title: H3K27me3, Intestine, FA


title: DNAK-NI,Stress_OS,Slevel_HIGH,T24,REPLICATE_2

status: Public on Oct 03 2024

type: SRA

city: Amherst

first: Peter

last: Chien

state: MA

address: 240 Thatcher Rd, Life Science Laboratories Room N325

department: Biochemistry and Molecular Biology

country: USA

institute: University of Massachusetts Amherst

library_source: genomic

data_processing:
Samples were de-multiplexed, and unique molecular identifiers (UMIs) were added during PCR steps removed using Je
The clipped reads were mapped to the Caulobacter crescentus NA1000 genome (NCBI Reference Sequence: NC011916.1) using bwa and sorted with samtools.
Duplicate transposon reads removed by Je and indexed with samtools.
Genome positions are assigned to the 5′ position of transposon insertions using bedtools genomecov.
bedtools map is used to count either the total number of transposon insertions per gene using the bedtools map -o sum argument or the unique number of insertions using the bedtools map -o count argument
Assembly: NCBI Reference Sequence: NC011916.1
Supplementary files format and content: tab delimited text files include raw total or unique insertion counts for each gene.
Library strategy: Tn-seq

molecule: genomic DNA

organism: Caulobacter vibrioides

source_name: DNAK-NI RB-TN Library

growth_protocol: Transposon mutagenesis libraries were thawed and recovered in PYE or PYE + %0.2 Xylose overnight at saturating concentrations to minimize growth during recovery. Only for dnaK-NI library, overnights were recovered in saturating Xylose concentrations (%0.2), and treatment and T24 control conditions were grown in minimal Xylose concentrations. (%0.002)

extract_protocol:
Following overnight growth, 1 ml of saturated culture from each Tn library was pelleted at 8000xg for 2 minutes. Genomic DNA was extracted by Monarch Genomics DNA Preparation Kit (NEB) according to the manufacturer’s protocol.
The sequencing libraries for Next-generation sequencing were prepared using a customized three-step PCR protocol. Genomic DNA input was normalized to a concentration of 100 ng/μl. The initial transposon junction amplification (PCR1) was carried out using an arbitrary PCR amplification method. This step utilized a forward primer designed to align with one end of the transposon and three reverse arbitrary primers. The PCR1 process employed a 2-step cycling protocol with annealing temperatures set at 42°C and 58°C, and number of cycles at 6 and 15, respectively.  Subsequently, the second PCR step (PCR2) involved the addition of 16S adapters for Illumina indexing, along with unique molecular identifiers (UMI), and amplification of the library for 36 cycles. Post-PCR2 cleanup was performed using Aline PCRClean DX magnetic beads. The final PCR step (PCR3) incorporated NexteraXT indexing in accordance with the manufacturer's protocol. Post-indexed library (PCR3) cleanup was carried out using Aline PCRClean DX magnetic beads.

treatment_protocol:
Control condition: Libraries were back diluted to OD 0.008 into 7 ml of PYE or PYE+0.002% xylose and grown overnight until they reached saturation at OD ∼1.6.
Heat stress: Libraries diluted to OD of 1 and heat-stressed at low, medium, or high (37, 42, 43.8◦C, respectively) for 45 minutes in a Biorad Thermocycler. After 45 minutes, cells diluted back to a final OD of 0.008 in 7 ml media for 24-hour growth.
Oxidative stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (0.025mM, 0.05mM, 0.1mM) level hydrogen peroxide. Cells were grown for 24 hours in these chronic stress conditions.
L-canavanine stress: Libraries were directly diluted back to OD of 0.008 in 7 ml media that contains low, medium, or high (25ug/ml, 50ug/ml, 100ug/ml) levels of L-canavanine. Cells were grown for 24 hours in these chronic stress conditions.

tag: cell line

value: DNAK-NI RB-TN Library

tag: cell type

value: transposon mutagenesis library

tag: genotype

value: DNAK-NI

tag: treatment


title: H3K27me3, Brain, FB

city: Murfreesboro

first: Rafet

last: Al-Tobasei

state: TN

address: 358 KOM

department: Computer Science Department

institute: Middle Tennessee State University

data_processing:
The raw sequencing data was subjected to quality control using FastQC (version v0.11.8). Adapter sequences were removed from the reads using trim galore (version 0.6.4) (https://github.com/FelixKrueger/TrimGalore).
Trimmed reads were aligned to the rainbow trout reference genome using Bowtie2 (version 2.3.5.1) with the "--end-to-end" and "--very-sensitive" parameters.
The aligned reads were stored in BAM format for subsequent analysis. MACS3 (Model-based Analysis of ChIP-Seq 3) (version 3.0.0a6) was used for peak calling. The aligned reads in BAM format were utilized as input, and specific parameters were adjusted for each histone modification. For H3K27me3, which represents broad peaks, we set the q-value threshold to 0.05. For the rest of the histone modifications, which represent narrow peaks, we set the q-value threshold to 0.01.
Assembly: GCF_013265735.2
Supplementary files format and content: bed, narrowPeak (except for Input sample)

organism: Oncorhynchus mykiss

source_name: Brain

extract_protocol:
20–30 mg of tissue powder was cross-linked with 1% formaldehyde for 8 minutes, and quenched for 10 minutes with 100 μl of glycine. Centrifugation at 2000 g for 5 min yielded the nuclei, which were then resuspended in 600 μl of iS1 buffer and incubated for 30 min on ice. Depending on the tissues, the Bioruptor Pico sheared chromatin between 10 and 15 cycles.
Libraries were constructed using the NEBNext Ultra DNA library prep kit (New England Biolabs #E7645L, Ipswich, MA)

