chip antibody

value: H3K4me3 Rabbit Polyclonal antibody ChIP-grade, Diagenode  C15410003-50


title: Sample 3 H3K9me3 CUT&RUN

value: H3K9me3 Rabbit Polyclonal antibody ChIP-grade, abcam ab8898


title: T+R_P8_rep3

description:
P8_R_RT_3
P8_T_RT_3
P8_Rpom_RV_RT_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx

organism:
Ruegeria pomeroyi DSS-3
Thalassospira sp. HF15


title: Sample 2 H3K4me3 CUT&RUN


title: T+R_P8_rep4

description:
P8_R_RT_4
P8_T_RT_4
P8_Rpom_RV_RT_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: Sample 2 H3K9me3 CUT&RUN


title: T+R_P8_rep2

description:
P8_R_RT_2
P8_T_RT_2
P8_Rpom_RV_RT_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: T+R_P8_rep1

description:
P8_R_RT_1
P8_T_RT_1
P8_Rpom_RV_RT_RVT.xlsx
P8_Tha_RT_VT_RVT.xlsx


title: 3 pooled In-utero natural embryos, E8.5

status: Public on Jul 31 2022

city: Rehovot

first: Noa

last: Novershtern

address: Weizmann Institute

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
InUtE85-3pooled
3 pooled In-utero natural embryos, E8.5 (same as GSM4498733).
Single-cell RNA-seq

library_source: transcriptomic single cell

data_processing:
Demultiplexing was done with cellranger/3.1.0 mkfastq.
Alignment and quantification of single cell features was done with cellranger counts.
Aggregation of multiple GEM wells was done using- cellranger aggr.
Cells with under 200 expressing genes, over 4000 expressing genes or over 10% mitochondrial gene expression were filtered out for the rest of the analysis.
Assembly: mm10
Supplementary files format and content: Processed data is divided into three different matrices created using Seurat 3.0: raw_counts.csv - contains raw counts of all genes across all cells, normalized_counts.csv - contains normalized counts of all genes across all cells, cell2sample.csv - contains information of each of the cells.

source_name: E8.5 mouse embryo

growth_protocol: Ex utero culture protocol for sEmbryos. E8.5 in utero control were dissected and used for experiment directly.

extract_protocol:
RNA extracted according to 10x Genomics Chromium v3.1 Dual Index system kit instructions.
10x Genomics Chromium v3.1 Dual Index system (5000 cell target cell recovery).

treatment_protocol: Doxycycline treatment for sEmbryos.

value: embryo

tag: embryo growth condition

value: in utero

tag: embryonic day

tag: original cells

value: natural


title: T+R_P4_rep1

description:
Rpom_duet_RT_1
Tha_duet_RT_1
P4_Rpom_RT_RV_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: T+R_P4_rep3

description:
Rpom_duet_RT_3
Tha_duet_RT_3
P4_Rpom_RT_RV_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: A single In-utero natural embryo, E8.5, replicate 2

description:
InUtE85-1emb-r2
A single in-utero embryo (natural), E8.5.
Single-cell RNA-seq

tag: tissue


title: Sample 1 H3K4me3 CUT&RUN


title: A single In-utero natural embryo, E8.5, replicate 1

description:
InUtE85-1emb-r1
A single in-utero embryo (natural), E8.5.
Single-cell RNA-seq


title: T+R_P4_rep2

description:
Rpom_duet_RT_2
Tha_duet_RT_2
P4_Rpom_RT_RV_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: 2 pooled synthetic-embryos, ex utero, from established early passage embryo derived TSCs (eTSC)

description:
TSCbl-2pooled
2 pooled synthetic-embryos, ex utero, from established embryo derived early passage TSCs (eTSCs).
Single-cell RNA-seq

source_name: E8.5 mouse synthetic-embryo (sEmbryo)

value: synthetic-embryo

value: ex utero

value: ESCs, iGata4, eTSCs


title: A single synthetic-embryo, ex utero, from 3-days induced iCdx2 cells, replicate 2

description:
Cdx2-3d-1emb
synthetic embryo, ex utero, from 3-days induced iCdx2 cells.
Single-cell RNA-seq

value: ESCs, iGata4, iCdx2


title: 2 pooled synthetic-embryos, ex utero, from 10-days induced iCdx2 cells, replicate 2

description:
Cdx2-10d-2pooled-r2
2 pooled synthetic-embryos, ex utero, from 10-days induced iCdx2 cells.
Single-cell RNA-seq


description:
InUtE85-1emb-r5
A single In-utero natural embryo, E8.5, replicate 5 (same as GSM4498732).
Single-cell RNA-seq


title: 2 pooled synthetic-embryos, ex utero, from 10-days induced iCdx2 cells, replicate 1

description:
Cdx2-10d-2pooled-r1
2 pooled synthetic-embryos, ex utero, from 10-days induced iCdx2 cells.
Single-cell RNA-seq


title: Reh-sgROSA

status: Public on Jul 27 2022

first: Soobeom

last: Lee

address: 550 First Avenue, Smilow 1307 New York NY

institute: NYU

data_processing:
The libraries were sequenced in paired-end by NovaSeq 6000 at 100 cycles.
RNA-seq reads were aligned to the human reference genome (GRCh37/hg19) using STAR aligner8 with default parameters.
Quantification of mapped reads to each gene was performed using FeatureCount of the Subread package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Raw counts matrix in the CSV file format

source_name: Reh

growth_protocol: All cell lines were cultured in RPMI-1640 media supplemented with 20% fetal bovine serum, 55 μM β-mercaptoethanol (Gibco # 21985023) and penicillin, streptomycin (Gibco #15140122).

