title: RPE1 genomic DNA

data_processing:
Duplicates were removed, adaptors were trimmed, and low quality reads were removed using fastp.
Reads were aligned to the genome and allele-specific counts by gene were measured using PAC
Assembly: hg38
Supplementary files format and content: vcf format file containing corrected SNPs for RPE-1 cells
Library strategy: DNA-seq

extract_protocol:
Genomic DNA was exrtracted using the NEB Monarch Genomic DNA extraction kit
Sequencing libraries were constructed using the NEBNext UltraExpress® FS DNA Library Prep Kit
Genomic DNA sequencing

value: WT


title: gcn1delta_3_csm_t0

status: Public on May 14 2025

type: SRA

city: stockholm

first: yujie

last: zhang

address: Tomtebodavägen 23

country: Sweden

institute: Karolinska institutet

description: Library name: gcn1delta_3_csm_t0

library_source: transcriptomic

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
SLAM-Seq data analysed was performed with slamdunk (v0.4.3) provided by nfcore pipeline(v1.0.0)(https://nf-co.re/slamseq). Firstly, fastq compressed files (fastq.gz) were first converted to reverse complementary reads method in order to feed into slamdunk nf core pipeline as stranded libraries were prepared with dUTP.  Adapter contamination and low-quality bases were trimmed using TrimGalore(v 0.6.4) (trim length 27bp). Slamdunk was used for mapping, quantifying nucleotide-conversions and collapsing quantifications on gene level.  At least 2 T>C conversions per read was regarded as a confident call for labelled RNA reads. Genes with less than 10 reads were filter out. SNP masking was employed to distinguish filter T>C SNPs from converted nucleotides. T > C reads counts in each library were normalized to total library read counts. To calculate RNA half-lives , T>C conversions were normalized to chase-onset (t0). Curve fitting was performed followed by non-linear decay model equations in R using the minpack.lm package.  Degradation rate is calculated as 60 * ln(2) / t1/2 (t1/2 is half-time of gene).
Assembly: Saccharomyces cerevisiae R64-1-1
Supplementary files format and content: Bedgraph files for collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.
Library strategy: SLAM-seq

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: S. cerevisiae (wildtype and upf1 mutant) were grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose) or  Complete Supplement Mixture (CSM from Formedium™).

extract_protocol:
Metabolic labelling of newly synthesized RNA molecules was performed as previously described [PMID: 28945705, PMID: 36838506].  Briefly, 4tU (Sigma)  was dissolved in NaOH (83 mM) used for labelling RNA molecules. The final concentration of 4tU for YPD and CSM is 5mM (PMID: 26941319) and 0.2 mM (PMID: 30192227), respectively. MES buffer (pH 5.9) with a final concentration 10 mM was prepared with media to avoid the PH change due to 4tU addition. To perform pulse and chase experiment, RNA molecules were labelled with 4tU (prepared as above) for 1h during cell grown at mid exponential phase. Cells were washed and resuspend in prewarmed medium (YPD with MES buffer or CSM with MES buffer) without  4tU and time points were collected at 0, 15 and 30 mins by centrifugation and snap frozen in liquid nitrogen immediately.
To perform thiol(SH)-linked alkylation, the reaction including 5 μg of RNA  was incubated with iodoacetamide (final concentration at 0.5 M) at 50 oC for 15 minutes [PMID: 28945705]. The reaction was stopped by adding 0.1 M DTT (final concentration at 20 mM). RNA was then precipitated by 3 M of sodium acetate and pure ethanol.  Purified RNA was subjected for ribosomal RNA depletion using RiboPools Depletion Kit (siTOOLs Biotech). Libraries were prepared by  Ultra™ II Directional RNA Library Prep Kit for Illumina® following manufacture instructions.  Sequencing was performed on Illumina Nextseq 2000 sequencer with single end read length for 150 cycles.

tag: tissue

value: yeast cells

tag: genotype

value: gcn1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1delta)

tag: treatment

value: Pulse for 1 h and chase for 0 min


title: SAFA depletion, K3K4Me3, rep2

city: Boston

first: Michael

middle: D

last: Blower

state: MA

address: 72 E. Concord St. K123C

department: Biochemistry and Cell Biology

country: USA

institute: Boston University

library_source: genomic

data_processing:
Duplicates were removed, adaptors were trimmed, and low quality reads were removed using fastp.
Reads were aligned to the genome and allele-specific counts by gene were measured using PAC
Assembly: hg38
Supplementary files format and content: tab-delimited text file of allele-specific counts per gene for each library
Supplementary files format and content: tab-delimited text file compaing allele-specific counts for each antigen between replicates and genotypes.
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: hTERT-RPE-1 cells were cultured in DMEM/F-12 supplemented with 10% FBS (HyClone Laboratories), penicillin/streptomycin, 2 mM glutamine, and 7.5% sodium bicarbonate.

extract_protocol:
Cut&Run enriched DNA was extracted using EpiCypher CUTANA ChIC/CUT&RUN Kit Version 3 (14-1048) with anti-H3K4me3 (EpiCypher 13-0060), anti-H3K27Ac (Invitrogen, MA5-23516) or IgG.
ng of CUT&RUN enriched DNA were used as input for library construction with EpiCypher CUT&RUN Library Prep Kit (14-1001).

treatment_protocol: To induce SAF-A depletion +/- SAF-A-GFP expression, cells were treated with 0.5 μg/mL doxycycline (D3447; MilliporeSigma) and 100 μg/mL 3-indole acetic acid (IAA, I-5148 MilliporeSigma) for 24 hours.

tag: cell line

tag: cell type

value: Retinal Pigment Epithelial Cells

value: SAFA depletion

value: dox, aux


title: SAFA depletion, IgG, rep2


title: gcn1delta_2_csm_t30

description: Library name: gcn1delta_2_csm_t30

value: Pulse for 1 h and chase for 30 min


title: Targeted bisulfite sequencing, 9394464, Tumor

city: Seoul

first: Yeongun

last: Lee

state: State...

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei university

description: paired-end 101bp

data_processing:
The generated sequencing data was quality controlled with FastQC (version 0.11.9). Trim Galore (version 0.6.7) and Cutadapt (version 2.8) were used to remove the adaptor sequences and low-quality sequences. Based on the human CpG island reference hg19, Bismark (version 0.22.3) was used to align sequencing reads with Bowtie2 (version 2.4.4). Alignment of each data was assessed by Picard CollectHsMetrics and every QC data was summarized by multiQC. Sort and index commands from Samtools were utilized. The number of methylated and unmethylated cytosines at each CpG site was listed using Bismark methylation extractor from post-indexed data, and only those 10X or higher were selected for downstream analysis. Finally, the methylation values of CpG sites included in the same CpG island were calculated by averaging the methylation value based on the hg19.
Assembly: hg19
Supplementary files format and content: DNA methylation levels of CpG sites extracted in a text file by Bismark methylation extractor

source_name: Papillary thyroid cancer

extract_protocol:
genomic DNA was extracted from the collected tissue samples using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany). as outlined in the manufacturer's recommendations and guideline. After DNA extraction, the DNA concentration and purity were assessed using Nanodrop (Thermo Fisher, Carlsbad, CA, US).
A total 500ng of genomic DNA was fragmented using M220 Focused-ultrasonicator (Covaris, Woburn, MA, US) with low-EDTA TE buffer. The quality, quantity, and fragment size (major peak in 250–300 bp) of sheared genomic DNA was verified using a 2100 Bioanalyzer system (Agilent Technologies, Santa Clara, CA, USA) prior to library preparation. The DNA library was bisulfite-converted using the EZ DNA Methylation-Gold™ Kit (Zymo Research, Irvine, CA, USA). Then, the library was prepared using the Accel-NGS® Methyl-Seq DNA library kit (Swift Biosciences, Ann Arbor, MI, USA) and other specified enzymes, buffers, and reagents in manufacturer’s protocol. Finally, 8 libraries were pooled and incubated with probe pool designed for targeting the regions of our interest. After clean-up, the libraries were sequenced on HiSeq2500 sequencer (Illumina, San Diego, CA, US) with 2 X 100bp pair-end reads with unique dual index and generated 2Gb of sequencing data from each sample.

value: Papillary thyroid cancer

tag: Sex

value: Female

tag: age

tag: metastasis

value: N


title: gcn1delta_2_csm_t15

description: Library name: gcn1delta_2_csm_t15

value: Pulse for 1 h and chase for 15 min


title: 231-D input

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

country: Japan

institute: University of Tokyo

description:
Library name: 231-D_input
specific superenhancers of parental (210325_Only231P_style-superhistone_hg19_cts.bed) and MDA-231-D clone (210325_Only231D_style-superhistone_hg19_cts.bed), respectively

data_processing:
Reference files of the human reference sequence assembly (UCSC hg19 and hg38) were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
ChIP-seq reads were trimmed down to 50 bp with the SamToFastq command and replicate data were combined with the cat command.
Combined read data were aligned using Bowtie (version 2.2.2.6) (Langmead et al., 2009) with the command “bowtie -p 8 -S -a --best --strata -n 1 -m 1”.
Super-enhancer regions and OCT-2 binding regions were identified using HOMER software (Model based analysis of ChIP-seq) (version) (Heinz et al, 2010) with the command "findpeaks -style superhistone" for H3K27ac ChIP-seq and "findpeaks -style factor" for POU2F2 ChIP-seq.
Identified Super-enhancer regions were compared among replicates and common Super-enhancers  among replicates were listed with the command "mergePeaks -d given". Identified OCT-2 binding regions were annotated with the annotatePeaks.pl command. RPM score were caliculated with the command bedtools multicov.
Assembly: hg19 or hg38 (specified in each sample)
Supplementary files format and content: BED files were generated using HOMER (version) as described above.

source_name: breast cancer cell line

growth_protocol: 231Pa_Luc+GFP cells and 231Pa_Luc+OCT-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; #11965; Gibco, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS (#SH30910.03; Thermo Fisher Scientific or #10270-106; Gibco, Thermo Fisher Scientific), 50 U·mL-1 penicillin, 50 μg·mL-1 streptomycin (penicillin–streptomycin; #15070-063; Gibco, Thermo Fisher Scientific). MDA-MB-436 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). MDA-MB-436_Luc2 (436_Luc2) cells and MDA-MB-436_Luc2_No3a (436-3a) cells are cultured in RPMI 1640 medium (#11875; Gibco, Thermo Fisher Scientific supplemented with 10% FBS (#SH30910.03; Thermo Fisher Scientific or #10270-106; Gibco, Thermo Fisher Scientific), 50 U·mL-1 penicillin, 50 μg·mL-1 streptomycin (penicillin–streptomycin; #15070-063; Gibco, Thermo Fisher Scientific). These cells were maintained in a 5% CO2 atmosphere at 37°C.

extract_protocol:
ChIP-seq was performed using 5 μg of anti-H3K27ac antibody (#MABI009-100) or 5 ug of anti-OCT-2 antibody (#sc-377475, Santa Cruz Biotechnology, Dallas, TX, USA), as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

value: breast cancer cell line

value: cancer

tag: clone

value: highly metastatic clone MDA-231-D

tag: transgenes

value: luciferase

tag: chip antibodies

value: input genome


title: 231Pa input

description:
Library name: 231Pa_input
specific superenhancers of parental (210325_Only231P_style-superhistone_hg19_cts.bed) and MDA-231-D clone (210325_Only231D_style-superhistone_hg19_cts.bed), respectively

value: parental cell line


title: Targeted bisulfite sequencing, 9389355, Normal thyroid tissue

description: paired-end 101bp

source_name: Normal thyroid

value: Normal thyroid


title: SAFA depletion, H3K27Ac, rep2


title: gcn1delta_2_csm_t0

description: Library name: gcn1delta_2_csm_t0

value: yeast cells

value: gcn1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 gcn1delta)


title: Targeted bisulfite sequencing, 9395019, Normal thyroid tissue

description: paired-end 101bp

value: Y


title: 231-D H3K27ac rep2

description:
Library name: 231-D_H3K27ac_2
specific superenhancers of parental (210325_Only231P_style-superhistone_hg19_cts.bed) and MDA-231-D clone (210325_Only231D_style-superhistone_hg19_cts.bed), respectively


title: Targeted bisulfite sequencing, 9395019, Tumor

description: paired-end 101bp


title: SAFA depleletion, H3K4Me3, rep1

value: Retinal Pigment Epithelial Cells

value: SAFA depletion


title: gcn1delta_1_csm_t30

description: Library name: gcn1delta_1_csm_t30

value: Pulse for 1 h and chase for 30 min


title: 231Pa H3K27ac rep2

description:
Library name: 231Pa_H3K27ac_2
specific superenhancers of parental (210325_Only231P_style-superhistone_hg19_cts.bed) and MDA-231-D clone (210325_Only231D_style-superhistone_hg19_cts.bed), respectively


title: 231-D H3K27ac rep1

description:
Library name: 231-D_H3K27ac_1
specific superenhancers of parental (210325_Only231P_style-superhistone_hg19_cts.bed) and MDA-231-D clone (210325_Only231D_style-superhistone_hg19_cts.bed), respectively. 210325_overlap231D_P_style-superhistone_hg19_cts.bed: superenhancers common to 231P and MDA-231-D.