tag: tissue

value: Brain

tag: chip antibody


title: evoCDA, replicate 3, presort, pooled, endogenous

city: Boston

first: Eric

last: Che

address: 531 Newbury St

institute: Harvard Medical School

description: pooled, endogenous

data_processing:
After sequencing, the sequencing core facility performed the primary demultiplexing based on the P7 index. Subsequently, our laboratory conducted a secondary demultiplexing step using the P5 index, which is located internally within the read.
For each demultiplexed FASTQ, “raw” guide mapping was performed using CRISPR-SURF Count in base-editing mode. To identify significant regions based on the mapped guide RNA counts, we ran CRISPR-SURF Deconvolution on both the ABE8e and evoCDA datasets.
The paired-end FASTQs were also quality controlled with FastQC and MultiQC to ensure sufficient sequencing quality of our samples. Next, the paired-end FASTQs were passed into CRISPResso2 for read merging, alignment, and quantification of the edited alleles. The CRISPResso2 allele frequency tables were encoded into a feature indicator matrix containing columns for all possible REF>ALT variants across the amplicon and rows for all unique alleles. The matrices are then modeled by Millipede, a PyTorch-based Bayesian variable selection model, to generate beta coefficients and posterior inclusion probabilities for each feature (per-nucleotide).
The encoding matrix from CRISPR-Millipede, along with a design matrix describing the conditions of each sample (replicate and sorting population), was also passed into into pyDESeq2, a statistical package used to calculate differential expression of alleles between the CD19 positive and CD19 negative populations. The log fold change and adjusted p-value were plotted for the alleles observed across the cellular populations.
Assembly: N/A
Supplementary files format and content: "encoding" tsv file, produced by encoding the CRISPresso2 allele frequency tables into a feature indicator matrix, fed into CRISPR-Millipede
Supplementary files format and content: "hit_table" csv file, table of scores for hits modeled by CRISPR-Millipede

organism: Homo sapiens

growth_protocol: NALM6 cells (CVCL_0092) were cultured in RPMI 1640 (Thermo Fisher Scientific) with 10% Fetal Bovine Serum, 100U/mL Penicillin-Streptomycin and 2mM L-Glutamine (referred to as RPMI complete) at 37°C, 5% CO2.

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen).
For sgRNA count, the sgRNA cassette was PCR amplified from genomic DNA using primers carrying partial Illumina adaptor. PCR products were then re-amplified using primers carrying sample-specific barcode combinations. The endogenous CD19 enhancer sequence was PCR-amplified and barcoded using a similar strategy.
Distributions of edits within a 346 bp fragment of the CD19 enhancer were obtained by targeted amplicon sequencing using MiSeq at PE250 and PE300 configuration. Guide RNAs were enumerated by NGS as previously reported (Seruggia et al. Mol Cell 2019).

treatment_protocol: ABE8e-SpRY and evoCDA expressing NALM-6 cell lines were produced through lentiviral transduction and and selected with 10 ug/mL Blasticidin for five days. Expression of base editors was confirmed by Western Blot using a Cas9 antibody.