extract_protocol: RNA isolation was performed using Qiagen RNEasy Mini Kit (Qiagen, #74134). RNA-seq libraries were prepared using NEXTflex Rapid Illumina Directional RNA-seq Library prep kit as per manufacturer’s guidelines.

treatment_protocol: All lentiviral transfections were performed in HEK293T cells using Polyethylenimine (PEI) reagent at 4:2:3 ratios of sgRNA or Cas9 construct: pVSVG: pPax2 in OPTI-MEM solution. All retroviral transfections were performed in Platinum-E cells using Polyethylenimine (PEI) reagent with 10 μg transfer plasmid in OPTI-MEM solution. All amphitropic retroviral transfections were performed Polyethylenimine (PEI) reagent at 5:2:5 ratios of MSCV-based construct: pVSVG: pCL-Ampho retrovirus packaging construct (Novus Biologicals, NBP2-29541) in OPTI-MEM solution Viral supernatant was collected 48-hrs post-transfection. Spin infections were performed at room temperature at 1,500g for 90 mins with polybrene reagent (Fisher Scientific). Reh, 697, NALM6, K562, HG3, TMD8 Cas9-expressing cell lines were generated by lentiviral transduction with retroviral Cas9-2A-blast (Addgene, plasmid #73310). Human GM12878 Cas9 lines were generated by lentiviral transduction with Cas9-2A-EGFP (Addgene plasmid #63592). 697 Cas13d-expressing cell line was generated by transduction with lentiviral tet-inducble RfxCas13d (Addgene, plasmid # 138149). Doxycycline (Sigma) treatment was performed at 0.5 μg/mL supplemented every two days in culture.

tag: guide rna

value: sgROSA

tag: batch


title: Sample 1 H3K9me3 CUT&RUN


title: NALM6-sgROSA


title: NALM6-sgZNF143-2


title: Reh-sgZNF143-1


title: T+R_P4_rep4

description:
Rpom_duet_RT_4
Tha_duet_RT_4
P4_Rpom_RT_RV_RVT.xlsx
P4_Tha_T_RT_VT_RVT.xlsx


title: NALM6-sgZNF143-1


title: 697-sgROSA


title: 697-sgZNF143-2


title: 697-sgZNF143-1


title: A single In-utero natural embryo, E8.5, replicate 4

description:
InUtE85-1emb-r4
A single in-utero natural embryo, E8.5.
Single-cell RNA-seq


title: 2 pooled In-utero natural embryos, E8.5

description:
InUtE85-2pooled
2 pooled In-utero natural embryos, E8.5.
Single-cell RNA-seq


title: Reh-sgNUDT21-2


title: Reh-sgNUDT21-1


title: NALM6-sgNUDT21-2


title: NALM6-sgNUDT21-1


title: 697-sgNUDT21-1


title: HiC_Reh_sgZNF143.h5

description:
H5 format of filtered Hi-C
5_REHB6_S5

data_processing:
Raw data was preprocessed using Cutadapt5 to eliminate poly-A-tails as well as bad-quality base reads. FastQC was used to assess the quality of sequencing after trimming
Cleaned reads were mapped to a reference genome using Bowtie2.
Quantification of mapped reads to each gene was performed using HT-seq.
ENSEMBL-GTF data was used to provide genomic locations for quantification as well as additional data for annotation (such as gene name, gene description, GO-Terms etc).
APA  usage was analyzed as described in QAPA using SALMON for quantifying 3’UTRs of PolyASite.
Genome_build: GRCh37/hg19

extract_protocol:
1 million of cells were used and lysed using the commercial Arima Genomics HiC kit according to the maufacture's instructions.
Hi-C were processed with the commercial Arima Genomics HiC kit according to the manufacturer’s guidelines.

value: Reh


title: HiC_NALM6_sgZNF143.h5

description:
H5 format of filtered Hi-C
3_NALM6B6_S3


title: HiC_Reh_sgROSA.h5

description:
H5 format of filtered Hi-C
6_REHB11_S6


title: HiC_NALM6_sgROSA.h5

description:
H5 format of filtered Hi-C
4_NALM6B11_S4


title: 2 pooled synthetic-embryos, ex utero, from 3-days induced iCdx2 cells, replicate 1

description:
Cdx2-3d-2pooled
2 pooled synthetic embryos, ex utero, from 3-days induced iCdx2 cells.
Single-cell RNA-seq


title: 21-WT-8hr biol rep 3

status: Public on Jul 20 2022

city: Laramie

first: Elizabeth

middle: Di Russo

last: Case

state: WY

address: 1174 Snowy Range Rd

department: Veterinary Sciences

institute: Univeristy of Wyoming

data_processing:
Trimmed with Trimmomatic
mapped to to Mus musculus (mm10) genome assembly with version 2.1
transcript-wise counts generated with "featureCounts" tool fromm SUBREAD package
Differential gene expression tests performed with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimted text file includes log-transformed gene expression values for all replicates

source_name: Bone marrow

growth_protocol: Primary BMDM were differentiated for 7 days in L929-conditioned medium prior to infection

extract_protocol:
Total RNA was extracted withTRIzol (Invitrogen) according to the manufacturer’s instructions at the indicated timepoints.
Stranded mRNA sequencing libraries were generated with Illumina TruSeq Stranded mRNA library kit with rRNA depletion.