title: Targeted bisulfite sequencing, 9395071, Normal thyroid tissue

description: paired-end 101bp


title: SAFA depletion, IgG, rep1

value: dox, aux


title: gcn1delta_1_csm_t15

description: Library name: gcn1delta_1_csm_t15


title: SAFA depletion, H3K27Ac, rep1


title: 231Pa H3K27ac rep1

description:
Library name: 231Pa_H3K27ac_1
specific superenhancers of parental (210325_Only231P_style-superhistone_hg19_cts.bed) and MDA-231-D clone (210325_Only231D_style-superhistone_hg19_cts.bed), respectively


title: Targeted bisulfite sequencing, 9395071, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer

value: Female


title: gcn1delta_1_csm_t0

description: Library name: gcn1delta_1_csm_t0

value: Pulse for 1 h and chase for 0 min


title: Targeted bisulfite sequencing, 9394464, Normal thyroid tissue

description: paired-end 101bp

value: N


title: dhh1delta_3_ypd_t30

description: Library name: dhh1delta_3_ypd_t30

value: dhh1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 dhh1delta)


title: RPE1, H3K4Me3, rep2

value: WT


title: treatment 3_ICM

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

country: China

institute: Tianjin Medical University

description: Library name: Sample 6

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: Mus musculus (mm39)
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample ...

organism: Mus musculus

source_name: heart

growth_protocol: Sham

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: ICM model

value: heart


title: RPE1, IgG, rep2


title: treatment 2_ICM

description: Library name: Sample 5


title: Targeted bisulfite sequencing, 9395392, Tumor

description: paired-end 101bp


title: RPE1, H3K27Ac, rep2


title: Targeted bisulfite sequencing, 9395975, Normal thyroid tissue

description: paired-end 101bp


title: dhh1delta_3_ypd_t15

description: Library name: dhh1delta_3_ypd_t15

value: Pulse for 1 h and chase for 15 min


title: dhh1delta_3_ypd_t0

description: Library name: dhh1delta_3_ypd_t0


title: Targeted bisulfite sequencing, 9395975, Tumor

description: paired-end 101bp


title: treatment 1_ICM

description: Library name: Sample 4


title: RPE1, H3K4Me3, rep1


title: dhh1delta_2_ypd_t30

description: Library name: dhh1delta_2_ypd_t30


title: control 3_Sham

description: Library name: Sample 3


title: RPE1, IgG, rep1


title: Targeted bisulfite sequencing, 9399569, Normal thyroid tissue

description: paired-end 101bp


title: control 1_Sham

description: Library name: Sample 1


title: SAFA depletion, rep2

data_processing:
Duplicates were removed, adaptors were trimmed, and low quality reads were removed using fastp.
for allele-specific gene expression analysis reads were aligned and quantified against hg38 using PAC
Assembly: hg38
Supplementary files format and content: tab-delimited text format of allele-specific counts per gene determine by PAC.

extract_protocol:
5 x 105 cells were collected for library preparation
Libraries were prepared by Zymo-Seq ATAC Library Kit (Zymo #D5458) following manufacturer's instructions


title: control 2_Sham

description: Library name: Sample 2


title: dhh1delta_2_ypd_t0

description: Library name: dhh1delta_2_ypd_t0


title: dhh1delta_2_ypd_t15

description: Library name: dhh1delta_2_ypd_t15


title: RPE1, H3K27Ac, rep1


title: Targeted bisulfite sequencing, 9399569, Tumor

description: paired-end 101bp


title: Targeted bisulfite sequencing, 9400111, Normal thyroid tissue

description: paired-end 101bp


title: dhh1delta_1_ypd_t30

description: Library name: dhh1delta_1_ypd_t30


title: CGNs, shKDM6B dCat Rescue 5

city: Durham

first: Rebecca

last: Li

state: North Carolina

address: 311 Research Drive

department: Neurobiology

institute: Duke University

data_processing:
nf-core/rnaseq pipeline v3.14.0
Sequencing reads were trimmed, aligned, counted, and normalized using nf-core/rnaseq pipeline with default parameters
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Cerebellar granule neurons

extract_protocol:
RNA was harvested using RNAqueous Micro Kit (Invitrogen)
RNA samples were sent to Novogene for library construction

value: Cerebellar granule neurons

value: shKDM6B dCat Rescue


title: SAFA depletion, rep1


title: Targeted bisulfite sequencing, 9400111, Tumor

description: paired-end 101bp


title: dhh1delta_1_ypd_t15

description: Library name: dhh1delta_1_ypd_t15

value: yeast cells


title: Targeted bisulfite sequencing, 9395392, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: CGNs, shKDM6B dCat Rescue 4


title: RPE1, rep2


title: Targeted bisulfite sequencing, 9402448, Normal thyroid tissue

description: paired-end 101bp

value: Male


title: RPE1, rep1

value: Retinal Pigment Epithelial Cells


title: dhh1delta_1_ypd_t0

description: Library name: dhh1delta_1_ypd_t0


title: CGNs, shKDM6B dCat Rescue 3


title: CGNs, shKDM6B dCat Rescue 2


title: CGNs, shKDM6B dCat Rescue 1


title: dhh1delta_3_csm_t30

description: Library name: dhh1delta_3_csm_t30


title: dhh1delta_3_csm_t15

description: Library name: dhh1delta_3_csm_t15


title: Targeted bisulfite sequencing, 9403428, Normal thyroid tissue

description: paired-end 101bp


title: AN05086.insula

city: Belmont

first: Weiqian

last: Jiang

address: 115 Mill St

institute: McLean Hospital

data_processing:
bcbio-nextgen Bulk RNA-seq pipeline
Paired-end sequence reads were aligned to human genome UCSC GRCh38.p14 using STAR
Quality metrics were assessed using Samtools
Transcript counts from aligned reads were quantified using Salmon, then summarized to the gene level using the R package Tximport
Assembly: GRCh38
Supplementary files format and content: comma-seperated file includes raw counts for all samples

source_name: Post mortem brain

extract_protocol:
rRNA depletion sequencing libraries were prepared by using QIAGEN Fastselect HMR
RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations

value: Post mortem brain

tag: brain region

value: insula

tag: group

value: control

value: male


title: AN18943.insula


title: Targeted bisulfite sequencing, 9403428, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer

value: Female


title: dhh1delta_3_csm_t0

description: Library name: dhh1delta_3_csm_t0

value: Pulse for 1 h and chase for 0 min


title: AN00331.insula


title: CGNs, shKDM6B Cat Rescue 4

value: shKDM6B Cat Rescue


title: Targeted bisulfite sequencing, 9408734, Normal thyroid tissue

description: paired-end 101bp

value: N


title: dhh1delta_2_csm_t15

description: Library name: dhh1delta_2_csm_t15

value: dhh1delta(MATa his3delta1 leu2delta0 met15delta0 ura3delta0 dhh1delta)


title: Targeted bisulfite sequencing, 9408734, Tumor

description: paired-end 101bp


title: AN02671.insula


title: dhh1delta_2_csm_t30

description: Library name: dhh1delta_2_csm_t30

value: Pulse for 1 h and chase for 30 min


title: CGNs, shKDM6B Cat Rescue 5

value: Cerebellar granule neurons


title: AN15823.insula


title: dhh1delta_2_csm_t0

description: Library name: dhh1delta_2_csm_t0


title: CGNs, shKDM6B Cat Rescue 2


title: AN17896.insula


title: Targeted bisulfite sequencing, 9402448, Tumor

description: paired-end 101bp


title: Targeted bisulfite sequencing, 9412424, Tumor

description: paired-end 101bp


title: dhh1delta_1_csm_t30

description: Library name: dhh1delta_1_csm_t30


title: AN12979.insula


title: dhh1delta_1_csm_t15

description: Library name: dhh1delta_1_csm_t15

value: Pulse for 1 h and chase for 15 min


title: CGNs, shKDM6B 5


title: AN08675.insula


title: AN08855.insula


title: CGNs, shKDM6B 3


title: dhh1delta_1_csm_t0

description: Library name: dhh1delta_1_csm_t0

value: yeast cells


title: Targeted bisulfite sequencing, 9416346, Tumor

description: paired-end 101bp


title: CGNs, shKDM6B 4


title: Targeted bisulfite sequencing, 9412424, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: Targeted bisulfite sequencing, 9420735, Normal thyroid tissue

description: paired-end 101bp


title: CGNs, shKDM6B Cat Rescue 3


title: dcp2delta_3_ypd_t15

description: Library name: dcp2delta_3_ypd_t15

value: DCP2-7::KanR;  his3delta1 leu2delta0 ura3delta0 met15delta0


title: dcp2delta_3_ypd_t30

description: Library name: dcp2delta_3_ypd_t30


title: Targeted bisulfite sequencing, 9423358, Normal thyroid tissue

description: paired-end 101bp


title: Targeted bisulfite sequencing, 9420735, Tumor

description: paired-end 101bp


title: CGNs, shKDM6B 1


title: CGNs, shKDM6B 2


title: AN08013.insula

value: female


title: AN06400.insula

value: Post mortem brain


title: CGNs, shKDM6B Cat Rescue 1


title: dcp2delta_3_ypd_t0

description: Library name: dcp2delta_3_ypd_t0


title: CGNs, Control 5

value: Control


title: Targeted bisulfite sequencing, 9423358, Tumor

description: paired-end 101bp


title: AN06429.insula

value: insula

value: control


title: Targeted bisulfite sequencing, 9416346, Normal thyroid tissue

description: paired-end 101bp


title: dcp2delta_2_ypd_t15

description: Library name: dcp2delta_2_ypd_t15


title: dcp2delta_2_ypd_t30

description: Library name: dcp2delta_2_ypd_t30


title: Targeted bisulfite sequencing, 9424511, Normal thyroid tissue

description: paired-end 101bp


title: CGNs, Control 4


title: AN01733.insula


title: Targeted bisulfite sequencing, 9424511, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: AN02737.insula

value: male


title: dcp2delta_2_ypd_t0

description: Library name: dcp2delta_2_ypd_t0

value: Pulse for 1 h and chase for 0 min


title: AN05086.BA32


title: CGNs, Control 3


title: dcp2delta_1_ypd_t30

description: Library name: dcp2delta_1_ypd_t30


title: Targeted bisulfite sequencing, 9427250, Normal thyroid tissue

description: paired-end 101bp

value: Female

value: Y


title: Targeted bisulfite sequencing, 9427250, Tumor

description: paired-end 101bp


title: AN00331.BA32


title: dcp2delta_1_ypd_t15

description: Library name: dcp2delta_1_ypd_t15


title: CGNs, Control 2


title: AN07243.BA32


title: Targeted bisulfite sequencing, 9430026, Normal thyroid tissue

description: paired-end 101bp

value: Male

value: N


title: dcp2delta_1_ypd_t0

description: Library name: dcp2delta_1_ypd_t0


title: scRNAseq of CD8+ TILs from human melanoma tumors

first: Or-Yam

middle: GENERAL

last: Revach

address: 55 fruit street

institute: MGH

description:
Library name: Sample 1
melanoma CD8+ TILs expression data

library_source: transcriptomic single cell

data_processing:
Samples were sequenced on a NextSeq 500 sequencer (Illumina), and the data was preprocessed using Cell Ranger v7.0.0
Assembly: GRCh38-2020-A
Supplementary files format and content: CD8.normalized.data.rds.gz

source_name: melanoma tumor

extract_protocol:
Tumors were rapidly dissociated after the surgical procedure using the Miltenyi Biotec Human Tumor Dissociation kit (cat# 130-095-929). Each lesion was minced into 1-2mm fragments with surgical scissors in a separate 1.5ml Eppendorf tube containing 932µl DMEM, 42µl of enzyme H, 21µl od enzyme R, and 5µl of enzyme A. Next, tubes were briefly vortexed and placed in a thermomixer for 15 minutes at 37°C, 350rpm. Finally, the dissociated samples were washed through a 50µm filter and counted using a manual hemocytometer to determine cell viability and concentration.
Libraries were constructed using the VDJ NextGEM v2 10x Genomics Chromium kit according to the manufacturer's instructions. Assessment of libraries quality was performed after cDNA and library generation, measuring the nucleic-acid concentration (Qubit dsDNA High Sensitivity kit; Invitrogen, cat# Q32854) and size distribution (High Sensitivity BioA DNA kit; Agilent, cat# 5067-4626).