value: B cell precursor leukemia

value: CD19 enhancer pertubation

tag: condition

value: presort

value: Cytosine base editing


title: DNAK-NI,Stress_HS,Slevel_LOW,T24,REPLICATE_2


title: DNAK-NI,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_2


title: DNAK-NI,Stress_HS,Slevel_HIGH,T24,REPLICATE_2


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_2


title: H3K27me3, Brain, FA


title: H3K27ac, WhiteMuscle, FB

source_name: White muscle

value: White muscle


title: DCLPA,Stress_CAN,Slevel_LOW,T24,REPLICATE_2

source_name: DCLPA RB-TN Library

value: DCLPA RB-TN Library

value: DCLPA


title: DCLPA,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_2


title: evoCDA, replicate 2, CD19 positive, pooled, endogenous

description: pooled, endogenous

value: CD19 positive


title: DCLPA,Stress_CAN,Slevel_HIGH,T24,REPLICATE_2


title: H3K27ac, WhiteMuscle, FA


title: DCLPA,Stress_OS,Slevel_LOW,T24,REPLICATE_2


title: evoCDA, replicate 1, CD19 negative, pooled, endogenous

description: pooled, endogenous

value: CD19 negative


title: DCLPA,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_2


title: H3K27ac, Spleen, FB

source_name: Spleen

value: Spleen


title: evoCDA, replicate 1, CD19 positive, pooled, endogenous

description: pooled, endogenous


title: DCLPA,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_2


title: H3K27ac, Liver, FB

source_name: Liver

value: Liver


title: DCLPA,Stress_HS,Slevel_HIGH,T24,REPLICATE_2


title: DCLPA,Stress_HS,Slevel_LOW,T24,REPLICATE_2


title: evoCDA, replicate 3, CD19 positive, pooled, endogenous

description: pooled, endogenous


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_2


title: DLON,Stress_CAN,Slevel_LOW,T24,REPLICATE_2

source_name: DLON RB-TN Library

value: DLON RB-TN Library

value: DLON


title: evoCDA, replicate 1, presort, pooled, endogenous

description: pooled, endogenous


title: H3K27ac, Liver, FA


title: evoCDA, replicate 2, CD19 negative, pooled, endogenous

description: pooled, endogenous


title: H3K27ac, Kidney, FB

source_name: Kidney

value: Kidney


title: DLON,Stress_CAN,Slevel_HIGH,T24,REPLICATE_2

value: transposon mutagenesis library


title: DLON,Stress_OS,Slevel_LOW,T24,REPLICATE_2


title: ABE8e, replicate 3, CD19 positive, sg218

description: single guide, endogenous

value: Adenine base editing


title: ABE8e, replicate 3, CD19 negative, sg218

description: single guide, endogenous


title: DLON,Stress_OS,Slevel_HIGH,T24,REPLICATE_2


title: ABE8e, replicate 3, presort, sg218

description: single guide, endogenous


title: DLON,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_2


title: H3K27ac, Intestine, FB

source_name: Intestine

value: Intestine


title: H3K27ac, Kidney, FA


title: DCLPA,Stress_OS,Slevel_HIGH,T24,REPLICATE_2


title: evoCDA, replicate 2, presort, pooled, endogenous

description: pooled, endogenous

value: B cell precursor leukemia


title: DLON,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_2


title: ABE8e, replicate 2, CD19 negative, sg218

description: single guide, endogenous

value: CD19 enhancer pertubation


title: DLON,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_2


title: H3K27ac, Spleen, FA


title: H3K27ac, Brain, FB

value: Brain


title: WT,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_2

source_name: WT RB-TN Library

value: WT RB-TN Library

value: WT


title: H3K27ac, Brain, FA


title: ABE8e, replicate 2, presort, sg218

description: single guide, endogenous

value: presort


title: WT,Stress_OS,Slevel_LOW,T24,REPLICATE_2


title: DLON,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_2


title: ABE8e, replicate 1, CD19 negative, sg218

description: single guide, endogenous


title: WT,Stress_CAN,Slevel_LOW,T24,REPLICATE_2


title: DLON,Stress_HS,Slevel_HIGH,T24,REPLICATE_2


title: H3K27ac, Intestine, FA


title: WT,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_2


title: ABE8e, replicate 1, CD19 positive, sg218

description: single guide, endogenous


title: WT,Stress_CAN,Slevel_HIGH,T24,REPLICATE_2


title: DLON,Stress_HS,Slevel_LOW,T24,REPLICATE_2


title: WT,Stress_HS,Slevel_LOW,T24,REPLICATE_2


title: Whole embryo, monosome footprints, 4 hpf rep2

city: Kita-ku, Kyoto

first: Kota

last: Ishibashi

state: Kyoto

address: Kamigamo-motoyama

department: Department of Frontier Life Sciences

country: Japan

institute: Kyoto Sangyo University

description: Ribosome profiling

library_source: transcriptomic

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a with --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 options
Read quantitation using custom scripts
Assembly: GRCz11
Supplementary files format and content: text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

molecule: total RNA

organism: Danio rerio

source_name: whole embryo

growth_protocol: Fertilized eggs were obtained by natural breeding and developed in system water at 28.5ºC.

extract_protocol:
Embryos were lysed in cycloheximide-containing buffer and treated with RNase I. Ribosomes were isolated using MicroSpin S-400 HR column (Cytiva). Ribosome footprints were extracted using Trizol reagent (Thermo Fisher Scientific), Direct-zol RNA Microprep Kit (Zymo Research) and size selection by gel electrophoresis.
preadenylated linker ligation, rRNA depletion, reverse transcription, cDNA circularization, PCR amplification for ribosome profiling

treatment_protocol: Reporter mRNA mix was injected in 1-cell stage embryos.

value: whole embryo

value: Wild type AB strain

value: injected with sfGFP mRNAs at 1-cell stage


title: Whole embryo, monosome footprints, 4 hpf rep1

description: Ribosome profiling


title: WT,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_2


title: ABE8e, replicate 1, presort, sg218

description: single guide, endogenous


title: WT,Stress_HS,Slevel_HIGH,T24,REPLICATE_2


title: WT,Stress_OS,Slevel_HIGH,T24,REPLICATE_2


title: WT,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_2


title: ABE8e, unedited, pooled, endogenous

description: pooled, endogenous

value: CD19 enhancer unedited

value: unedited


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_2

value: DNAK-NI RB-TN Library

value: DNAK-NI


title: Whole embryo, disome footprints, 4 hpf rep1

description: Ribosome profiling


title: ABE8e, replicate 2, CD19 positive, sg218

description: single guide, endogenous

value: CD19 positive


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_2

value: DCLPA RB-TN Library

value: transposon mutagenesis library

value: DCLPA


title: ABE8e, replicate 3, CD19 negative, pooled, endogenous

description: pooled, endogenous

value: B cell precursor leukemia

value: CD19 negative

value: Adenine base editing


title: DLON,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_2

value: DLON RB-TN Library

value: DLON


title: mES-E14TG2a, biological replicate 3

city: Amsterdam

first: Max

last: Trauernicht

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Reads were aligned to GRCh38 (for human cells) or GRCm38 (for mouse cells) and counted in gencode v38 (human) or M10 (mouse) genes with STAR 2.5.4a
Assembly: mm10/hg38
Supplementary files format and content: File contains raw read counts per gene.

organism: Mus musculus

source_name: embryonic

growth_protocol: Cells were cultured as previously described (https://www.biorxiv.org/content/10.1101/2024.07.26.605239v1).

extract_protocol:
1x10^6 cells were resuspended in 600 uL RLT buffer (Qiagen). RNA was extracted using RNeasy plus kit (Qiagen).
Libraries were prepared using Illumina stranded RNA Library kit following manufacturer's instructions.

value: embryonic

value: mouse embryonic stem cell


title: WT,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_2

value: WT RB-TN Library

value: WT


title: ABE8e, replicate 3, CD19 positive, pooled, endogenous

description: pooled, endogenous

value: CD19 enhancer pertubation


title: WT,Stress_OS,Slevel_LOW,T24,REPLICATE_1


title: mES-E14TG2a, biological replicate 2


title: WT,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_1


title: ABE8e, replicate 3, presort, pooled, endogenous

description: pooled, endogenous

value: presort


title: mES-E14TG2a, biological replicate 1


title: ABE8e, replicate 2, CD19 positive, pooled, endogenous

description: pooled, endogenous


title: WT,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_1


title: Whole embryo, disome footprints, 4 hpf rep2

description: Ribosome profiling

value: whole embryo

value: Wild type AB strain

value: injected with sfGFP mRNAs at 1-cell stage


title: WT,Stress_HS,Slevel_LOW,T24,REPLICATE_1


title: WT,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_1


title: ABE8e, replicate 2, CD19 negative, pooled, endogenous

description: pooled, endogenous


title: WT,Stress_HS,Slevel_HIGH,T24,REPLICATE_1


title: ABE8e, replicate 2, presort, pooled, endogenous

description: pooled, endogenous


title: Klf9 KO-1

city: Tianjin

first: Lei

last: Zhang

address: qixiangtai 22

country: China

institute: Tianjin Medical University

data_processing:
A total of 4 samples were tested using the BGISEQ platform, with each sample yielding an average of 1.14G of data.
Assembly: NCBI
Supplementary files format and content: The average alignment rate of the sample compared to the genome is 97.38%, and the average alignment rate of the gene set is 56.38%; a total of 17,485 genes were detected.