treatment_protocol: BMDM were infected with the stated C. burnetii strains for either 8- or 24 hours prior to total RNA extraction. A total of 4 independent experiments were conducted.

value: Bone marrow

tag: cell type

value: macrophage

tag: genotype

value: wild-type C. burnetii NMII infected


title: 23-WT-24hr biol rep 3

tag: treatment


title: Reh-sgZNF143-2


title: HiC_697_sgROSA.h5

description:
H5 format of filtered Hi-C
2_697B11_S2

tag: cell line


title: HiC_697_sgZNF143.h5

description:
H5 format of filtered Hi-C
1_697B6_S1


title: 22-WT-8hr biol rep 4


title: 24-WT-24hr biol rep 4


title: 20-dot-24hr biol rep 4

value: dotA::Tn C. burnetii NMII infected


title: 17-dot-8hr biol rep 3


title: 16-Mock-24hr biol rep 4

value: uninfected control


title: 18-dot-8hr biol rep 4


title: 11-dot-8hr biol rep 2


title: 15-Mock-24hr biol rep 3


title: 09-WT-8hr biol rep 2


title: 13-Mock-8hr biol rep 3


title: 12-dot-24hr biol rep 2


title: 14-Mock-8hr biol rep 4


title: 07-Mock-8hr biol rep 2


title: 10-WT-24hr biol rep 2


title: 08-Mock-24hr biol rep 2


title: 06-dot-24hr biol rep 1


title: 01-Mock-8hr biol rep 1


title: 03-WT-8hr biol rep 1


title: 02-Mock-24hr biol rep 1


title: Clr3-Myc ChIP

status: Public on Jul 12 2022

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
Reads were quality trimmed with fastp, aligned with the BWA aligner  to the S. pombe V2 reference sequence in which the Pombase provided 20 kb mat contig was replaced with the sequence of the full 40kb mat region. In addition, both the mat region on chromosome 2 (chrII 2109748:2138781) and the mat1M locus on the 40 kb mat contig (MAT:4489-5615) were masked from alignment. Bedgraphs of ChIP enrichment over input were produced using the MACS2 callpeaks function to make broad calls with options "--nomodel --extsize 147", followed by the bdgcmp function to compute fold-enrichment over the input background.
Assembly: S. pombe V2 reference sequence
Supplementary files format and content: bedgraph

organism: Schizosaccharomyces pombe

source_name: Md-log phase cells

growth_protocol: Standard conditions were used to produce exponentially growing cultures in rich media (YEA) at 32˚C.

extract_protocol:
Fixed cells were lysed with glass-beads in Biospec Mini-Beadbeater 16, DNA was sheared by sonication to ~ 250 bp fragments, cleared by centrifugation at 3,000 g and immunoprecipitated with 2ug of MYC antibody (sc40, Santa Cruz Biotechnology). Immunoprecipitated DNA was recovered by incubation with protein G slurry and the crosslink reversed at 65˚C. Input and immunoprecipitated DNA was treated with RNase A (5ug) and Protease K (40ug) and column purified by Qiaquick PCR purification kit (Qiagen).
Sequencing libraries were constructed from ~1 ng of input or immunoprecipitated DNA using NextUltra II DNA Library Prep (New England Biolabs) according to the manufacturer’s instructions. Libraries were purified with AMPure XP magnetic beads (Beckman Coulter) and analyzed on Bioanalyzer 2100 (Agilent) prior to sequencing using the NextSeq 500 sequencer (Illumina).

treatment_protocol: Md-log phase cells were fixated with 3% paraformaldehyde and subsequently treated with 10 mM dimethyl adipimidate for  45 min.

value: Md-log phase cells


title: C-PPn-53

status: Public on Jul 05 2022

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
Ion Torrent S5TL XL
processed_data_mm9.txt

data_processing:
Mapping to the mouse genome was performed using the T-Map algorithm from Torrent Suite Server.
Integration sites were analyzed using the program InSiDeR. https://github.com/UppsalaGenomeCenter/InSiDeR
Assembly: mm9 or mm10
Supplementary files format and content: Tab-delimited file with integration sites together with nr of reads that supports integration.

source_name: Cell line

extract_protocol:
Genomic DNA was extracted using the MagAttract HMW DNA Kit (Qiagen), according to the manufacturer’s protocol.
Library was prepared accordingusing the Ion Xpress™ Plus protocol and the Ion Plus Library Preparation for the AB Library Builder™ System (Thermo Fisher)
Hybridization-based sequencing

tag: cell line name

tag: genotype (backgound)