value: melanoma tumor

value: CD8+ T cells


title: Targeted bisulfite sequencing, 9430026, Tumor

description: paired-end 101bp


title: AN02671.BA32


title: AN08675.BA32


title: dcp2delta_3_csm_t15

description: Library name: dcp2delta_3_csm_t15

value: yeast cells

value: Pulse for 1 h and chase for 15 min


title: GM58 D100 sAD E3_TRN_1_biolRepl_3

city: Brno

first: Katerina

last: Amruz Cerna

state: Czech Republic

address: Kamenice 3

department: Department of Histology and Embryology

country: Czech Republic

institute: Faculty of Medicine, Masaryk University

description: Library name: GM58_E3_TRN_1

data_processing:
The raw reads were initially trimmed using Trimmomatic (Bolger et al., 2014) and subsequently mapped to the human reference genome hg38 with STAR (v.2.7.3) (Dobin et al., 2013).
Transcript-level expression quantification was carried out using RSEM (Dobin et al., 2013), with results aggregated at the gene level according to GENCODE (v.30) (Frankish et al., 2019).
RNA-SeqQC (DeLuca et al., 2012) and  Picard (v2.2.4) tools were employed to assess the quality control metrics, which included the number of aligned reads (minimum average of 8.740 ± 0.593 million), the fractions of duplicate reads (0.723 ± 0.057), the fractions of uniquely mapped reads (0.75 ± 0.020), and the mean GC content (40.597% ± 0.630%).
Assembly: The raw reads were initially trimmed using Trimmomatic (Bolger et al., 2014) and subsequently mapped to the human reference genome hg38 with STAR (v.2.7.3) (Dobin et al., 2013).
Supplementary files format and content: To identify genes that showed differential expression between treatments (NTR/TRN/TMP), a differential gene expression (DGE) analysis was performed.
Supplementary files format and content: The read count matrix was adjusted for technical confounders, i.e., sequencing batch and two principal components (PC1 and PC2) calculated on the matrix of 15 sample-level covariates including the fractions of intronic/intergenic/mRNA/coding/ribosomal bases, fractions of uniquely mapped reads / duplicate reads, mean GC content, estimated fractions of GABAergic neurons / glutamatergic neurons / astrocytes / oligodendrocytes, the fractions of uniquely mapped reads, chimeric reads and too-short reads.
Supplementary files format and content: Normalized counts for each sample are counted in the .csv table.

source_name: cerebral organoids

growth_protocol: With a few modifications, the generation of COs followed the protocol described in (Vanova et al., 2023; Camp et al., 2015; Lancaster and Knoblich, 2014).

extract_protocol:
RNA was isolated with RNABlue (TopBio, R013)  combined with column extraction with Dnase I pretreatment (Direct-zol RNA Microprep kit (ZymoResearch)). 300 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared with QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD and Lexogen i5 6 nt Unique Dual Indexing Add-on Kit (Lexogen) with 14 - 18x PCR cycles according to the manufacturer’s instructions.

treatment_protocol:
The treatment with TRN or TMP was performed for 50 days, from day 50 (D50) to day 100 (D100).
During the treatment, CODM was continuously supplemented with 100 µM TRN or 100 µM tramiprosate diluted in the cell culture medium.
Samples were harvested from two independent batches of CO differentiation. Control samples (NTR) were treated with medium only.

value: cerebral organoids

value: iPSC cell lines

value: taurine


title: Targeted bisulfite sequencing, 9430426, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: GM58 D100 sAD E3_TMP_1_biolRepl_3

description: Library name: GM58_E3_TMP_1

value: tramiprosate


title: dcp2delta_3_csm_t0

description: Library name: dcp2delta_3_csm_t0

value: DCP2-7::KanR;  his3delta1 leu2delta0 ura3delta0 met15delta0


title: Targeted bisulfite sequencing, 9430426, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: GM58 D100 sAD E3_NTR_1_biolRepl_3

description: Library name: GM58_E3_NTR_1

value: non-treated


title: AN08855.BA32

value: Post mortem brain

value: control

value: male


title: dcp2delta_3_csm_t30

description: Library name: dcp2delta_3_csm_t30

value: Pulse for 1 h and chase for 30 min


title: AN12979.BA32


title: Targeted bisulfite sequencing, 943119, Normal thyroid tissue

description: paired-end 101bp

value: Female

value: N


title: GM57 D100 sAD E4_TMP_1_biolRepl_3

description: Library name: GM57_E4_TMP_1


title: dcp2delta_2_csm_t15

description: Library name: dcp2delta_2_csm_t15


title: AN02737.BA32


title: CGNs, Control 1

value: Cerebellar granule neurons

value: Control


title: AN06400.BA32

value: female


title: GM57 D100 sAD E4_TRN_1_biolRepl_3

description: Library name: GM57_E4_TRN_1

value: cerebral organoids


title: Targeted bisulfite sequencing, 943119, Tumor

description: paired-end 101bp


title: dcp2delta_2_csm_t0

description: Library name: dcp2delta_2_csm_t0

value: yeast cells

value: Pulse for 1 h and chase for 0 min


title: GM57 D100 sAD E4_NTR_1_biolRepl_3

description: Library name: GM57_E4_NTR_1

value: iPSC cell lines


title: Targeted bisulfite sequencing, 9443038, Tumor

description: paired-end 101bp


title: AN04446.BA32


title: dcp2delta_1_csm_t30

description: Library name: dcp2delta_1_csm_t30


title: AN01733.BA32


title: GM51 D100 sAD E4_TMP_2_biolRepl_2

description: Library name: GM51_E4_TMP_2

value: tramiprosate


title: Targeted bisulfite sequencing, 9443516, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: AN06954.insula

value: insula

value: AD


title: GM51 D100 sAD E4_NTR_2_biolRepl_2

description: Library name: GM51_E4_NTR_2

value: non-treated


title: dcp2delta_1_csm_t0

description: Library name: dcp2delta_1_csm_t0

value: DCP2-7::KanR;  his3delta1 leu2delta0 ura3delta0 met15delta0


title: Targeted bisulfite sequencing, 9443516, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer


title: GM51 D100 sAD E4_TRN_2_biolRepl_2

description: Library name: GM51_E4_TRN_2

value: taurine


title: dcp2delta_1_csm_t15

description: Library name: dcp2delta_1_csm_t15

value: Pulse for 1 h and chase for 15 min


title: AN05918.insula

value: Post mortem brain

value: male


title: Targeted bisulfite sequencing, 9444981, Normal thyroid tissue

description: paired-end 101bp

value: Female

value: N


title: dcp2delta_2_csm_t30

description: Library name: dcp2delta_2_csm_t30

value: Pulse for 1 h and chase for 30 min


title: srna_AID_CSR1_1mM_rep4

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

library_source: other

data_processing:
Reads were first trimmed to remove adapter sequences using Trim Galore (Krueger et al., 2012), with options --illumina --max_length 35 --length 18 -q 0 --stringency 3: this retains only reads between 18-35 bp post-trimming.
Reads were further split according to size: 22 bp (CSR-1 and WAGO siRNAs plus miRNAs), 21 bp (PRG-1 piRNAs) and 26 bp (ERGO-1 and ALG-3/4-dependent siRNAs), and aligned to ce10 using bowtie2 (Langmead and Salzberg, 2012) in --end-to-end --very-sensitive mode.
Uniquely mapped reads were extracted (mapQ >= 2), and converted into strand-specific coverage tracks using DeepTools (Ramírez et al., 2016) bamCoverage --binSize 10 --normalizeUsing CPM --filterRNAstrand [forward/reverse]. Counts over genes were obtained using the htseq-count function from the HTSeq python package (Anders et al., 2015) v2.0.2 with options --nonunique none -m intersection-strict, and using the WS230 C. elegans annotations, and log2(fold change) estimates between wild-type and mutants were estimated using DESeq2 (Love et al., 2014).
TPM values were calculated using StringTie with the WS230 annotations, with options -e -s1 -t --rf.
Assembly: ce10/WBcel215
Supplementary files format and content: srnaseq_raw_counts.txt contains the raw counts for each library obtained from htseq-count. Both genes and TEs are included.
Supplementary files format and content: srnaseq_processed_data.txt contains TPM estimates from stringtie for all libraries. This file also contains DESeq2 estimates of log2 fold change and adjusted p-value estimates for comparisons between (1) csr1(G560R) and N2, and (2) aid::csr-1 treated with 0mM auxin vs. 1mM auxin.

molecule: other

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: C.elegansstrains were maintained using standard procedures at 15°C or 20°C (Brenner, 1974) unless indicated otherwise. In all cases, Bristol N2 strain was used as the wild-type control. Worms were fed OP50E.colifor all experiments except ChIP-seq and those involving RNAi. Worms for ChIP were fed HB101 E.coli and worms for RNAi experiments were fed with HT115E.coli.

extract_protocol:
Worms were collected in TriReagent (Thermo Fisher Scientific) and were subjected to three freeze-thaw cycles. Phase separation was achieved via 1-bromo-3-chloropropane (BCP) and the aqueous phase was precipitated in isopropanol at -80°C for 2 hrs. To pellet RNA, samples were centrifuged at 21,000 x g for 30 min at 4°C. The pellet was washed three times in 75% ethanol then resuspended in water.
Small RNA-seq libraries were made using the NEBNext Multiplex Small RNA Library Prep Set (NEB) according to manufacturer’s instructions. All RNA libraries were sequenced on the NovaSeq6000 Sequencer (Illumina).

treatment_protocol: In experiments in which auxin (3-indoleacetic acid) (Sigma-Aldrich) was used, NGM plates were poured containing the indicated concentration of auxin. In ChIP-seq experiments in which worms were grown in liquid culture, the auxin was added directly to the cultures.

value: whole worms

value: 1 mM auxin


title: Targeted bisulfite sequencing, 9444981, Tumor

description: paired-end 101bp


title: AN11698.insula


title: srna_AID_CSR1_0mM_rep4

value: 0 mM auxin


title: Targeted bisulfite sequencing, 9443038, Normal thyroid tissue

description: paired-end 101bp


title: AN00561.insula


title: GM51 D100 sAD E3_TRN_1_biolRepl_2

description: Library name: GM51_E3_TRN_1

value: cerebral organoids

value: iPSC cell lines


title: GM51 D100 sAD E3_NTR_2_biolRepl_2

description: Library name: GM51_E3_NTR_2


title: srna_G560R_rep4


title: Targeted bisulfite sequencing, 9594391, Normal thyroid tissue

description: paired-end 101bp

value: Normal thyroid


title: AN17703.insula

value: insula

value: AD


title: srna_N2_rep4


title: AN07534.insula


title: C5_Ni_0mM_D5

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

description: Library name: C5_D5

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (Bolger, Lohse, and Usadel 2014) (version 0.39) using the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:12 MINLEN:20.
Trimmed sequences were mapped to the C. merolae reference genome provided by ENSEMBL, (version ASM9120v1) using Hisat2 (Kim, Langmead, and Salzberg 2015) with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK (McKenna et al. 2010) package (version 4.2.3.0) with default parameters except OPTICAL_DUPLICATE_PIXEL_DISTANCE set to 12000.
Mapped reads were associated with transcripts from Ensembl (Zerbino et al. 2018) (version 54) using HTSeq-count (Anders, Pyl, and Huber 2015) (version 0.9.1) with default parameters except –stranded set to “reverse”.
Differentially expressed genes were selected using the DESeq2 package (Love, Huber, and Anders 2014) (version 1.38.3).
Assembly: C. merolae ASM9120v1
Supplementary files format and content: Counts generated by Htseq-count

organism: Cyanidioschyzon merolae

source_name: algal cell

growth_protocol: The microalgae culture was cultivated in a Panasonic® Plant Growth Chamber (FL40SS-ENW/37H) using a modified 2x Allen medium (Allen 1959). Cell suspensions (125 mL) were grown at pH 2.5, in continuous white light of 90 µE m-2 s-1 intensity (400-700 nm), with gentle shaking (110 rpm), at 42°C. These conditions were maintained throughout the experiment.