source_name: hearts

growth_protocol: 8-weeks old WT and Klf9 KO mice are used to investigate the expression of genes

extract_protocol:
The cardiac tissues are collected from the 8-weeks old WT and Klf9 KO mice。
Extract total RNA of  heart tissues from 8-weeks old WT and Klf9 KO mice for transcriptome sequencing

treatment_protocol: Random food and drink

value: hearts

tag: Sex

value: male


title: Klf9 KO-2


title: WT,Stress_CAN,Slevel_LOW,T24,REPLICATE_1

value: transposon mutagenesis library


title: WT,Stress_CAN,Slevel_HIGH,T24,REPLICATE_1


title: ABE8e, replicate 1, CD19 negative, pooled, endogenous

description: pooled, endogenous

value: B cell precursor leukemia


title: WT-2


title: WT,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_1


title: WT,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_1


title: WT-1


title: ABE8e, replicate 1, CD19 positive, pooled, endogenous

description: pooled, endogenous

value: CD19 positive


title: DLON,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_1


title: DLON,Stress_OS,Slevel_LOW,T24,REPLICATE_1


title: KO-Control_GTN_10w_rep3

city: Gainesville

first: Karyn

middle: A

last: Esser

state: Florida

address: 1345 Center Drive M5-44

department: Department of Physiology and Aging

institute: University of Florida

data_processing:
Alignment was performed by using HISAT2 software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
Assembly: GRCm38 (mm10)
Supplementary files format and content: DESeq2 normalized counts are reported in normalized_counts_data.csv

source_name: Gastrocnemius

extract_protocol:
Samples were homogenized in TRIzol reagent and RNA was isolated using Qiagen’s RNeasy mini kit
Poly-A selected RNA-seq libraries were prepared using Illumina mRNA Prep kit following manufacturer's protocols.

value: Gastrocnemius

value: Male

tag: age

value: 10 weeks

value: KO

tag: site

value: Novogene


title: WT,Stress_OS,Slevel_HIGH,T24,REPLICATE_1

value: WT RB-TN Library


title: KO-Control_GTN_10w_rep2


title: ABE8e, replicate 1, presort, pooled, endogenous

description: pooled, endogenous

value: Adenine base editing


title: ADE N(6), 500 nM

city: Marburg

first: Julia

middle: E.

last: Weigand

address: Marbacher Weg 6

department: Pharmacy

country: Germany

institute: University of Marburg

data_processing:
NGS data were analyzed using a custom Python script. Briefly, it searches for each occurrence of a used partial random stem-loop and calculates its enrichment. The enrichment value "E" of a given random region is defined as follows E_loop=(freq_pulldown)/(freq_input)
Assembly: other
Supplementary files format and content: Excel files containing the sRBNS E-values generated by the sRBNS analysis pipeline. E represents the enrichment of a specific random region and is defined as the frequency of the random region in the reads of the pulldown divided by its frequency in the input reads.
Library strategy: RNA Bind-n-Seq

organism: synthetic construct

source_name: synthetic construct based on mouse Rc3h1

extract_protocol:
For the sRBNS experiment, a Twin-Strep tagged coreROQ domain and different pre-structured RNA input pools were used. The three different RNA input pools [CDE pool N(3), CDE pool N(3-5), ADE pool N(6)] were generated by in vitro transcription. For the sRBNS experiment, we adapted the protocol from https://doi.org/10.1016/bs.mie.2015.02.007. The protein was equilibrated in binding buffer (25 mM Tris-HCl pH 7.5, 150 mM KCl, 3 mM MgCl2, 0.01% Tween, 500 µg/mL BSA, 1 mM DTT) at three different concentrations (10, 50, 500 nM) for 30 min at 4°C. Second, the folded RNA was added to a final concentration of 1 µM together with 40 U of ribonuclease inhibitor (moloX, Berlin) and incubated for 1 h at room temperature. Pulldown was performed by incubating the RNA pool/coreROQ mixture with 1 μL of washed MagStrep "type3" XT beads (IBA Lifesciences, Göttingen, Germany) for 1 h at 4°C. Unbound RNA was then removed by washing three times with wash buffer (25 mM Tris-HCl pH 8.0, 150 mM KCl, 60 μg/ml BSA, 0.5 mM EDTA, 0.01% Tween). The RNA/coreROQ complexes were then eluted twice with 25 µL of Elution Buffer (wash buffer containing 50 mM biotin). RNA was then extracted using the Zymo RNA Clean & Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer's instructions.
The RNA extracted after pulldown was transcribed into cDNA. The cDNA was then amplified by PCR, using primers to insert an index for each concentration and Illumina adapters. Deep sequencing was then performed at GENEWIZ (Leipzig, Germany).