tag: reference genome

tag: mutagen

tag: successful integration

value: TRUE

tag: transgene

value: P/tv-a

tag: age

value: newborn


title: C-NPn-50

value: N/tv-a


title: C-NPn-49


title: C-NPn-48


title: C-NAn-46

value: Arf-/-

value: FALSE


title: C-NAn-45


title: C-NAn-47


title: C-CAa-7

value: C/tv-a

value: adult


title: C-NAa-41


title: C-CAa-4


title: C-GAa-20

value: G/tv-a


title: C-GWn-Control

value: WT


title: C-GAa-21


title: C-GAn-28


title: C-GAn-27


title: C-NAa-38


title: C-GAa-19


title: Clr3-Myc-Input


title: C-GAn-26


title: Clr3-HA-CDx2 in  tetR-clr4-ON wt cells

type: genomic

description: Clr3-HA-CDx2 HAChIP  V3

hyb_protocol: Equal amounts of Cy5-labeled immunoprecipitated DNA and Cy3-labeled input DNA were mixed with human Cot1 DNA, blocking agent and hybridization buffer, and hybridized to Agilent high-density microarrays at 65˚C for 24 hours, 10 rpm. After hybridization, slides were processed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (ChIP_1200_Jun14). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

source_name: log. growing cells

label_protocol: ChIP and input DNA was random-primed PCR amplified and conjugated with Cy5 (ChIP DNA) or Cy3 (input DNA).

growth_protocol: Standard conditions were used to produce exponentially growing cultures in minimal media (EMM) at 32˚C. Cells were pre-cultured for 20 generations in thiamine-free EMM and grown to mid-log phase.

extract_protocol: Fixed cells were lysed with glass-beads in Biospec Mini-Beadbeater 16, DNA was sheared by sonication to ~ 1,000 bp fragments, cleared by centrifugation at 3,000 g and immunoprecipitated with 2ug of HA antibody (HA.11, Santa Cruz Biotechnology). Immunoprecipitated DNA was recovered by incubation with protein G slurry and the crosslink reversed at 65˚C.Input and immunoprecipitated DNA was treated with RNase A (5ug) and Protease K (40ug) and column purified by Qiaquick PCR purification (Qiagen).

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 32˚C and subsequently treated with 10 mM dimethyl adipimidate for 45 min.

value: clr3-CDx2 tetR-clr4ON

tag: molecule type

value: HA immunoprecipitated DNA

value: Whole-cell extract DNA


title: 04-WT-24hr biol rep 1

value: Bone marrow

value: macrophage

value: wild-type C. burnetii NMII infected


title: 05-dot-8hr biol rep 1

value: dotA::Tn C. burnetii NMII infected


title: C-NPn-52

value: TRUE


title: C-CAn-A


title: C-GAn-29


title: C-GWn-80

description:
Ion Torrent S5TL XL
processed_data_mm10.txt


title: C-GWn-79


title: C-GWn-88


title: C-NAa-40


title: C-GWn-85


title: C-CAa-1


title: C-GWn-77


title: C-GWn-81


title: C-GWn-76


title: C-GWn-82


title: C-GWn-75


title: T-GWn-61

source_name: Tumor biopsy

value: Tumor biopsy


title: T-GWn-57

value: newborn


title: untagged Clr3 in  tetR-clr4-ON wt cells

description: untagged Clr3 HAChIP V3

value: wt tetR-clr4ON


title: C-GAn-33

value: Arf-/-


title: T-GWn-54


title: T-GWn-71


title: C-CAn-10


title: T-GWn-59


title: C-CAa-2


title: T-GWn-72


title: C-GAn-32


title: T-GWn-56


title: C-GAn-31


title: C-GWn-69

value: FALSE


title: C-GWn-68


title: C-GWn-64


title: C-GWn-67


title: C-GWn-66


title: C-GWn-62


title: C-GWn-63


title: C-CAn-B

value: C/tv-a


title: C-GWn-70


title: C-GWn-61


title: C-GWn-60


title: C-GWn-59


title: C-GWn-56


title: C-GWn-57


title: C-GWn-55


title: T-GWn-96


title: T-GWn-92


title: C-GWn-94


title: C-GWn-95


title: T-GWn-93


title: C-GWn-96


title: C-GWn-92


title: C-GWn-58


title: C-GWn-54


title: T-GWn-90


title: C-GWn-93


title: T-GWn-94


title: T-GWn-91


title: PFEIFFER

status: Public on Jul 01 2022

first: Laura

last: Pasqualucci

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

institute: Columbia University

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
PFEIFFER_GCB_EL029

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (GRCh37) using STAR v2.7.2.
Reads were mapped to exons using FeatureCounts and a curated version of GENCODE.v29lift37 (obtained by removing transcript types tagged as readthrough, antisense RNA, rRNA, miRNA) to produce count tables, which were converted to transcript per million (TPM) values using the sum of the exons as the transcript length.
genome build/assembly: GRCh37
Supplementary files format and content: tab-delimited text files containing the normalized transcripts per million mapped reads (TPM) values, the read counts per gene counts for genes.

source_name: PFEIFFER

growth_protocol: DLBCL cell lines were grown in Iscove’s modified Dulbecco’s medium (IMDM) supplemented with 10% heat-inactivated fetal calf serum (FCS), 100 U/ml penicillin and 100 μg/ml streptomycin, except for OCI-LY10 cells, which were grown in IMDM supplemented with 20% human plasma, 0.1% β-mercaptoethanol, 100 U/ml penicillin and 100 μg/ml streptomycin.