extract_protocol:
Microalgae cell suspensions were centrifuged at 2,200 g for 15 min at 4°C. Then, the samples were frozen and stored at -80°C. RNA extraction was performed using TRIzol reagent (Invitrogen, Carlsbad, CA, USA).
RNA-Seq

treatment_protocol: At the onset of each experiment, the stock C. merolae inoculum, NiSO4 6(H2O) and an adequate volume of the modified 2x Allen culture medium were mixed to reach the cell suspension optical density (OD) at 750 nm of 0.15.

value: algal cell

tag: strain

tag: time


title: GM47 D100 sAD E4_TMP_2_biolRepl_1

description: Library name: GM47_E4_TMP_2

value: tramiprosate


title: GM47 D100 sAD E4_TRN_2_biolRepl_1

description: Library name: GM47_E4_TRN_2

value: taurine


title: C5_Ni_0mM_D10

description: Library name: C5_D10


title: srna_AID_CSR1_1mM_rep2


title: srna_AID_CSR1_0mM_rep2


title: GM47 D100 sAD E4_NTR_2_biolRepl_1

description: Library name: GM47_E4_NTR_2

value: non-treated


title: AN08533.insula

value: Post mortem brain


title: GM51 D100 sAD E3_TMP_2_biolRepl_2

description: Library name: GM51_E3_TMP_2


title: C4_Ni_0mM_D5

description: Library name: C4_D5


title: GM47 D100 sAD E3_TMP_2_biolRepl_1

description: Library name: GM47_E3_TMP_2


title: srna_G560R_rep2


title: AN08122.insula

value: male


title: C4_Ni_0mM_D15

description: Library name: C4_D15


title: AN07275.insula


title: srna_N2_rep2


title: srna_AID_CSR1_1mM_rep1


title: GM47 D100 sAD E3_NTR_2_biolRepl_1

description: Library name: GM47_E3_NTR_2


title: C3_Ni_0mM_D5

description: Library name: C3_D5


title: AN06897.insula


title: Targeted bisulfite sequencing, 9594391, Tumor

description: paired-end 101bp

value: Papillary thyroid cancer

value: Female


title: C4_Ni_0mM_D0

description: Library name: C4_D0


title: GM47 D100 sAD E3_TRN_2_biolRepl_1

description: Library name: GM47_E3_TRN_2


title: srna_AID_CSR1_0mM_rep1


title: H358 Drug, scATACseq

city: New York

first: Hideo

last: Watanabe

state: NY

address: One Gustave L. Levy Place

department: Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
10x genomics
H358AMGD8_fragments.tsv.gz

library_source: genomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using default Cell Ranger settings for scATAC-seq
Assembly: hg38
Supplementary files format and content: tsv, fragment files

extract_protocol:
DTP cells or untreated control cells were washed twice with PBS to remove dead floating cells. All cells were trypsinized and collocted. Cell pallete were resuspend at a concentration of 1 million cells/ml in PBS +0.04% BSA
Libruary was performed according to manufactor's instruction. Briefly,  Single Nuclei were isolated from the cell sample using standard procedures of microfluidics-based techniques. Transposition reaction were perform for the tagmentation of DNA and barcode incorporation using the Tn5 transposase enzyme according to the manufacturer's. Amplify the tagmented DNA fragments by PCR to generate scATAC-seq libraries.

value: tumor cell line

value: 500nM Sotorasib for 8days


title: srna_G560R_rep1

value: whole worms


title: AN16022.insula


title: AN01535.insula


title: AN11711.insula


title: C3_Ni_0mM_D10

description: Library name: C3_D10


title: PC9 Drug, library4, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz

value: 150nM Osimertinib for 11days


title: C2_Ni_0mM_D0

description: Library name: C2_D0


title: rna_morcOE_L2F2_neo_rep3

data_processing:
Sequencing data were first checked for quality using fastqc v0.11.8
Reads were filtered and trimmed to remove poor quality sequences and adapter sequences using Trim Galore v0.6.7 with options --stringency 3 -q 25 --length 20
Reads were aligned to ce10/WBcel215 with the WS230 annotations, obtained from WormBase (https://wormbase.org) using STAR v2.7.9a with options --outFilterMismatchNoverReadLmax 0.05 --alignIntronMin 70 --alignIntronMax 5000 --alignMatesGapMax 100000 --outFilterIntronMotifs RemoveNoncanonical --alignEndsType EndToEnd
PCR duplicates were removed using MarkDuplicates from the Picard tools suite.
Counts over genes were obtained using the htseq-count function from the HTSeq python package v2.0.2 with options --nonunique none -m intersection-strict, and using the WS230 C. elegans annotations.
Assembly: ce10/WBcel215
Supplementary files format and content: tab-delimited text file contains a matrix of all the raw counts for each library obtained from htseq-count. Both genes and TEs are included. Rows represent genes/TEs, columns represent samples.

molecule: polyA RNA

growth_protocol: C.elegansstrains were maintained using standard procedures at 15°C or 20°C unless indicated otherwise. In all cases, Bristol N2 strain was used as the wild-type control. Worms were fed OP50E.coli. Worms were shifted to 25 C for all RNA-seq experiments.

extract_protocol:
Worms were collected in TriReagent (ThermoFisher) and were subjected to three freeze-thaw cycles. Phase separation was achieved via 1-bromo-3-chloropropane (BCP) and the aqueous phase was precipitated in isopropanol at -80°C for 2 hrs. To pellet RNA, samples were centrifuged at 21,000 x g for 30 min at 4°C. The pellet was washed three times in 75% ethanol then resuspended in water.
RNA-seq libraries were generated using the KAPA stranded mRNA-seq kit (Roche) according to the manufacturer’s instructions.

treatment_protocol: In experiments in which auxin (3-indoleacetic acid) (Sigma-Aldrich) was used, NGM plates were poured containing the indicated concentration of auxin.

value: morcOE

value: neomycin

tag: batch

tag: mcherry status


title: AN07668.insula

tag: tissue


title: AN02028.insula


title: C1_Ni_0mM_D10

description: Library name: C1_D10


title: PC9 Drug, library2, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz


title: PC9 Drug, library3, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz


title: C1_Ni_0mM_D15

description: Library name: C1_D15


title: rna_morcOE_L2F2_ChON_rep3

tag: genotype

value: ON


title: AN13062.insula

value: insula


title: 3E_Ni_3mM_D5

description: Library name: 3E_D5

tag: treatment


title: C1_Ni_0mM_D0

description: Library name: C1_D0


title: PC9 Drug, library1, scATACseq

description:
10x genomics
PC9Osi_fragments.tsv.gz

tag: cell line


title: H358 Ctrl, scATACseq

description:
10x genomics
H358DMSO_fragments.tsv.gz

tag: cell type

value: without treatment


title: PC9 Ctrl, library2, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz


title: AN07311.insula

value: AD

tag: Sex


title: rna_morcOE_L1F2_ChOFF_rep3

value: OFF


title: PC9 Ctrl, library4, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz


title: C3_Ni_0mM_D15

description: Library name: C3_D15

value: algal cell


title: rna_morcOE_L2F1_neo_rep3


title: 3E_Ni_3mM_D15

description: Library name: 3E_D15


title: AN13493.insula

value: female


title: PC9 Ctrl, library3, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz


title: 3D_Ni_3mM_D5

description: Library name: 3D_D5


title: AN15043.insula

value: Post mortem brain


title: rna_morcOE_L2F1_rep3


title: rna_morcOE_L2F2_ChOFF_rep3


title: srna_N2_rep1


title: PC9 Ctrl, library1, scATACseq

description:
10x genomics
PC9Ctrl_fragments.tsv.gz


title: AN00675.insula

value: male


title: 3D_Ni_3mM_D15

description: Library name: 3D_D15


title: rna_morcOE_L1F1_rep3


title: AN11178.insula


title: AN05080.insula


title: 3C_Ni_3mM_D5

description: Library name: 3C_D5


title: rna_morcOE_P0_neo_rep3


title: PC9 and H358, scRNAseq (GEX)

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using default Cell Ranger settings
Assembly: hg38
Supplementary files format and content: tsv, matrix files

source_name: PC9 and NCI-H358

extract_protocol:
DTP cells or untreated control cells were washed twice with PBS to remove dead floating cells. All cells were trypsinized and collocted. Cell pallete were resuspend at a concentration of 1 million cells/ml in PBS +0.04% BSA
Libruary was performed according to manufactor's instruction. Briefly,  different samples were labeled with barcoded antibodies and conbined to one scRNAseq sample(cell hashing). Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead in emulsion. the poly A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, unique molecular identifier, and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with silane dynabeads, amplified by PCR and the appropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequence and a sample index were added.

value: PC9 and NCI-H358

value: untreated, 150nM Osimertinib treated for 4 or 11 days, or 500nM Sotorasib treated for 8 days


title: AN09220.insula


title: rna_morcOE_P0_rep3


title: PC9 non-target sgRNA2, H3K27me3, ChIP

data_processing:
macs2 callpeak --broad --broad-cutoff 0.1 --nolambda
Assembly: hg38
Supplementary files format and content: Bed, BroadPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 minutes. After quenching and cell lysis, chromatin was sonicated for 6 minute using QSONICA
Protein G magnetic beads and indicated antibodies were used to immunoprecipitated the DNA fragment. 10 ng DNA was used for the library construction using NEBNext Ultra II DNA Library Prep Kit complemented with DNA barcode primers. Libraries were amplified using PCR, and purified  by AMPure beads. Libraries were validated using the Agilent High sensitivity kit

value: 150nM Osimertinib for 4 days


title: AN13338.insula


title: PC9 non-target sgRNA1, H3K27me3, ChIP


title: rna_morcOE_ctrl_rep3


title: 3B_Ni_3mM_D10

description: Library name: 3B_D10


title: rna_morcOE_L2F2_ChOFF_rep2


title: PC9 non-target sgRNA2, H3K9me3, ChIP

value: H3K9me3 (Abcam, #ab8898)


title: AN18637.insula


title: rna_morcOE_L2F2_neo_rep2

value: whole worms


title: PC9 non-target sgRNA1, H3K9me3, ChIP


title: rna_morcOE_L1F2_ChON_rep3


title: AN11052.insula


title: rna_morcOE_L2F2_ChON_rep2


title: AN18056.insula


title: PC9 and H358, cell hashing (HTO)

description: 10x genomics

value: tumor cell line


title: 1E_Ni_1mM_D15

description: Library name: 1E_D15


title: 3A_Ni_3mM_D10

description: Library name: 3A_D10


title: Failing Sample 6 [HRT-F6_S12]

city: Pittsburgh

first: Heth

last: Turnquist

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench
Assembly: hg38
Supplementary files format and content: tab-delimited txt file including total counts and CPM data for each sample

source_name: Left ventricle

extract_protocol:
RNA was isolated using the Qiagen miRNeasy Mini Kit according to the manufacturers instructions
miRNA libraries were prepared using the QIAseq miRNA Library Kit

value: Left ventricle

value: Failing


title: 1D_Ni_1mM_D10

description: Library name: 1D_D10


title: Failing Sample 5 [HRT-F5_S11]


title: rna_morcOE_L2F1_neo_rep2

value: morcOE

value: neomycin


title: AN11669.insula

value: insula


title: 1C_Ni_1mM_D5

description: Library name: 1C_D5


title: rna_morcOE_L2F1_rep2


title: Failing Sample 4 [HRT-F4_S10]