title: DLON,Stress_HS,Slevel_HIGH,T24,REPLICATE_1

value: DLON RB-TN Library

value: DLON


title: DLON,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_1


title: ADE N(6), 50 nM

value: synthetic construct based on mouse Rc3h1


title: DLON,Stress_CAN,Slevel_HIGH,T24,REPLICATE_1


title: DLON,Stress_HS,Slevel_LOW,T24,REPLICATE_1


title: DLON,Stress_CAN,Slevel_LOW,T24,REPLICATE_1


title: ADE N(6), 10 nM


title: DLON,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_1


title: DLON,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_1


title: DNAK-NI,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_1

value: DNAK-NI RB-TN Library

value: DNAK-NI


title: KO-GFP_GTN_10w_rep2


title: DNAK-NI,Stress_OS,Slevel_LOW,T24,REPLICATE_1


title: KO-GFP_GTN_10w_rep1


title: DNAK-NI,Stress_OS,Slevel_HIGH,T24,REPLICATE_1


title: Smarcd1_KD6_3 spheroids

city: Bethesda

first: Kent

last: Hunter

state: MD

address: 37/4048 37 Convent Drive

department: Center for Cancer Research

institute: National Cancer Institute

description:
ATAC-seq
15_6DT1_shSmarcd1_6_S15

library_source: other

data_processing:
fastq files were uploaded to PartekFlow. Unaligned reads were filtered and aligned using STAR 2.7.8a alignment rool.
Gene and transcript counts were then normalized and a batch removal was perfromed.
Gene specific analysis was performed in order to compare changes in gene and transcript expression between Smarcd1 KD or OE and their respective controls.
Gene set enrichment analysis was performed to compare gene expression pathways altered between Smarcd1 KD or OE and their respective controls.
Assembly: Reads were mapped to mm39
Supplementary files format and content: ATAC seq peaks, text file format
Supplementary files format and content: ATAC seq peaks, text file format

molecule: other

source_name: mammary

growth_protocol: These cells were grown in 3D culture. 24-well ultralow attachment plates (Corning #3473) were prepared with 500 µl of a 1:1 ratio of MethoCult H4100 (Stemcell Technologies Cat# 04100) and complete MammoCult Media (MammoCult (StemCell Technologies Cat #05620) supplemented with 10% MammoCult Proliferation Supplement (StemCell Technologies Cat#05622), 1% hydrocortisone stock solution (StemCell Technologies Cat#07925), and 0.04% heparin (StemCell Technologies Cat #07980). Cells were then seeded at 5x103 cells/well in 100 µl of complete MammoCult Media. Cells were collected after 10 days of growth in 3D culture by dilution of the methylcellulose with 1ml PBS and transfer to a microcentrifuge tube. Cells were then washed 3 times by centrifucation to pellet the cells and addition of 1ml fresh PBS.

extract_protocol:
RNA was extracted from cells 10 days after seededing. Each biological replicate was seeded from a different pasage of cells on subsequent days. Cells were collected and washed with PBS and then collected in 1ml TriPure isolation reagent, followed by organic extraction with chloroform and precipitation by isopropanol. RNA was then purified using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion. RNA quality was tested using the Agilent 2200 TapeStation electrophoresis system, and samples with an RNA integrity number (RIN) score >7 were sent to the Sequencing Facility at Frederick National Laboratory
Preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.

treatment_protocol: These cells were not treated.

value: mammary

value: mammary cancer

value: knockdown


title: KO-GFP_GTN_10w_rep3


title: DNAK-NI,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_1

value: transposon mutagenesis library


title: DNAK-NI,Stress_HS,Slevel_LOW,T24,REPLICATE_1


title: control_rep2

first: Bei

last: Lan

state: 天津Tianjin

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

data_processing:
Reads were aligned to the human genome (UCSC hg38) using HISAT2 (v2.2.1) with the following parameters: --no-mixed --no-discordant
Gene expression levels were quantified by StringTie (v2.2.1).
DESeq2 (v1.34.0) was used to perform differential expression analysis.
Assembly: hg38
Supplementary files format and content: gene_count.csv: comma-separated table file includes raw count for each example

molecule: polyA RNA

source_name: liver

growth_protocol: HepG2 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard DNBSEQ-G400 protocols.

treatment_protocol: HepG2 cells were infected with lentiviruses expressing Cas9 together with control sgRNA or USP22 sgRNA to establish control and USP22 knockout HepG2 cells, followed by treatment with Sorafenib for 24 hours.

value: liver

value: human hepatocellular carcinoma cell

value: HepG2 cells were infected with lentiviruses expressing cas9 and control sgRNA to establish control cells, followed by treatment with Sorafenib for 24 hours.


title: DNAK-NI,Stress_HS,Slevel_HIGH,T24,REPLICATE_1

source_name: DNAK-NI RB-TN Library


title: sgUSP22_rep2

value: HepG2 cells were infected with lentiviruses expressing cas9 and USP22 sgRNA to establish USP22 knockout cells, followed by treatment with Sorafenib for 24 hours.


title: DLON,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_1


title: Smarcd1_KD4_3 spheroids

description:
ATAC-seq
14_6DT1_shSmarcd1_4_S14


title: DNAK-NI,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_1


title: control _rep1


title: KO-Control_GTN_10w_rep1

value: Gastrocnemius

value: Male

value: 10 weeks

value: KO


title: Ctrl_KDScr_3 spheroids

description:
ATAC-seq
13_6DT1_shScr_S13

value: wildtype


title: DNAK-NI,Stress_CAN,Slevel_LOW,T24,REPLICATE_1


title: DNAK-NI,Stress_CAN,Slevel_HIGH,T24,REPLICATE_1


title: LP patient 7 PBMC scRNA-seq

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The scRNA sequencing data was mapped to the GRCh38 reference genome to generate gene count and cell barcode matrices using the “cellranger count” function from cellranger pipeline (version 5.0.1, 10X Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
The skin punch biopsies were incubated in 200 μl of Dispase solution (2mg/mL) for 30 minutes at  37 C. Following the incubation, the epidermis was peeled from dermis with curved forceps, washed in PBS and successively minced into < 1 mm3 pieces, using scalpel in a serum free RPMI 1640 media with DNase I (0.2 mg/mL), 20 mM HEPES and 0.25 mg/ml Liberase TM, Roche. The suspension was incubated for 90 minutes at 37 C. The digestion was stopped by adding 100 μl FBS and 3 μl of 0.5 M EDTA and filtered through a 70-mm cell strainer. The cells were pelleted and washed twice with PBS containing 1% BSA. Finally the cells were resuspended in PBS containing 0.04% BSA and an aliquot was taken for counting.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion. The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated 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 sequences and a sample index were added.