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions
RNA-seq libraries were generated using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus following the manufacturer's protocol

value: PFEIFFER

value: Diffuse large B cell lymphoma

tag: group

value: GCB-DLBCL


title: LY3

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
LY3_ABC_EL028

value: ABC-DLBCL


title: SUDHL2

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
SUDHL2_ABC_EL027


title: C-GWn-71

value: WT

value: G/tv-a


title: TMD8

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
TMD8_ABC_EL025


title: RL

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
RL_GCB_EL026

source_name: RL

value: RL


title: HLY1

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
HLY1_ABC_EL024


title: C-GWn-72


title: TOLEDO

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
TOLEDO_GCB_EL023

source_name: TOLEDO

value: TOLEDO


title: C-GWn-91


title: U2932

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
U2932_ABC_EL022


title: SUDHL16

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
SUDHL16_GCB_EL021


title: SUDHL5

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
SUDHL5_GCB_EL019


title: SUDHL6

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
SUDHL6_GCB_EL020


title: SUDHL4

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
SUDHL4_GCB_EL018


title: C-GWn-90


title: NU-DHL1

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
NU-DHL1_GCB_EL017


title: SUDHL10

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
SUDHL10_GCB_EL016


title: RIVA

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
RIVA_ABC_EL015

source_name: RIVA

value: RIVA


title: OCI-LY8

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
OCI-LY8_GCB_EL013


title: OCI-LY7

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
OCI-LY7_GCB_EL012


title: RCK8

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
RCK8_ABC_EL014


title: OCI-LY18

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
OCI-LY18_GCB_EL009


title: OCI-LY10

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
OCI-LY10_ABC_EL008


title: WSU-DLCL2

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
WSU-DLCL2_GCB_EL011


title: OCI-LY1

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
OCI-LY1_GCB_EL010


title: HT

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
HT_GCB_EL006

source_name: HT

value: HT


title: KARPAS 422

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
KARPAS_422_GCB_EL007

source_name: KARPAS 422

value: KARPAS 422


title: DB

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
DB_GCB_EL002

source_name: DB

value: DB


title: BJAB

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
BJAB_GCB_EL001

source_name: BJAB

value: BJAB


title: FARAGE

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
FARAGE_GCB_EL004

source_name: FARAGE

value: FARAGE


title: DOHH2

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
DOHH2_GCB_EL003


title: HBL1

description:
Illumina Stranded Total RNA Prep with Ribo-Zero Plus
HBL1_ABC_EL005


title: Ecoli_H2O2_rep2

status: Public on Jun 22 2022

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

data_processing:
Libraries were sequenced on Illumina Hi-Seq or NEXT-seq platform. First, paired end reads were split by barcode sequence using Je demultiplex with options BPOS=BOTH BM=READ_1 LEN=4:6 FORCE=true C=false 6. BM and LEN options were adjusted for samples with a 3 nt barcode instead of 4, and for samples where the barcode is located in read 2
Next read 2 files were used to map with bowtie2 with the following parameters: -q -p 10 --local —no-unal. Reads were mapped to curated list of non-redundant tRNA genes with tRNAScane score >40 for respective organisms (human and E. Coli)
Bowtie2 output sam files were converted to bam files, then sorted using samtools. Next IGV was used to collapse reads into 1 nt window. IGV output .wig files were reformatted using custom python scripts (available on GitHub at https://github.com/ckatanski/Q_paper).
The bowtie2 output Sam files were also used as input for a custom python script using PySam, a python wrapper for SAMTools ( https://github.com/pysam-developers/pysam) to sum all reads that mapped to each gene
Data was visualized with custom R scripts (available on GitHub at https://github.com/ckatanski/Q_paper)
Genome_build: Hg19
Supplementary_files_format_and_content: Tab separated values. Rows for each base of every gene in the reference. Columns for base, position, gene, pileup, mutation, deletion, insertion, stop rate, number of reads that map an “A” at each position, and “C”, “G”, “T”, “N”.

organism: Escherichia coli

source_name: RNA was extracted from E. coli MG1655 cells grown in LB until mid-log growth then treated with 0.5% H2O2 for 10 minutes

growth_protocol: E. coli MG1655 cells were grown in LB to a A600 of 0.4 before subjecting to the stress conditions. Cells were harvested by centrifuging 25 mL culture for 1 min at 12 000 rcf and decanting media. HEK293T cells were cultured with complete DMEM medium under normal conditions. 0Q HEK293T cells were obtained by culturing the cells with dialyzed FBS for certain passages, and 100Q HEK293T cells were obtained by treating 0Q cells with 1 μM queuine for 24 hours(Zhang et al. 2020; Wang et al. 2018) . Briefly, HEK293T cells were grown in complete DMEM medium (Cytiva Hyclone SH30022.01) with 10% dialyzed FBS ((Thermo Fisher Scientific 26400044) and 1% Penicillin-Streptomycin (Thermo Fisher Scientific 15070063) to 80% confluency and passaged.