title: 3C_Ni_3mM_D15

description: Library name: 3C_D15


title: 3C_Ni_3mM_D10

description: Library name: 3C_D10


title: rna_morcOE_L1F2_neo_rep2


title: Failing Sample 3 [HRT-F3_S9]


title: 1C_Ni_1mM_D15

description: Library name: 1C_D15


title: 1B_Ni_1mM_D5

description: Library name: 1B_D5


title: AN11050.insula

value: AD


title: rna_morcOE_L1F2_ChOFF_rep2

value: OFF


title: AN11729.insula


title: rna_morcOE_L1F2_ChON_rep2

value: ON


title: AN13841.insula

value: female


title: Failing Sample 2 [HRT-F2_S8]


title: Failing Sample 1 [HRT-F1_S7]


title: rna_morcOE_L1F1_neo_rep2


title: AN08338.insula

value: Post mortem brain


title: Healthy Sample 6 [HRT-H6_S6]

value: Healthy/non-failing


title: 1A_Ni_1mM_D5

description: Library name: 1A_D5

value: algal cell


title: AN03989.insula


title: Healthy Sample 5 [HRT-H5_S5]


title: 1A_Ni_1mM_D10

description: Library name: 1A_D10


title: rna_morcOE_L1F1_rep2


title: rna_morcOE_P0_neo_rep2


title: Healthy Sample 4 [HRT-H4_S4]


title: Aconitum_japonicum_Rootlet

city: Chiba

first: Mami

last: Yamazaki

state: Chiba

address: 1-8-1 Inohana, Chuo-ku, Chiba City Pharmaceutical Research Building II

department: Department of Molecular Biology and Biotechnology

institute: Chiba University

data_processing:
We pre-processed raw reads, and removed adapter sequences, empty reads, reads with ambiguous ‘N’ bases > 5%, raw reads of low quality (Q<20), and raw reads with an average length less than 30 bases. Filtering of raw reads was performed using Trimmomatic program (Bolger et al., 2014), resulting into paired end raw reads, and unpaired reads which lost its corresponding sequence partner due to quality control.
Assembly: The Trinity program ver 3.0 was used for the de novo transcriptome assembly using clean reads from all the samples. Trinity program derived de novo transcriptome assembly was further processed through CD-HIT-EST program (Li and Godzik 2006) to remove transcripts redundancies, resulting in our final assembly of 129,760 unigenes with N50 value as 811bps. We then processed these contigs for read alignment and abundance estimation using Bowtie2.0 (Langmead et al., 2009) and RSEM (Li et al., 2011), respectively. To calculate unigene expression, we used Fragments per Kilobase exon per Million mapped fragments (FPKM) method. FASTA file is available on the series record.
Supplementary files format and content: Leaf_Aj_FPKM.csv
Supplementary files format and content: It is a .csv file containing FPKM values of the transcripts in the leaf
Supplementary files format and content: Mother_Root_Aj_FPKM.csv
Supplementary files format and content: It is a .csv file containing FPKM values of the transcripts in the mother root
Supplementary files format and content: Daughter_Root_Aj_FPKM.csv
Supplementary files format and content: It is a .csv file containing FPKM values of the transcripts in the daughter root
Supplementary files format and content: Rootlet_Aj_FPKM.csv
Supplementary files format and content: It is a .csv file containing FPKM values of the transcripts in the rootlet
Supplementary files format and content: Aconitum_japonicum_all_tissues_FPKM_values
Supplementary files format and content: It is a .txt file containing FPKM values of the transcripts in all the tissues

organism: Aconitum japonicum

source_name: Rootlet

growth_protocol: All four tissues, namely leaf, mother root, daughter root, and rootlet were harvested from A. japonicum growing at Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido

extract_protocol:
Frozen samples of A. japonicum were powdered using a Multi Beads Shocker (Yasui Kikai, Japan) for subsequent RNA extraction. Total RNA for each of the four tissues was extracted using RNeasy Plant Mini Kit (Qiagen, USA), according to the manufacturer’s instruction.
cDNA library was then prepared using SureSelect Strand Specific RNA Library kit (Agilent 150 Technologies, USA) according to the manufacturer’s specifications. mRNA was isolated from total RNA of each tissue using beads containing oligo(dt), which was then added with fragmentation buffer to shear mRNA into short fragments and used as a template for the synthesis of first strand cDNA synthesis using random hexamer primers. The cDNA library for Illumina sequencing was prepared using SureSelect Strand Specific RNA Library kit (Agilent, USA) according to the manufacturer’s instruction.

value: Rootlet


title: AN14331.insula


title: Aconitum_japonicum_Daughter_Root

description: Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido

source_name: Daughter Root

value: Daughter Root


title: AN18901.insula


title: Healthy Sample 3 [HRT-H3_S3]


title: AN03564.insula


title: Aconitum_japonicum_Mother_Root

source_name: Mother Root

value: Mother Root


title: 1B_Ni_1mM_D10

description: Library name: 1B_D10


title: AN07303.insula


title: rna_morcOE_ctrl_rep2

value: whole worms


title: Aconitum_japonicum_Leaf

source_name: Leaf

value: Leaf


title: Healthy Sample 1 [HRT-H1_S1]

value: Left ventricle


title: rna_morcOE_L2F2_neo_rep1


title: AN05797.insula


title: AN14576.insula


title: rna_morcOE_L2F2_ChOFF_rep1


title: Healthy Sample 2 [HRT-H2_S2]


title: AN06706.insula


title: 01_0GAO_027HUAMS_JE-1B16-GLU_input_mm_i84

city: Little Rock

middle: Anton

last: Bauer

state: United States

address: 4301 W Markham  Slot 782

department: Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: Library name: GLU_input

data_processing:
bcl2fastq2 (v2.20)
reads aligned using bwa (v0.7.12)
The 5′-ends of aligned reads were extended to 200 bp to approximate ChIP fragment lengths. Fragment density was then calculated in 32-nt genomic bins, and the resulting signal map was stored as a bigWig (wigToBigWig v4) file for genome browser visualization.
Assembly: mm10
Supplementary files format and content: bw files contatining read coverage for each sample

source_name: skin

growth_protocol: 20 million B16F10 cells growing under GLU or GAL conditions were fixed in 1.1% PFA solution for 15 minutes.

extract_protocol:
According to Active Motif protocol, cells were lysed, sonicated, and then DNA-protein complexes were isolated with antibodies. Samples were reverse-crosslinked and DNA was purified.
DNA Library Prep Kit for Illumina (Cat. No. 53220)

value: skin

value: Cells were cultured under normal glucose (GLU) conditions


title: AN12633.insula


title: rna_morcOE_L2F2_ChON_rep1

value: morcOE


title: AN13999.insula

value: insula


title: Exp5,iNKT (ATOCs) and PITL enriched population  (ATOCs) sorts, VDJ

city: Hannover

first: Ahmed

last: Hassan

address: Carl-Neuberg-Straße 1

country: Germany

institute: Hannover Medical School

data_processing:
Cellranger-7.0.1
Assembly: mm10-2020-A, vdj-GRCm38-alts-ensembl-7.0.0
Supplementary files format and content: Cellranger output file: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cellranger output file: airr_rearrangement.tsv

source_name: Thymus

extract_protocol:
Cell were sorted and mixed then used to generate 5’end V1.1 or V2 GEMs following 10x genomics protocol
Following the recommendation of 10x genomics

value: Thymus


title: rna_morcOE_L2F1_neo_rep1

value: neomycin


title: rna_morcOE_P0_rep2


title: rna_morcOE_L2F1_rep1


title: Exp5,iNKT (ATOCs) and PITL enriched population  (ATOCs) sorts, HTO_ADT

molecule: protein


title: Exp6,Total live cells (ATOCs) sorts, VDJ


title: 04_0GC2_027HUAMS_s2-JE-2-B16-GAL_H3K27me3_mm_i64

description: Library name: GAL_H3K27me3

value: Cells were cultured under glucose-deprived (GAL) replaced with galactose conditions


title: AN06954.BA32

value: AD

value: male


title: Exp6,Total live cells (ATOCs) sorts, GEX


title: rna_morcOE_P0_neo_rep1


title: AN05918.BA32

value: Post mortem brain


title: m6A-RNA, IA-KA injected mice, 2weeks, mouse 9

city: Dublin 4

first: Justine

last: Mathoux

address: Belfield

country: Ireland

institute: FutureNeuro Research Center

description: Library name: KA 2weeks9

data_processing:
fastq files were uploaded to Biojupies website for further analysis (Torre, D., Lachmann, A., and Ma’ayan, A. (2018). BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. Cell Systems.)
Assembly: mm10
Supplementary files format and content: tab delimited text files

source_name: Hippocampus

extract_protocol:
Trizol extraction of totalRNA and then m6A-immunoprecipitation of 5ug total RNA for polyA-RNA. 10ng of m6A-samples or 50ng of totalRNA (INPUT) were used for the library construction.
SMARTer® Stranded Total RNA-Seq Kit v2.

value: Hippocampus


title: rna_morcOE_P0_rep1


title: m6A-RNA, IA-KA injected mice, 2weeks, mouse 7

description: Library name: KA 2weeks7


title: Exp6,Total live cells (ATOCs) sorts, HTO_ADT


title: AN11698.BA32


title: 03_0GC1_027HUAMS_s1-JE-1-B16-GLU_H3K27me3_mm_i57

description: Library name: GLU_H3K27me3


title: rna_morcOE_ctrl_rep1


title: m6A-RNA, IA-KA injected mice, 2weeks, mouse 21

description: Library name: KA 2weeks21


title: bsubs_minimal-media_rep3

last: zhang

address: Tomtebodavägen 23

institute: Karolinska institutet

data_processing:
Base-calling was done using bcl2fastq v2.20.0.422  and for demultiplex, we allowed one mismatch in index1 and one mismatch in index2
HT5Pseq reads were demultiplexed using bcl2fastq (v2) and  trimmed 3’-sequencing adapter using cutadapt V1.16 (http://gensoft.pasteur.fr/docs/cutadapt/1.6/index.html). After that the 8-nt random barcodes located on the 5´ ends of reads were extracted and added to the fastq file header as UMIs using UMI-tools (Smith, Heger and Sudbery, 2017). Reads were mapped to the reference genome (SGD R64-1-1 for S. cerevisiae genome, GCF_000009045.1_ASM904v1 for B. subtilis  genome) by star/2.7.0 (Dobin et al., 2013) with the parameter --alignEndsType Extend5pOfRead1 to exclude soft-clipped bases on the 5´ end. Duplicated 5´ ends of read introduced by PCR during library preparation were removed based on random barcodes sequences using UMI-tools (Smith, Heger and Sudbery, 2017).
Analysis of 5´ ends positions was performed using Fivepseq package (Nersisyan, Ropat and Pelechano, 2020) (http://pelechanolab.com/software/fivepseq). This included analysis of the relative positions of the 5' ends of the mRNA reads with respect to the start codon, stop codon, and codon-specific pausing. Specifically, the unique 5´mRNA reads in biological samples were averaged and normalized to reads per million (rpm). The relative position of 5´mRNA reads at each codon were summed up  and used for all additional analyses. Metagene plots for frame preference were showed as the sum value (in rpm) of each frame versus the relative from the sliding window's average (in rpm) for 20 codons located at the beginning, middle, and end of each gene.
Assembly: Saccharomyces cerevisiae R64-1-1, GCA_000009045.1 for B. subtilis
Supplementary files format and content: Bedgraph files for UMI collapsed reads for positive and negative strand. Reads were collapsed to the first 5´nucleotide.

organism: Bacillus subtilis

source_name: bacteria

growth_protocol: All yeast experiments were performed using Saccharomyces cerevisiae strain BY4741 (MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0). S. cerevisiae was grown to mid exponential phase (OD600~0.6) at 30 °C with rotating using YPD (1% yeast extract, 2% peptone, 2% glucose), Complete Supplement Mixture (CSM from Formedium™) or Synthetic Complete (SC from MP Biomedicals™) medium. Bacteria of the strain B. subtilis 168 (trpC2) were pre-cultivated at 37°C with rotating in LB and minimal growth medium (per 50 ml:  5X minimal salts solution,10 ml;  glucose (50% (w/v)), 0.5 ml; casamino acids (2% (w/v)), 0.5 ml; tryptophan (10 mg/ml), 0.1 ml; iron ammonium citrate (2.2 mg/ml), 0.05 ml, demonized water, 39 ml) with tryptophan supplementation at OD600 < 0.8. Cultures were diluted to  OD600~0.05 and collected until reaching the mid-exponential phase (OD600~0.6).