value: Blood

tag: subject status

value: Lichen planus (LP) patient

value: PBMCs


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_1

value: DNAK-NI RB-TN Library

value: DNAK-NI


title: DNAK-NI,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_1


title: sgUSP22_rep1


title: Smarcd1_KD4_2 spheroids

description:
ATAC-seq
11_6DT1_Empty_Vector_2pt5_S11

value: mammary

value: mammary cancer


title: DCLPA,Stress_OS,Slevel_MEDIUM,T24,REPLICATE_1

value: DCLPA RB-TN Library

value: transposon mutagenesis library

value: DCLPA


title: LP patient 5 PBMC scRNA-seq

description: 10x Genomics


title: DCLPA,Stress_HS,Slevel_MEDIUM,T24,REPLICATE_1


title: Ctrl_KDScr_2 spheroids

description:
ATAC-seq
10_6DT1_shSmarcd1_6_S10


title: LP patient 4 PBMC scRNA-seq

description: 10x Genomics


title: DCLPA,Stress_OS,Slevel_LOW,T24,REPLICATE_1


title: DCLPA,Stress_CAN,Slevel_MEDIUM,T24,REPLICATE_1


title: LP patient 3 PBMC scRNA-seq

description: 10x Genomics


title: DCLPA,Stress_HS,Slevel_HIGH,T24,REPLICATE_1


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T0,REPLICATE_1


title: LP patient 2 PBMC scRNA-seq

description: 10x Genomics


title: Smarcd1_KD4_1 spheroids

description:
ATAC-seq
8_6DT1_shScr_S8

value: knockdown


title: DCLPA,Stress_CAN,Slevel_LOW,T24,REPLICATE_1


title: Smarcd1_KD6_1 spheroids

description:
ATAC-seq
9_6DT1_shSmarcd1_4_S9


title: DCLPA,Stress_CONTROL,Slevel_CONTROL,T24,REPLICATE_1


title: Ctrl_KDScr_1 spheroids

description:
ATAC-seq
7_6DT1_Smarcd1_Over_Epxression_2_S7


title: LP patient 1 PBMC scRNA-seq

description: 10x Genomics


title: Smarcd1_OverExpression_3 spheroids

description:
ATAC-seq
6_6DT1_Empty_Vector_2pt5_S6

value: over expression


title: Structure-seq, HEK293T, STM2457, NAI, Rep2

city: Hong Kong

first: Yuwei

last: ZHANG

state: Hong Kong

address: Rm503, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital, Shatin, NT, HK

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

description: HEK293T_STM2457_statistic_reactivity.csv

data_processing:
The adapters were first removed using Cutadapt v1.15 and the reads shorter than 20nt or with quality score lower than 30 were filtered out.
The remaining reads were mapped to human or mouse transcriptome reference using Bowtie2 v2.3.3.1.
Next, the mapped reads with more than 3 mismatches or mismatch at the first base were removed, RT stops were counted and reactivity scores were calculated using StructureFold2 package.
Assembly: hg38
Supplementary files format and content: comma-delimited text file includes SHAPE reactivity score of each transcript
Library strategy: Structure-seq

extract_protocol:
poly(A)-selected RNAs
Each library was prepared with 500 ng poly(A)-selected RNAs after 2 rounds of selection (Thermo Fisher Scientific, AM1922). The poly(A) RNAs were fragmented to around 300 nt length at 95°C for 1 min and purified using RNA clean and concentrator (Zymo research, R1016). The fragmented RNA was then subjected to a 5' dephosphorylation reaction at 37°C for 30 min by adding rSAP (NEB, M0371L) and PNK enzyme (NEB, M0201S) in 1× T4 PNK buffer (NEB, B0201S). Next, the 3’adapter was ligated to the dephosphorylated RNA using T4 RNA ligase 2 KQ (NEB, M0373L) at 25°C for 1 h. Excess adapters were digested and removed by adding RecJf (NEB, M0331) and 5’ deadenylase (NEB, M0331) for 30 min at 30°C followed by column purification (Zymo research, R1016). The following reverse transcription (RT) was performed in 1 X RT buffer (20 mM Tris, pH 7.5, 4 mM MgCl2, 1 mM DTT, 0.5 mM dNTPs, 150 mM LiCl) with SuperScript III enzyme (Thermo Scientific, 18080093) at 42°C for 40 min. RNA was digested by 2M NaOH and the reaction was neutralized with 1M Tris-HCl (pH 7.5) followed by column purification (Zymo research, R1016). The 5’adapter (for C2C12 libraries) or dU adapter (for HEK293T libraries) was ligated to the cDNA with Quick T4 DNA ligase (NEB, M2200L) and incubated in 37°C overnight. For the C2C12 library, the ligated product was run on the 10% denaturing urea-TBE acrylamide gel (Thermo Scientific, EC68752BOX), and the 100–400 nt region was cut and dissolved in 1X TEN250 buffer (1X TE 7.4, 0.25 M NaCl) at 80°C for 30 min followed by column purification (Zymo research, R1016). For the HEK293T libraries, the ligated product was first purified by column (Zymo research, R1016), then USER II enzyme (NEB, M5509) was added to cleave the product followed by a second column purification (Zymo research, R1016). The purified product was used for PCR cycle test and amplification with different barcoded reverse primer. PCR products with 150–400 bp were then cut and purified with 2% agarose gel and column (Zymo research, D4008).

treatment_protocol: For HEK293T cells, the control and STM2457-treated cells were harvested in 1X PBS buffer (Thermo Fisher Scientific, 10010049) and probed with NAI (50 mM in final) or 5% DMSO as negative control for 15 min at 37°C, 500 rpm. Then DTT (200mM in final) was added immediately to quench each probing reaction. After spinning down the cells (~ 500 g) for 3 min at room temperature, total RNAs were extracted and quantified using RNeasy Plus Mini Kit (Qiagen, 74136) and Nanodrop ND-1000 Spectrophotometer.