extract_protocol:
For HEK293T cells, TRIzol reagent (Thermo Fisher Scientific 15596026) was used to extract total RNAs at each passage by following the manufacturer’s manual. For E. coli, RNA was extracted by a hot acid-phenol protocol.  Briefly, 0.5 mL of acid-buffer phenol (pH 4.5 citrate) was added to frozen samples.  Samples were incubated in a heat block with shaking at 50°C for 30 min.  The aqueous phase was extracted for another round of phenol extraction and 2 rounds of chloroform extraction before ultimately precipitating with glycoblue, 300 mM sodium acetate, and 3 volumes of ethanol.  Samples were incubated for 1 hour at -80°C, then centrifuged at maximum speed (20k RCF) for 45 min to pellet RNA.  Pellets were washed twice with 70% ethanol, then resuspended in water.
Libraries were prepared as previsouly described: 33337498. Briefly, Samples were incubated overnight at 16 °C in a 50 μL ligation solution with the following final concentration: 15% PEG 8000, 1x NEB T4 RNA ligase I buffer, 50 μM ATP, 5% DMSO, 1 mM hexaamine cobalt (III) chloride, 0.8 μM barcode ligation oligo, and 1 U/μL NEB T4 RNA ligase I. After overnight ligation, 50 μL of 100 mM EDTA were added to each sample to inactivate the ligase. The samples were then combined and 8 μL of ThermoFisher Streptavidin MyOne C1 Dynabeads per sample were added to the combined samples. The biotinylated samples were allowed to bind the beads for 15 minutes. After binding, the beads were magnetized, the supernatant was removed, and the samples were washed once with a high salt Tween wash buffer (1 M NaCl, 0.1% Tween 20, and 20 mM TrisHCl, pH 7.4) and once with low salt wash buffer (100 mM NaCl, 20 mM TrisHCl, pH 7.4). Periodate treatment was included when indicated - either before first ligation, or before reverse transcription. Before reverse transcription, A 50 µL dephosphorylation mix containing the following was added to the multiplexed sample on bead: 0.04 U/µL calf intestine phosphatase (Roche), 10 mM MgCl2, 0.5 mM ZnCl2, 20 mM HEPES, pH 7.3. The sample was incubated at 37 °C for 30 minutes. The sample was then washed once with high salt wash buffer and once with low salt wash buffer, then resuspended in 20 µL water. For reverse transcitpion, 5 µL of SuperScript IV VILO 5x master mix (ThermoFisher) was added to the dephosphorylated sample (final volume of 25 µL) and then incubated at 55 °C for 10 minutes, then incubated at 30 C overnight. Beads were then resuspended into 50 µL of RNase H master mix containing 0.4 U/uL RNase H (NEB) and 1x NEB RNase H buffer and incubated at 37 °C for 15 minutes. Beads were resuspended into 50 µL of a ligation master mix with the following components:  2U/µL T4 RNA ligase I (NEB), 1x NEB T4 RNA ligase I buffer, 2 µM second ligation oligo (Table S1), 25% PEG 8000, 50 µM ATP, 7.5% DMSO, and 1 mM hexaamine cobalt chloride. After incubation at room temperature overnight (12+ hours), the reaction was diluted with 50 µL water to reduce viscosity, washed once with high salt wash buffer and once with low salt wash buffer, and then resuspended in water. The amount of water was 6 µL per sample in the first ligation reaction, before pooling the barcoded samples. A 50 µL PCR reaction was run using 5-10% of the bead slurry products from the second ligation reaction using Q5 DNA polymerase (NEB) and following the manufacturer’s instructions: 0.02 U/µL Q5 DNA polymerase, 1x Q5 reaction buffer, 0.2 mM dNTPs, 0.5 µM Illumina index primer. Following desalting, PCR products were run on 10% non-denaturing TBE gel with dsDNA size markers; lanes were cut for inserts between 20ng and 300nt, mashed by pipette tip, and then resuspended in crush-and-soak buffer

treatment_protocol: For E. coli stress, Mock treated cells, 25 mL, were left to grow for 10 min. Hydrogen peroxide stress was done by adding H2O2 to 25 mL cells to a final concentration of 0.5% for 10 min. Glucose phosphate stress was done by adding to 25 mL cells α-methyl glucoside-6-phosphate (αMG) to a final concentration of 1 mM for 10 min. Iron depletion stress was done by adding to 25 mL cells 2,2’-dipyridl (DIP) to 250 µM final concentration for 10 min. Cells were resuspended in 0.5 mL ice cold lysis buffer (150 mM KCl, 2 mM EDTA, 20 mM HEPES pH 7.5) then flash frozen in liquid nitrogen

tag: cell line/strain

tag: queuine added

value: No


title: Ecoli_DIP_rep2

source_name: RNA was extracted from E. coli MG1655 cells grown in LB until mid-log growth then treated with 250uM 2,2’-dipyridl (DIP) for 10 minutes


title: Ecoli_aMG_rep2

source_name: RNA was extracted from E. coli MG1655 cells grown in LB until mid-log growth then treated with 1mM α-methyl glucoside-6-phosphate (αMG) for 10 minutes


title: Ecoli_none_rep2

source_name: RNA was extracted from E. coli MG1655 cells grown in LB until mid-log growth