extract_protocol:
Total RNA was isolated by the standard phenol chloroform method and DNA was removed by DNase I treatment, as described in Zhang & Pelechano, 2021 (PMID:33870233). RNA concentration was measured with Qubit and RNA quality was checked by 1.2% Agarose Gel or on a BioAnalyzer using an RNA Nano 6000 chip according (Agilent Technologies).
HT-5Pseq libraries were prepared following a previously established protocol (Zhang & Pelechano, 2021) if not stated otherwise. To briefly summarize, 6 μg of RNA was subjected to DNase treatment, and the resulting DNA-free total RNA was ligated with an RNA/RNA oligo containing UMI (RNA rP5_RND oligo). The ligated RNA was reverse transcribed using Illumina PE2 compatible oligos with random hexamers and oligo-dT as primers. To eliminate RNA in RNA/DNA hybrids, samples were treated with sodium hydroxide at 65°C for 20 minutes. Ribosomal RNAs were depleted using DSN (Duplex-specific nuclease) and a mixture of ribosomal DNA probes. To deplete Ribosomal RNAs in B. subtilis 168 (trpC2), we used the in-house rRNA DNA oligo depletion mixes described previously (Huch, Nersisyan et.al, doi.org/10.1101/2021.04.08.439066). Finally, the samples were amplified by PCR and sequenced on an Illumina NextSeq 2000 instrument using average of 45 cycles for read1.
OTHER: 5PSeq

treatment_protocol:
B. subtilis was collected after reaching the mid-exponential phase (OD600~0.6) in Minimal growth medium
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.

value: bacteria

value: 168 trpC2


title: AN00561.BA32


title: rna_G560R_morc1_rep4


title: AN17703.BA32


title: bsubs_minimal-media_rep1


title: m6A-RNA, IA-KA injected mice, 2weeks, mouse 6

description: Library name: KA 2weeks6


title: bsubs_minimal-media_rep2


title: rna_AID_CSR1_1mM_rep4

value: 1mM auxin


title: AN07534.BA32


title: Exp5,iNKT (ATOCs) and PITL enriched population  (ATOCs) sorts, GEX


title: bsubs_ctrl_rep3

treatment_protocol:
B. subtilis was collected after reaching the mid-exponential phase (OD600~0.6) in LB
Stress-induced S. cerevisiae cells were subjected to heat shock (42°C for 30 minutes), oxidative stress (0.2 mM H2O2 for either 5 or 30 minutes), and amino acid deprivation (CSM medium lacking amino acids for 30 mins). S. cerevisiae cells grown with amino acid addition were individually supplemented with arginine, proline, and serine as single amino acids to achieve a comparable concentration to that of SC medium. The concentration of each added amino acid ranged from 50 to 85.6 mg/L for arginine and from 0 to 85.6 mg/L for proline and serine. For B. subtilis,  cells were grown in both LB and minimal media. Cells were fast spined down and flash-frozen in liquid nitrogen.


title: m6A-RNA, IA-PBS injected mice, 2weeks, mouse 4

description: Library name: PBS 2weeks4


title: rna_AID_CSR1_0mM_rep4

value: whole worms

value: 0mM auxin


title: bsubs_ctrl_rep2


title: m6A-RNA, IA-KA injected mice, 2weeks, mouse 5

description: Library name: KA 2weeks5


title: m6A-RNA, IA-KA injected mice, 2weeks, mouse 42

description: Library name: KA 2weeks42


title: AN08533.BA32


title: bsubs_ctrl_rep1


title: rna_N2_rep4


title: m6A-RNA, IA-PBS injected mice, 2weeks, mouse 3

description: Library name: PBS 2weeks3


title: AN16022.BA32


title: AN07275.BA32


title: Multiplexed WT-KO-TG TSC

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

institute: University of Michigan

data_processing:
The library was sequenced with a NovaSeq S4 (300 cycle). Total 6860 cells with 51,167 median reads per cell and 2284 median UMI per cell were captured. Mapping rate to the genome (mm10) was 87.23%. General gene expression was analyzed using the Loupe Browser (10x Genomics).
Raw Fastq sequencing files were demultiplexed and analyzed with 10X Genomics Cell Ranger (6.1.0) software using the standard default settings and the cell ranger count command to generate quality control metrics and cloupe files.
Cell type-specific marker genes and tSNE clustering were used to identify immune cell subsets. For example, CD8 T cells were identified based on the expression of Cd8a within the T cell cluster.
The log2-fold change of significantly differentially expressed genes with an average count of >0.1 were analyzed. p-values are adjusted using the Benjamin-Hochberg correction for multiple tests. Differences in TCR genes were omitted from the analysis. TCR clonotypes (CDR3 region) were analyzed using the Loupe VDJ Browser 4.0 (10x Genomics).
Assembly: Mus_musculus/GRCm38/refdata-gex-mm10-2020-A
Supplementary files format and content: 10x CLOUPE file

organism: Mus

source_name: Spleen

growth_protocol: WT, RARα-KO, or RARα-TG mice bearing MC38 tumors were sacrificed on day 16 post tumor cell-injection

extract_protocol:
Tumor cell suspensions were stained, respectively, with anti-mouse TotalSeq™-C0301, C0302, and C0303 Hashtag antibodies (Biolegend #155861, #155863, #155865) together with fluorochrome-labelled antibodies against CD45.2, CD3, CD4, and CD8 cell sorting. 30,000 T cells (CD45.2+ CD3+) and 10,000 total cells for each mouse genotype were sorted by FACS Melody (BD Biosciences) and pooled for multiplexed single-cell RNA and TCR repertoire sequencing by 10X genomics Chromium Single Cell 5' Reagent Chromium Single Cell Mouse TCR Amplification Kits.
10X genomics Chromium Single Cell 5' Reagent Chromium Single Cell Mouse TCR Amplification Kits.
Single Cell 5' Reagent Chromium Single Cell Mouse TCR Amplification

value: Spleen

value: Primary

value: Naive CD8 T cells

value: T cell activation with anti-CD3/28+IL-2


title: rna_G560R_morc1_rep3


title: AN01535.BA32


title: m6A-RNA, IA-PBS injected mice, 2weeks, mouse 2

description: Library name: PBS 2weeks2


title: rna_AID_CSR1_1mM_rep3


title: AN11711.BA32


title: m6A-RNA, IA-PBS injected mice, 2weeks, mouse 78

description: Library name: PBS 2weeks78


title: Multiplexed WT-KO-TG T cells


title: rna_G560R_rep4


title: Multiplexed WT-KO-TG


title: m6A-RNA, IA-KA injected mice, 24h, mouse 8

description: Library name: KA 24h8


title: AN07668.BA32


title: Rara IgG control

description: Rara IgG

data_processing:
Fastq files were processed for QC, trimming, and aligned by Bowtie2 to obtain Bam files and to generate Bigwig files.
Bam files and to generate Bigwig files. Motif analysis (MACS v2, Homer) was performed at P values of 1e-4 (RARa) or 1e-5 (BATF) to identify ChIP-Seq peaks and transcription binding motifs.
Assembly: Aligned on GRCm38 - mm10 - Genome – Assembly by Bowtie2
Supplementary files format and content: MACS2 files to show annonated peak information.

growth_protocol: CD8 T cells, activated for 24 h with anti-CD3, anti-CD28, and IL-2 and then rested for 24 h in IL-2 (100 U/ml), were further treated with or without RA (50 nM) for 1 h.

extract_protocol:
The cultured cells were fixed with 1% formaldehyde and processed with the SimpleChIP ® Enzymatic Chromatin IP Kit (Cell Signaling Technology) as previously described. The chromatin fragments were incubated with anti-RARα (CST #62294), anti-BATF (CST #8638), or Normal Rabbit IgG (CST #2729) overnight at 4°C with rotation.
The DNA samples were sent for library preparation and subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq).
Illumina DNA (low input) Library Prep

value: WT

value: T cell activation with anti-CD3/28+IL-9

tag: antibody

value: Normal Rabbit IgG (CST #2729)


title: rna_G560R_rep3


title: m6A-RNA, IA-KA injected mice, 24h, mouse 79

description: Library name: KA 24h79


title: AN02028.BA32

data_processing:
bcbio-nextgen Bulk RNA-seq pipeline
Paired-end sequence reads were aligned to human genome UCSC GRCh38.p14 using STAR
Quality metrics were assessed using Samtools
Transcript counts from aligned reads were quantified using Salmon, then summarized to the gene level using the R package Tximport
Assembly: GRCh38
Supplementary files format and content: comma-seperated file includes raw counts for all samples

extract_protocol:
rRNA depletion sequencing libraries were prepared by using QIAGEN Fastselect HMR
RNA sequencing library preparation uses NEBNext Ultra II RNA Library Preparation Kit for Illumina by following the manufacturer’s recommendations


title: m6A-RNA, IA-KA injected mice, 24h, mouse 97

description: Library name: KA 24h97


title: BATF+RA (15+9) vs. IgG control

description: BATF+RA

value: T cell activation with anti-CD3/28+IL-10

value: anti-BATF (CST #8638)


title: rna_AID_CSR1_0mM_rep3


title: AN00675.BA32

value: AD

value: male


title: BATF (14+7) vs. IgG control

description: BATF


title: m6A-RNA, IA-KA injected mice, 24h, mouse 98

description: Library name: KA 24h98

value: Hippocampus


title: rna_AID_CSR1_1mM_rep2


title: AN13062.BA32

value: Post mortem brain


title: RARa (12+3) vs IgG control

description: RARa

value: T cell activation with anti-CD3/28+IL-7

value: anti-RARα (CST #62294)


title: m6A-RNA, IA-KA injected mice, 24h, mouse 67

description: Library name: KA 24h67


title: rna_G560R_morc1_rep2

value: whole worms


title: RAR+RA (13+5) vs. IgG control

description: RAR+RA

value: T cell activation with anti-CD3/28+IL-8


title: rna_AID_CSR1_0mM_rep2

value: 0mM auxin


title: AN15043.BA32

value: female


title: m6A-RNA, IA-PBS injected mice, 24h, mouse 1

description: Library name: PBS 24h1


title: AN07311.BA32


title: m6A-RNA, IA-PBS injected mice, 24h, mouse 73

description: Library name: PBS 24h73


title: RARA KO2-RA [8554-CK-24]

data_processing:
BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files. In general, Snakemake was used to manage the bioinformatics workflow
The reads were trimmed, examined for quality of data, and screened for various types of contamination.
In general, Snakemake was used to manage the bioinformatics workflow. The reads were trimmed, examined for quality of data, and screened for various types of contamination.  Hierarchical clusters were generated using the Gene Cluster software (3.0) with a cut-off of ≥1.5 log2 fold-change and data was presented using the Java TreeView software.
Assembly: Reads were mapped to the reference genome GRCm38 (ENSEMBL) and assigned count estimates to genes with RSEM v1.3.3 using STAR v2.7.8a 67.

growth_protocol: CD8 T cells were cultured on anti-CD3-coated (1µg/ml) 96-wells in RPMI medium supplemented with 10% charcoal-stripped FBS, anti-CD28 (2 ug/ml), and IL-2 (100 U/ml) for 20 h with or without RA (15 nM).  samples were prepared for each group. BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files. In general, Snakemake was used to manage the bioinformatics workflow 66. The reads were trimmed, examined for quality of data, and screened for various types of contamination. Reads were mapped to the reference genome GRCm38 (ENSEMBL) and assigned count estimates to genes with RSEM v1.3.3 using STAR v2.7.8a 67. Hierarchical clusters were generated using the Gene Cluster software (3.0) with a cut-off of ≥1.5 log2 fold-change and data was presented using the Java TreeView software.