value: WT


title: Structure-seq, HEK293T, STM2457, DMSO, Rep1


title: Structure-seq, HEK293T, STM2457, DMSO, Rep2


title: Smarcd1_KD6_2 spheroids

description:
ATAC-seq
12_6DT1_Smarcd1_Over_Epxression_2_S12


title: LP patient 7 unaffected skin scRNA-seq

description: 10x Genomics

source_name: Skin

value: Skin


title: LP patient 6 PBMC scRNA-seq

description: 10x Genomics


title: Structure-seq, HEK293T, STM2457, NAI, Rep1


title: DCLPA,Stress_OS,Slevel_HIGH,T24,REPLICATE_1

source_name: DCLPA RB-TN Library


title: Structure-seq, HEK293T, Control, DMSO, Rep2

description: HEK293T_control_statistic_reactivity.csv

value: DMSO+DMSO


title: Ctrl_ EmptyVector 3 spheroids

description:
ATAC-seq
5_6DT1_shSmarcd1_6_S5


title: Structure-seq, HEK293T, Control, DMSO, Rep1


title: LP patient 6 unaffected skin scRNA-seq

description: 10x Genomics


title: Smarcd1_OverExpression_2 spheroids

description:
ATAC-seq
4_6DT1_shSmarcd1_4_S4


title: Structure-seq, HEK293T, Control, NAI, Rep1

value: DMSO+NAI


title: Structure-seq, HEK293T, Control, NAI, Rep2


title: CLIP-seq, HEK293T, WT, Rep2

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

data_processing:
The pipeline includes adapter trimming using Cutadapt, mapping using BWA, duplicate removal, peak calling using the CIMS pipeline in CTK. Next, deepTools 89 was used to compare the signals of YTHDF1 binding within DHX36 binding sites between WT and DHX36-KO samples.
Assembly: hg38
Supplementary files format and content: bed format; peak location
Library strategy: CLIP-seq

extract_protocol:
Immunopreciptation was performed using 10 µg anti-YTHDF1 antibody, or normal IgG control respectively for overnight at 4°C with rotation. Next day, 125 µl washed Dynabeads Protein G was added to each reaction and incubated for another 4 hours with rotation. Beads were collected and washed twice with high salt wash buffer and twice with wash buffer. After washing, 1/10 volume of beads were saved to determine immunoprecipitation efficiency. The remaining cross-linked RNA complexes were dephosphorylated by incubating with Quick CIP for 20 min at 37°C, followed by treatment with T4 PNK enzyme in acid PNK buffer for 20 min at 37°C.
The RNA-protein complexes were used for on-bead 3’ RNA linker ligation and incubated in a 25 µl reaction volume. The beads were then denatured in loading buffer and resolved on a Novex NuPAGE 4-12% Bis-Tris gel and then transferred to 0.45 µm nitrocellulose membranes. The biotin reaction group was then subjected to biotin detection. For CLIP-seq, labeled YTHDF1-RNA bands were excised from the membrane and eluted. RNA was subsequently purified and 5’ ends phosphorylated with T4 PNK and then ligated to 5’ RNA adaptor. The resultant RNA was reverse transcribed with RP1 primer. The full-scale PCR amplification was performed.


title: Ctrl_ EmptyVector 2 spheroids

description:
ATAC-seq
3_6DT1_shScr_S3

value: wildtype


title: LP patient 3 unaffected skin scRNA-seq

description: 10x Genomics


title: CLIP-seq, HEK293T, WT, Rep1


title: LP patient 4 unaffected skin scRNA-seq

description: 10x Genomics


title: Smarcd1_OverExpression_1 spheroids

description:
ATAC-seq
2_6DT1_Smarcd1_Over_Epxression_2_S2


title: CLIP-seq, HEK293T, DHX36-KO, Rep1


title: CLIP-seq, HEK293T, DHX36-KO, Rep2


title: LP patient 2 unaffected skin scRNA-seq

description: 10x Genomics


title: Ctrl_ EmptyVector 1 spheroids

description:
ATAC-seq
1_6DT1_Empty_Vector_2pt5_S1


title: LP patient 1 unaffected skin scRNA-seq

description: 10x Genomics


title: DalgU_pH6.5modifiedKB_rep3

city: Ithaca

first: Bryan

last: Swingle

state: NY

address: 302 Plant Science Building

institute: USDA-ARS

data_processing:
Illumina pipeline software was used for base calling.
Sequenced reads were trimmed for 3' adaptor sequence and low-quality sequence and filtered to remove reads < 50nt with TrimGalore/cutadapt.
Processed reads were mapped to the reference genome/transcriptome with STAR using --quantMode GeneCounts to generate raw counts per gene.
Raw counts were analyzed in R with DEseq2.
Assembly: GCF_000007805.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Pseudomonas syringae pv. tomato str. DC3000

source_name: bacteria

growth_protocol: Pst DC3000 strainswere grown at 28°C in King’s B (KB) medium  and on KB medium solidified with 1.5% (w/v) agar.

extract_protocol:
Total RNA was isolated with Trizol, with an extra chloroform extraction to remove residual phenol and addition of glyco-blue as a carrier to promote RNA precipitation. RNA concentration was determined with a Nanodrop and integrity assessed on a Fragment Analyzer.
Directional RNA-seq libraries were prepared from 500ng total RNA using the NEBNext Directional Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), with initial rRNA depletion.