title: Ecoli_H2O2_rep1


title: Ecoli_plusIO4


title: Ecoli_none_rep1


title: Ecoli_minusIO4


title: HEK_calibration_100Q

source_name: RNA extracted from HEK293T cells grown with added queuine

value: HEK 293T

value: Yes


title: HEK_calibration_90Q

source_name: A mixture of RNA from HEK293T cells grown with and without queuine


title: HEK_calibration_80Q


title: HEK_calibration_70Q


title: HEK_calibration_60Q


title: HEK_calibration_30Q


title: HEK_calibration_40Q


title: HEK_calibraiton_20Q


title: T-GWn-95

description:
Ion Torrent S5TL XL
processed_data_mm10.txt

tag: tissue

value: Tumor biopsy

value: TRUE

value: newborn


title: HEK_100Q_rep2_plusIO4


title: Ecoli_aMG_rep1


title: HEK_100Q_rep2_minusIO4


title: HEK_100Q_rep1_minusIO4


title: HEK_0Q_rep2_minusIO4

source_name: RNA extracted from HEK293T cells grown without queuine


title: HEK_0Q_rep1_plusIO4


title: 17MO_MG_C9_KO_HOMO_2

status: Public on Jun 15 2022

city: Los Angeles

first: Shaughn

last: Bell

state: CA

address: 8700 Beverly Blvd

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

data_processing:
(RPKM generation) Raw sequencing reads were demultiplexed and FASTQ files were uploaded to the Galaxy web platform using the public server at usegalaxy.org.
(RPKM generation) FASTQ files were processed using FASTQ Groomer (Galaxy Version 1.1.1) and aligned to the mouse genome (mm10) via Tophat (Galaxy Version 2.1.1) using default settings.
(RPKM generation) BAM files were downloaded locally and annotated using Partek software v7.17.0918 to generate RPKM values for each gene.
(TPM generation) Raw sequencing reads were demultiplexed, and FASTQ files were used to generate estimated transcript counts against the mouse transcriptome (mm10) via Salmon v0.8.2.
(TPM generation)TPM values summed to the gene level were generated using the R Bioconductor package DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: comma delimited RPKM & TPM tables

source_name: Microglia

extract_protocol:
The meninges were removed from the mice brains of different genotypes and dissociated using the Neural Tissue dissociation kit, papain based (Miltenyi Biotech) and GentleMACSdissociator (NTDK Brain setting). The lysate was collected and passed through a 70μm strainer to obtain a single cell suspension. Next, myelin was removed from the cells by incubating with magnetic myelin beads (Myelin Removal Beads II, human, mouse, rat, Miltenyi Biotech) and removed using the AutoMACs. Cells were then incubated with CD11b+ magnetic beads CD11b MicroBeads, human and mouse, (Miltenyi Biotech) and sorted using the AutoMACs. After sorting, cells were pelleted and stored at -80°C until further downstream application.  RNA was isolated using Qiagen RNeasy Micro Kit (Cat #74004) according to manufacturer’s instructions.
RNA-seq libraries were generated using 75ng to 180ng total RNA as input for the TruSeq Stranded mRNA Library Prep kit (Illumina) according to the manufacturer’s protocol, and samples were indexed using TruSeq RNA Single Indexes (Illumina). Library preps were analyzed via bioanalyzer (Agilent) and quantified via Qubit fluorometric quantification (Thermo Fisher). Quantified libraries were normalized, pooled, and sequenced on a NextSeq 500 sequencer (Illumina) using the single-end 75 nucleotide setting