extract_protocol:
RNA was isolated using the RNAeasy kit (Qiagen #74104)
Illumina Total RNA (standard) Library Prep
poly-A-enrichment-based library preparation

value: Spleen

value: Primary

value: Naive CD8 T cells

tag: strain background

value: RARA KO


title: rna_G560R_rep2


title: rna_N2_rep3


title: AN13493.BA32


title: AN11178.BA32


title: m6A-RNA, IA-PBS injected mice, 24h, mouse 71

description: Library name: PBS 24h71


title: rna_G560R_morc1_rep1


title: BATF KO2 [8554-CK-21]

value: BATF KO

value: T cell activation with anti-CD3/28+IL-2


title: AN05080.BA32


title: INPUT, total RNA, IA-KA injected mice, 2weeks, mouse 6

description: Library name: INPUT KA 2weeks6


title: RARA KO2 [8554-CK-23]


title: INPUT, total RNA, IA-KA injected mice, 2weeks, mouse 9

description: Library name: INPUT KA 2weeks9


title: rna_AID_CSR1_1mM_rep1

value: 1mM auxin


title: WT2-RA [8554-CK-20]

value: WT


title: rna_AID_CSR1_0mM_rep1


title: AN11729.BA32

value: AD


title: AN18637.BA32


title: rna_N2_rep2


title: INPUT, total RNA, IA-KA injected mice, 2weeks, mouse 7

description: Library name: INPUT KA 2weeks7

value: Hippocampus


title: WT2 [8554-CK-19]


title: rna_N2_rep1


title: AN11052.BA32

value: Post mortem brain


title: RARA KO1 [8554-CK-17 ]


title: INPUT, total RNA, IA-KA injected mice, 2weeks, mouse 21

description: Library name: INPUT KA 2weeks21


title: RARA KO1-RA [8554-CK-18 ]


title: INPUT, total RNA, IA-KA injected mice, 2weeks, mouse 42

description: Library name: INPUT KA 2weeks42


title: AN18056.BA32


title: BATF KO2-RA [8554-CK-22]


title: BATF KO1-RA [8554-CK-16 ]


title: m6A-RNA, IA-PBS injected mice, 2weeks, mouse 50

description: Library name: PBS 2weeks50


title: morc1_csr1RNAi_F4_input_1

data_processing:
Sequencing data were first checked for quality using fastqc v0.11.8
Reads were filtered and trimmed to remove poor quality sequences and adapter sequences using Trim Galore v0.6.7 with options --stringency 3 -q 25 --length 20
Reads were aligned to ce10/WBcel215 with the WS230 annotations, obtained from WormBase (https://wormbase.org) using bowtie2 v2.3.4.3 with options -N 0 -L 22
Fragment size was estimated using the run_spp function from the phantompeakqualtools (49, 50) suite. Fragment size estimates averaged to approximately 175 bp across all samples, and this estimate was used for all analyses.
Read coverage tracks for each sample were generated using the bamCoverage function from DeepTools suite v.3.5.1, using options --extendReads 175 --binSize 10 and --normalizeUsing CPM, and excluding the mitochondrial chromosome.
Assembly: ce10/WBcel215
Supplementary files format and content: bigWig pileups contain normalized sequencing read depth for each library, obtained from deeptools bamCoverage with the "CPM" normalization option. bigWig files are the binary form of a four-column file, where column 1 == chromosome, column 2 == interval start, 3 == interval end, and 4 == signal (normalized read counts in this case)

growth_protocol: For purified germline nuclei ChIP, a synchronized population of worms was obtained by hypochlorite treatment of gravid worms followed by overnight nutation of the embryos in M9. Worms were grown in liquid culture at 20°C according and collected at 56 hours (young adult stage). For whole worm ChIP, worms previously maintained at 20°C were hypochlorite treated and shifted to 25°C; these worms became the “P0” population. Worms were propagated at 25°C for four successive generations (F1–F4); each generation was synchronized by hypochlorite treatment.

extract_protocol:
Purified germline nuclei ChIP: the 56 hour time point, the worms were cleansed via sucrose floatation. They were then live-crosslinked in 2.6% formaldehyde for 30 min at room temperature with nutation. The cross-linker was quenched with a 5 min nutation in glycine at a final concentration of 125 mM. Worms were washed in water and flash frozen in liquid nitrogen as ~1 mL pellets. Germline nuclei were purified and ChIP was performed according to Han, et al., 2019 with some modifications (see methods). For whole worm ChIP: chromatin sonication, immunoprecipitation, decrosslinking and DNA extraction were performed as in Weiser et al. 2017. For each immunoprecipitated sample, an input library was generated from 10% of the chromatin pre-IP and was de-crosslinked and extracted in parallel to the immunoprecipitated samples.
Libraries were prepared using the Ovation Ultra Low System V2 kit (NuGEN) according to manufacturer’s instructions and then sequenced on the NovaSeq6000 Sequencer (Illumina).

treatment_protocol: aid::csr-1 worms were grown in the presence of 50 µM auxin beginning at the L1 stage for purified germline nuclei ChIP. For whole worm ChIPs on samples treated w/ RNAi, it was fed to the worms beginning at the L1 stage only for the single generation prior to worm sample collection.

value: input

value: csr-1 RNAi


title: AN13338.BA32


title: INPUT, total RNA, IA-PBS injected mice, 2weeks, mouse 4

description: Library name: INPUT PBS 2weeks4


title: AN18901.BA32


title: BATF KO1 [8554-CK-15]


title: N2_csr1RNAi_F4_input_2

value: whole worms


title: rna_G560R_rep1


title: AN11050.BA32


title: INPUT, total RNA, IA-KA injected mice, 2weeks, mouse 5

description: Library name: INPUT KA 2weeks5


title: WT1-RA [8554-CK-14 ]


title: N2_csr1RNAi_F4_input_1


title: INPUT, total RNA, IA-PBS injected mice, 2weeks, mouse 3

description: Library name: INPUT PBS 2weeks3


title: morc1_csr1RNAi_F4_K36_2


title: WT1 [8554-CK-13]


title: AN10747.BA32


title: INPUT, total RNA, IA-PBS injected mice, 2weeks, mouse 2

description: Library name: INPUT PBS 2weeks2


title: morc1_csr1RNAi_F4_input_2


title: morc1_csr1RNAi_F4_K36_1


title: AN14576.BA32


title: morc1_csr1RNAi_F4_K9_2


title: INPUT, total RNA, IA-KA injected mice,24h, mouse 8

description: Library name: INPUT KA 24h8


title: INPUT, total RNA, IA-KA injected mice,24h, mouse h97

description: Library name: INPUT KA 24h97


title: AN07303.BA32


title: AN05797.BA32


title: morc1_csr1RNAi_F4_K9_1


title: INPUT, total RNA, IA-KA injected mice,24h, mouse 98

description: Library name: INPUT KA 24h98


title: AN17402.BA32


title: 02_0GAP_027HUAMS_JE-2B16-GAL_input_mm_i85

description: Library name: GAL_input

value: skin

value: Cells were cultured under glucose-deprived (GAL) replaced with galactose conditions


title: INPUT, total RNA, IA-KA injected mice,24h, mouse 67

description: Library name: INPUT KA 24h67


title: N2_csr1RNAi_F4_K36_2


title: AN06706.BA32

value: female


title: INPUT, total RNA, IA-PBS injected mice, 24h, mouse 73

description: Library name: INPUT PBS 24h73


title: N2_csr1RNAi_F4_K9_2


title: AN13999.BA32


title: Brain_PS19_3_rep1

type: RNA

first: Ami

last: Kobayashi

address: 60 Fenwood Rd

department: Neurology

institute: Brigham & Women's Hospital

description: Pull down with magnetic beads-Tau pS396 antibody complexes

hyb_protocol: The labeled RNAs were combined together and hybridized onto Arraystar Mouse small RNA Microarray (8x15K, Arraystar).

scan_protocol: The arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Raw intensities of IP (CLIP-bound, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After the normalization, probe signals having Present (P) or Marginal (M) QC flags in at least 2 out of 4 samples were retained. After QC flag filtering, Multiple probes from the same small RNA (miRNA, pre-miRNA, or tsRNA) were combined into one RNA level. “Binding abundance” was analyzed based on the Cy5-labelled IP (CLIP-bound RNA) normalized intensities.

source_name: brain, frozen tissue

label_protocol: 1ug RNA is used for labeling. The “IP” and “Supernatant” RNAs were enzymatically labeled with Cy5 and Cy3 respectively in separate reactions.

extract_protocol: RNA-Protein complexes were pull down using magnetic beads-antibody complexes.

treatment_protocol: Tissues were homogenized and UV-crosslinked.

tag: fraction

value: Supernatant unbinding RNA

value: CLIP RNA


title: N2_csr1RNAi_F4_K36_1


title: INPUT, total RNA, IA-PBS injected mice, 24h, mouse 71

description: Library name: INPUT PBS 24h71


title: Brain_PS19_2_rep1


title: rip_G560R_IP_rep3

description: Library name: rip_G560R_IP_rep3

data_processing:
Reads were first trimmed to remove adapter sequences using Trim Galore with options --illumina --max_length 35 --length 18 -q 0 --stringency 3, retaining only reads between 18-35 bp post-trimming. Reads were further split according to size, retaining 22 nt reads (CSR-1 and WAGO siRNAs plus miRNAs)
Reads were aligned to ce10 using bowtie2 in --end-to-end --very-sensitive mode. Uniquely mapped reads were extracted (mapQ >= 2), and converted into strand-specific coverage tracks using DeepTools bamCoverage --binSize 10 --normalizeUsing CPM --filterRNAstrand [forward/reverse].
Counts over genes were obtained using the htseq-count function from the HTSeq python package v2.0.2 with options --nonunique none -m intersection-strict, and using the WS230 C. elegans annotations, and log2(fold change) estimates between wild-type and mutants were estimated using DESeq2.
Assembly: ce10
Supplementary files format and content: CSR1_all_22nt_data.txt is a matrix of sRNA (raw) read count data across all samples. Column names match sample names, while rows correspond to genes.

growth_protocol: A synchronized population of worms was obtained by hypochlorite treatment of gravid adult worms followed by overnight nutation of the embryos in M9. Worms were grown in liquid culture at 20°C according to the protocol described in Zanin et al. 2011 Cell Biol. and collected at 56 hours (young adult stage) in water and flash frozen in liquid nitrogen as ~500 L pellets.

extract_protocol:
Frozen worms were homogenized in an MM400 Mixer Mill homogenizer (Retsch) for 2 rounds of 1 min at a frequency of 30-1 sec. An estimated equal amount of worm powder per genotype was added to a 15 mL conical and 1.5 mL IP buffer (10% glycerol, 10 mM EDTA,  30 mM Hepes (pH 7.4), 100 mM potassium acetate, 2 mM DTT, 0.1% NP40) was added. Worm powder was resuspended in the buffer by pipetting and vortexing. Worm lysis was transferred to a 2 mL LoBind microcentrifuge tube (Eppendorf) and spun at 18000 g for 5 min at 4°C. The lipid layer was aspirated off. 50 mL of the supernatant was reserved as the ‘input’ sample and stored in 1 mL TriReagent (ThermoFisher) at -80°C. The rest of the worm lysis was mixed with 50 mL Dynabeads conjugated with anti-FLAG antibody (Sigma-Aldrich, F1804) and nutated at 4°C for two hours. Immunoprecipitated material was washed 3x in cold IP buffer. Immunoprecipitated material (on Dynabeads) were stored in 1 mL TriReagent (ThermoFisher) at -80°C. Worms were collected in TriReagent (ThermoFisher) and subjected to three freeze-thaw cycles. Phase separation was achieved via 1-bromo-3-chloropropane (BCP) and the aqueous phase was precipitated in isopropanol at -80°C for 2 hrs. To pellet RNA, samples were centrifuged at 21,000 x g for 30 min at 4°C. The pellet was washed three times in 75% ethanol then resuspended in water.
RNA-seq libraries were generated using the KAPA stranded mRNA-seq kit (Roche) according to the manufacturer’s instructions. Small RNA-seq libraries were made using the NEBNext Multiplex Small RNA Library Prep Set (NEB) according to the manufacturer’s instructions. All RNA-seq libraries were sequenced on a NovaSeq 6000 Sequencer (Illumina).

treatment_protocol: Input vs. IP samples are described in extraction protocol.

value: IP


title: INPUT, total RNA, IA-PBS injected mice, 24h, mouse 1

description: Library name: INPUT PBS 24h1


title: N2_csr1RNAi_F4_K9_1


title: rip_CSR1_IP_rep3

description: Library name: rip_CSR1_IP_rep3


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp2_Control/Bleo-21dpi, scRNA-seq, HTO

first: Nicholas

last: Arpaia

department: Microbiology & Immunology

institute: Columbia University

data_processing:
Cell Ranger v5.0.0
Assembly: GRCh38
Supplementary files format and content: Processed RDS object for Experiment 1 (2021); full TCR sequences and V(D)J usage information is included in metadata within RDS file
Supplementary files format and content: Processed RDS object for Experiment 2 (2022); full TCR sequences and V(D)J usage information is included in metadata within RDS file

source_name: lung

extract_protocol:
10X Genomics Chromium Platform
10X Genomics Chromium Single Cell 5’ V(D)J with Feature Barcoding Reagent Kits (CG000186)

treatment_protocol: Thy1.1- (Areg non-producing) and Thy1.1+ (Areg-producing) lung Treg cells were sorted and prepared for single cell RNA-seq

value: lung

value: Treg cells

value: C57BL/6 male; Foxp3GFPAregThy1.1/Thy1.1

value: Control/Bleomycin


title: Brain_PS19_1_rep1


title: rip_N2_IP_rep3

description: Library name: rip_N2_IP_rep3


title: BMDC, KO, LPS, rep5

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

description: Library name: 19_ZJJ_KO_LPS

data_processing:
Reads were mapped to the reference genome GRCm39 using HISAT.
Reads were mapped to reference genes using Bowtie2
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: Tab-delimited text file contains FPKM, TPM, and raw counts for each sample

source_name: BMDC

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (Qiagen, 1071023)
RNA libraries were prepared by BGI genomics for their DNBSEQ platform for PE150 RNA resequencing

value: BMDC

value: KO

value: LPS


title: G560R_MORC1_IP_2

source_name: purified germline nuclei

value: purified germline nuclei

value: anti-FLAG


title: BMDC, WT, Control, rep4

description: Library name: 18_ZJJ_WT

value: WT

value: Control


title: AIDcsr1_MORC1_IP_2


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp2_Control/Bleo-21dpi, scRNA-seq, HTO


title: Brain_WT_3_rep1

value: Hippocampus


title: BMDC, WT, LPS, rep5

description: Library name: 17_ZJJ_WT_LPS


title: rip_G560R_input_rep3

description: Library name: rip_G560R_input_rep3

source_name: whole worms

value: whole worms

value: input


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, HTO

value: Control/Influenza A Virus/Bleomycin


title: G560R_MORC1_input_2


title: rip_CSR1_input_rep3

description: Library name: rip_CSR1_input_rep3


title: BMDC, KO, Control, rep3

description: Library name: 16_ZJJ_KO


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, HTO


title: AIDcsr1_MORC1_input_2


title: Brain_WT_2_rep1

value: Supernatant unbinding RNA

value: CLIP RNA


title: rip_N2_input_rep3

description: Library name: rip_N2_input_rep3


title: G560R_MORC1_IP_1


title: BMDC, KO, Control, rep4

description: Library name: 20_ZJJ_KO


title: BMDC, WT, Control, rep3

description: Library name: 14_ZJJ_WT


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp2_Control/Bleo-21dpi, scRNA-seq, TCR

value: lung


title: BMDC, KO, LPS, rep4

description: Library name: 15_ZJJ_KO_LPS


title: Brain_WT_1_rep1


title: BMDC, WT, LPS, rep4

description: Library name: 13_ZJJ_WT_LPS


title: rip_CSR1_IP_rep2

description: Library name: rip_CSR1_IP_rep2

value: IP


title: AIDcsr1_MORC1_IP_1


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, TCR

value: Treg cells

value: C57BL/6 male; Foxp3GFPAregThy1.1/Thy1.1


title: rip_N2_IP_rep2

description: Library name: rip_N2_IP_rep2


title: BMDC, KO, Control, rep2

description: Library name: 12_ZJJ_KO

value: BMDC


title: rip_G560R_input_rep2

description: Library name: rip_G560R_input_rep2


title: AIDcsr1_MORC1_input_1


title: BMDC, KO, LPS, rep3

description: Library name: 11_ZJJ_KO_LPS

value: KO


title: N2_MORC1_IP_2


title: rip_CSR1_input_rep2

description: Library name: rip_CSR1_input_rep2


title: BMDC, WT, Control, rep2

description: Library name: 10_ZJJ_WT


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp2_Control/Bleo-21dpi, scRNA-seq, GEX

value: Control/Bleomycin


title: N2_noflag_IP_2

value: purified germline nuclei


title: rip_N2_input_rep2

description: Library name: rip_N2_input_rep2


title: rip_G560R_IP_rep1

description: Library name: rip_G560R_IP_rep1


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp2_Control/Bleo-21dpi, scRNA-seq, GEX


title: rip_G560R_IP_rep2

description: Library name: rip_G560R_IP_rep2


title: N2_MORC1_input_2


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, GEXrun3


title: N2_noflag_input_2


title: rip_CSR1_IP_rep1

description: Library name: rip_CSR1_IP_rep1


title: BMDC, WT, LPS, rep3

description: Library name: 9_ZJJ_WT_LPS

value: LPS


title: BMDC, WT, LPS, rep2

description: Library name: 5_ZJJ_WT_LPS

value: WT


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, GEXrun2


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp2_Control/Bleo-21dpi, scRNA-seq, TCR


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, GEXrun3


title: G560R_MORC1_input_1


title: rip_N2_IP_rep1

description: Library name: rip_N2_IP_rep1


title: BMDC, KO, Control, rep1

description: Library name: 4_ZJJ_KO

value: Control


title: BMDC, KO, LPS, rep2

description: Library name: 7_ZJJ_KO_LPS


title: N2_MORC1_IP_1

value: anti-FLAG


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, GEXrun2


title: rip_G560R_input_rep1

description: Library name: rip_G560R_input_rep1

value: whole worms


title: BMDC, KO, LPS, rep1

description: Library name: 3_ZJJ_KO_LPS


title: N2_noflag_IP_1


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, TCR


title: N2_MORC1_input_1

value: input


title: rip_CSR1_input_rep1

description: Library name: rip_CSR1_input_rep1


title: Sorted Thy1.1+ (Areg-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, GEXrun1

value: Control/Influenza A Virus/Bleomycin


title: N2_noflag_input_1


title: BMDC, WT, LPS, rep1

description: Library name: 1_ZJJ_WT_LPS


title: rip_N2_input_rep1

description: Library name: rip_N2_input_rep1


title: N2_atac_1

data_processing:
Sequencing data were first checked for quality using fastqc v0.11.8
Reads were filtered and trimmed to remove poor quality sequences and adapter sequences using Trim Galore v0.6.7 with options --stringency 3 -q 25 --length 20
Reads were aligned to ce10/WBcel215 with the WS230 annotations, obtained from WormBase (https://wormbase.org) using bowtie2 v2.3.4.3 with options -N 0 -L 22 (-X 500 for paired-end data).
PCR duplicates were removed using MarkDuplicates from the Picard tools suite.
Aligned reads were analyzed using Genrich v.0.5 (47) to identify cut sites, excluding the mitochondrial chromosome. Cut site data were converted by Genrich into bigWig signal tracks.
Assembly: ce10/WBcel215
Supplementary files format and content: bigWig pileups represent the frequency of ATAC-seq cut sites at each location in the genome, at single-base resolution, obtained from Genrich. This is the binary form of a four-column file, where column 1 == chromosome, column 2 == interval start, 3 == interval end, and 4 == # of cut sites at this location (not normalized).

growth_protocol: ATAC-seq was performed on adult wild-type (N2) worms grown at 25°C.  Worms were fed OP50E.coli.

extract_protocol:
ATAC-seq was performed as in Zhong et al. 2021 (doi: 10.1073/pnas.2023347118). Briefly, worms were ground and filtered through 40 um mesh to isolate nuclei, all on ice, then pelleted at 10 min 3000g.
Extracted nuclei were treated with Tn5 transposase in a mix containing 25 uL 2x dimethylformamide + 2.5 uL Tn5 and 22.5 uL nuclei suspension at 37 C 30 min, then purified with a Zymo ChIP DNA Clean & Concentrator kit. Tagmented DNA was amplified using Phusion polymerase (NEB).


title: iNeuron_d7_NT_RNA-seq

status: Public on May 13 2025

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

description: Library name: Sample 37

data_processing:
Raw reads were trimmed by Trim Galore!.
Trimmed reads were mapped to reference genome using STAR.
Bigwig files were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM
Assembly: hg19, mm10
Supplementary files format and content: bw files include normliazed value
Supplementary files format and content: csv files include raw count expression matrix

source_name: iPSC-derived i3Neurons

growth_protocol: Human iPSC lines (WTC11) were cultured on Matrigel-coated dishes in Essential 8 Medium (E8) supplemented with 10 μM ROCK inhibitor at 37°C and 5% CO2. The medium was replaced every 1–2 days, and cells were passaged using Accutase and replated in E8 with ROCK inhibitor to promote survival, with the inhibitor removed once colonies formed. For iPSC-derived i3Neuron differentiation, NGN2-expressing iPSCs were plated in N2 medium with doxycycline and ROCK inhibitor. After two days, the cells were replated onto poly-L-ornithine-coated plates and cultured in iN Culture Media, including BrainPhys media, BDNF, NT-3, laminin, and doxycycline. The media was changed twice a week from day 6 onwards. For primary cortical neurons, cortices were dissected from E16.5 mouse embryos, digested with Papain and DNase I, and triturated in Neurobasal complete medium. The cells were then filtered, seeded on poly-d-lysine and laminin-coated plates, and aphidicolin was added to eliminate dividing cells.

extract_protocol:
For RNA-seq, total RNA was extracted from cells using TRIzol reagent (Thermo Fisher, 15596018) following the manufacturer’s instructions.
For RNA-seq, libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB; cat. No. E7760).

value: iPSC-derived i3Neurons

value: Neurons


title: day9_iNs_NT_CRISPRi_AX227_replicate2

description: Library name: Sample 8

data_processing:
sgRNA sequences were counted and normalized by MAGeCK (v 0.5.7) count subcommand. Beta score was calculated to select negatively/positively regulated genes by MAGeCK-MLE subcommand.
Assembly: hg19
Supplementary files format and content: xlsx file from CRISPRi_Screen includes beta score
Library strategy: CRISPR Screen

extract_protocol:
For CRISPRi-screen, genomic DNA was extracted from transduced iPSCs using the DNeasy Blood & Tissue Kit (QIAGEN). The extracted DNA was then amplified by PCR to enrich target fragments for sequencing.
For CRISPRi-screen, the PCR reaction included 10 μg of DNA, 1 μM of each forward and reverse primer containing Illumina sequencing indices, and 1× KAPA HiFi HotStart Ready Mix (Roche). The amplification process involved an initial 3-minute denaturation at 95°C, followed by 20 cycles of 30 seconds at 95°C, 30 seconds at 55°C, and 30 seconds at 72°C, concluding with a final 5-minute extension at 72°C. The amplified DNA was purified using AMPure XP beads (Beckman Coulter) with a 2× size selection, and the quality was assessed using the Agilent High Sensitivity D5000 ScreenTape System.

value: WT transduced with CRISPRi sgRNA library AX227

value: sgRNA library AX227 transduction


title: day9_iNs_AraC_CRISPRi_AX227_replicate1

description: Library name: Sample 10

value: sgRNA library AX227 transduction and AraC treatment for 3 days


title: day9_iNs_NT_CRISPRi_AX227_replicate1

description: Library name: Sample 7


title: day9_iNs_NT_CRISPRi_AX227_replicate3

description: Library name: Sample 9


title: day9_iNs_AraC_CRISPRi_AX227_replicate2

description: Library name: Sample 11


title: day3_iNs_CRISPRi_AX227_replicate1

description: Library name: Sample 4


title: day0_iPSCs_CRISPRi_AX227_replicate1

description: Library name: Sample 1

source_name: iPSCs

value: iPSCs