tag: strain

value: Homozygous C9orf72 (3110043O21Rik) Knock-Out

tag: age at collection

value: 17 months

tag: total rna input


title: HEK_0Q_rep2_plusIO4


title: 17MO_MG_C9_KO_HOMO_3

tag: genotype


title: HEK_calibraiton_0Q


title: HEK_calibration_50Q


title: Ecoli_DIP_rep1


title: 17MO_MG_C9_KO_HOMO_4


title: 17MO_MG_C9_KO_HET_4

value: Heterozygous C9orf72 (3110043O21Rik) Knock-Out


title: 17MO_MG_C9_KO_HOMO_1


title: 17MO_MG_C9_KO_HET_3


title: HEK_0Q_rep1_minusIO4


title: 17MO_MG_C9_KO_HET_2


title: HEK_calibration_10Q


title: 17MO_MG_C9_KO_HET_1


title: 17MO_MG_WT_1

value: Wild Type


title: HEK_100Q_rep1_plusIO4


title: 3MO_MG_C9_KO_HOMO_4

value: 3 months


title: 17MO_MG_WT_2


title: 3MO_MG_C9_KO_HOMO_3


title: 17MO_MG_WT_3


title: 17MO_MG_WT_4


title: 3MO_MG_C9_KO_HET_4


title: 3MO_MG_C9_KO_HOMO_1


title: 3MO_MG_C9_KO_HOMO_2


title: 3MO_MG_C9_KO_HET_3


title: 3MO_MG_C9_KO_HET_2


title: 3MO_MG_C9_KO_HET_1


title: 3MO_MG_WT_3


title: 3MO_MG_WT_2


title: 3MO_MG_WT_1


title: MG_C9_KO_HOMO_3

data_processing:
The demultiplexed raw reads were aligned to the transcriptome using STAR (version 2.5.1) with default parameters, using mouse mm10 transcriptome reference from Ensembl version 84 annotation, containing all protein coding genes, long non-coding RNA genes, and polymorphic pseudogenes. Expression counts for each gene in all samples were collapsed and normalized to unique molecular identifier (UMI) counts using Cell Ranger software version 4.0.0 (10X Genomics). The result is a large digital expression matrix with cell barcodes as rows and gene identities as columns.
Filtered digital expression matrices from the CellRanger output (filtered_feature_bc_matrix directory) were loaded into R (version 4.0.3) using the Seurat package (version 3.2.2) in Rstudio (version 1.3.1093), keeping all genes that were expressed in more than one cell. All samples were merged into a single Seurat object (30,872 cells) and filtered by removing all cells with counts, genes, or mitochondrial gene percentage outside of three standard deviations from the mean (30,065 cells).
The data were then normalized using SCTransform, regressing out the mitochondrial gene content. Dimensionality reduction was run with Principal Component Analysis (PCA) followed by Uniform Manifold Approximation and Projection (UMAP) using the default 50 principal components (PCs). After visualizing the UMAP plots, the cells appeared to cluster based on the order they were processed, the day they were processed, and the sex of the animal. Integration of the data was performed by using the Harmony R package (version 1.0.0), batch correcting for these covariates (process day, process order, and sex) resulting in a much more uniform clustering between these factors after rerunning UMAP with the Harmony-corrected PCs.
Cluster determination was performed using FindNeighbors and FindClusters with a resolution of 0.3 and resulting in an initial discovery of 19 clusters. Cluster markers were determined using FindAllMarkers with the default min.pct = 0.25 and logfc.threshold = 0.4. Investigating these markers, six distinct cell types were discovered (microglia, endothelial cells, astrocytes, granulocytes, neutrophils and lymphocytes). A seventh general cluster was positive for both monocyte and macrophage markers.
In order to investigate microglial state changes between genotypes, all non-microglia cells were removed (26,275 microglia), and the remaining cells were then normalized, centered and scaled (NormalizeData, FindVariableFeatures & ScaleData) followed by Jack Straw Analysis to determine which PCs to use for further analysis. A sharp drop-off of p-values was observed between PC 14 and 15, so 15 PCs were used for microglia analysis.
The microglia were then normalized with SCTransform regressed against mitochondrial gene content. Subsequent PCA and UMAP reductions showed similar day, order, and sex bias as the analysis with all the cells, and the microglia were again integrated with Harmony, using the same covariates as before, followed by UMAP. Using FindNeighbors and FindClusters with a resolution of 0.8 discovered 16 clusters.
Known ARM genes (Clec7a, Itgax, Apoe, and Cst7) were found to be highly expressed in Cluster 11, and known IRM genes (Ifit1, Ifit2, Ifi204, and Isg15) were found to be highly expressed in Cluster 13.  Using FindAllMarkers (min.pct = 0.25 and logfc.threshold = 0.4), 66 genes were discovered to have a positive average logfc in Cluster 11 (ARM cluster marker genes) and 86 genes were discovered to have a positive average logfc in Cluster 13 (IRM cluster marker genes).
These two gene lists were used with the AddModuleScore function to assign ARM and IRM module scores to each cell. Cells in the ARM or IRM clusters were compared across genotypes by ordinary one-way ANOVA (Dunnett’s multiple comparisons test with a single pooled variance) using GraphPad Prism (version 9.0.0 (86) for macOS).
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger 4.0 outs filtered_feature_bc_matrix (3 files per sample:  barcodes.tsv, features.tsv & matrix.mtx); excel spreadsheet with cell metadata including module scores

extract_protocol:
The meninges were removed from the mice brains of different genotypes and dissociated using the Neural Tissue dissociation kit, papain based (Miltenyi Biotech) and GentleMACSdissociator (NTDK Brain setting). The lysate was collected and passed through a 70μm strainer to obtain a single cell suspension. Next, myelin was removed fromthe cells by incubating with magnetic myelin beads (Myelin Removal Beads II, human, mouse, rat, Miltenyi Biotech) and removed using the AutoMACs. Cells were then incubated with CD11b+ magnetic beads CD11b MicroBeads, human and mouse, (Miltenyi Biotech) and sorted using the AutoMACs. After sorting, cells were counted and diluted according to the specifications in the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California) to capture about 4000 cells per sample.
Single-cell RNA-Seq libraries were prepared per the Single Cell 3′ v3.1 Reagent Kits User Guide (10x Genomics, Pleasanton, California). Cellular suspensions were loaded on a Chromium Controller instrument (10x Genomics) to generate single-cell Gel Bead-In-EMulsions (GEMs). GEM-RT was performed in a Veriti 96-well thermal cycler (Thermo Fisher Scientific, Waltham, MA). GEMs were then harvested, and the cDNA was amplified and cleaned up with SPRIselect Reagent Kit (Beckman Coulter, Brea, CA).  Indexed sequencing libraries were constructed usingChromium Single-Cell 3′ Library Kit for enzymatic fragmentation, end-repair, A-tailing, adapter ligation, ligation cleanup, sample index PCR, and PCR cleanup. The barcoded sequencing libraries were quantified by quantitative PCR using the Collibri LibraryQuantification Kit (Thermo Fisher Scientific). Libraries were sequenced on a NovaSeq 6000 (Illumina, San Diego, CA) as per the Single Cell 3′ v3.1 Reagent Kits User Guide, with a sequencing depth of ~40,000 reads/cell.
batching protocol: To minimize batch affect, samples were processed through the GEM-RT step in batches of three on three consecutive days. We attempted to mix the genotypes over all three days, however this was not done perfectly. In addition, the order each genotype was processed on a given day was also mixed, but again not perfectly. The process day and process order value is listed in the caracteristics column of the Samples Table. After all nine samples were taken to the GEM-RT stage, all samples were taken through the rest of the library construction protocol together on the same day.
10x Genomics Single Cell 3' v3.1

value: 12 months

tag: Sex

value: female

tag: process day

value: day 2

tag: process order


title: MG_C9_KO_HOMO_2

value: male


title: MG_C9_KO_HET_2


title: MG_C9_KO_HET_3

value: day 3


title: MG_C9_KO_HET_1

value: day 1


title: MG_C9_KO_HOMO_1


title: MG_WT_3


title: MG_WT_2