treatment_protocol: Wild type and ΔalgU mutant of Pst DC3000 strains were grown overnight in standard KB and then resuspended in 5 ml of pH-altered KB media at OD600 value of 0.4. These cultures were incubated for three hours at 28°C with shaking and subsequently collected for RNA extraction

value: bacteria

value: DalgU

value: pH6.5 modified KB


title: Smarcd1_KD6_3 RNA-Seq on plastic

data_processing:
fastq files were uploaded to PartekFlow. Unaligned reads were filtered and aligned using STAR 2.7.8a alignment rool.
Gene and transcript counts were then normalized and a batch removal was perfromed.
Gene specific analysis was performed in order to compare changes in gene expression between Smarcd1 KD or OE and their respective controls.
Gene set enrichment analysis was performed to compare gene expression pathways altered between Smarcd1 KD or OE and their respective controls.
Assembly: Reads were mapped to mm39
Supplementary files format and content: gene expression values, tab separated text file

growth_protocol: These cells were grown in monolayer culture on tissue culture plasticwear in DMEM + 10% FBS supplemented with 1% Penicillin and Streptomycin and 1% glutamine

extract_protocol:
RNA was extracted from cells 24hrs after seededing at 70% confluence. Each biological replicate was seeded from a different pasage of cells on subsequent days. Cells were washed with PBS and then collected in 1ml TriPure isolation reagent, followed by organic extraction with chloroform and precipitation by isopropanol. RNA was then purified using the RNeasy Mini Kit (Qiagen) with on-column DNase digestion. RNA quality was tested using the Agilent 2200 TapeStation electrophoresis system, and samples with an RNA integrity number (RIN) score >7 were sent to the Sequencing Facility at Frederick National Laboratory
Preparation of mRNA libraries and mRNA sequencing was performed by the Sequencing Facility using the HiSeq2500 instrument with Illumina TruSeq v4 chemistry.


title: DalgU_pH7.8modifiedKB_rep3

value: pH7.8 modified KB


title: WT_pH7.8modifiedKB_rep3


title: LP patient 7 affected skin scRNA-seq

description: 10x Genomics

value: Lichen planus (LP) patient


title: DalgU_pH5.5modifiedKB_rep3

value: pH5.5 modified KB


title: WT_pH6.5modifiedKB_rep3


title: LP patient 6 affected skin scRNA-seq

description: 10x Genomics


title: WT_pH5.5modifiedKB_rep3


title: Smarcd1_KD4_3 RNA-Seq on plastic

value: mammary

value: mammary cancer


title: DalgU_pH7.8modifiedKB_rep2


title: Smarcd1_KD6_2 RNA-Seq on plastic


title: DalgU_pH6.5modifiedKB_rep2


title: Ctrl_KDScr_3 RNA-Seq on plastic


title: LP patient 5 affected skin scRNA-seq

description: 10x Genomics


title: LP patient 4 affected skin scRNA-seq

description: 10x Genomics


title: WT_pH7.8modifiedKB_rep2


title: DalgU_pH5.5modifiedKB_rep2


title: Smarcd1_KD4_2 RNA-Seq on plastic


title: WT_pH5.5modifiedKB_rep2


title: Ctrl_KDScr_2 RNA-Seq on plastic


title: DalgU_pH7.8modifiedKB_rep1


title: Smarcd1_KD6_1 RNA-Seq on plastic


title: LP patient 2 affected skin scRNA-seq

description: 10x Genomics


title: DalgU_pH5.5modifiedKB_rep1


title: LP patient 1 affected skin scRNA-seq

description: 10x Genomics


title: WT_pH7.8modifiedKB_rep1


title: WT_pH5.5modifiedKB_rep1


title: ADE N(6), input library

source_name: synthetic sequence library

value: synthetic sequence library


title: WT_pH6.5modifiedKB_rep1


title: DalgU_pH6.5modifiedKB_rep1


title: Ctrl_KDScr_1 RNA-Seq on plastic


title: RBNS, RHAU53, Synthesized construct, 1300nM, Li+

data_processing:
RBNS data were analyzed using rbns_pipeline software (https://github.com/alexrson/rbns_pipeline).
Assembly: synthetic construct
Supplementary files format and content: Tab-delimited text file includes the enrichment levels of RBNS 6mers

source_name: N/A (synthetic construct)

extract_protocol:
RNAs with a random region of 40nt were prepared by in vitro transcription (NEB, E2040S) and incubated with an increasing concentration of RHAU53 (5, 20, 80, 320 and 1300nM). The RNA pool resolved by 10% PAGE gel and purified (Zymo Research, R1016). Concentrated RNAs were heated at 85C for 5 min in the presence of 150 mM KCl or LiCl and allowed to cool for at least 3 min to allow for folding. 10 µl NEBExpress® Ni-NTA Magnetic Bead (NEB, S1423L) was used to replace the Dynabeads MyOne Streptavidin T1 in old method to pull-down the His tagged protein-RNA complexes. All wash and binding buffers contained either 150 mM KCl or LiCl. Protein-RNA complexes were eluted in the final buffer concentration of 20 mM Tris-HCl (pH 7.5), 150mM KCl or LiCl, 500mM Imidazole (pH 7.4) and 8M Urea. RNAs were isolated and reversely transcribed for PCR amplification and sequencing
RNA Bind-n-Seq

value: N/A (synthetic construct)

value: Li+


title: CDE N(3-5), 500 nM

value: synthetic construct based on mouse Rc3h1


title: RBNS, RHAU53, Synthesized construct, 1300nM, K+

value: K+


title: RBNS, RHAU53, Synthesized construct, 320nM, Li+


title: Smarcd1_OverExpression_3 RNA-Seq on plastic

value: over expression


title: CDE N(3-5), 50 nM


title: Ctrl_ EmptyVector 3 RNA-Seq on plastic


title: CDE N(3-5), 10 nM


title: LP patient 3 affected skin scRNA-seq

description: 10x Genomics

value: Skin


title: RBNS, RHAU53, Synthesized construct, 320nM, K+


title: WT_pH6.5modifiedKB_rep2

value: WT


title: CDE N(3-5), input library


title: RBNS, RHAU53, Synthesized construct, 5nM, Li+


title: Smarcd1_KD4_1 RNA-Seq on plastic

value: knockdown


title: Ctrl_ EmptyVector 2 RNA-Seq on plastic

value: wildtype


title: CDE N(3), 50 nM


title: RBNS, RHAU53, Synthesized construct, 5nM, K+


title: Ctrl_ EmptyVector 1 RNA-Seq on plastic


title: RBNS, RHAU53, Synthesized construct, 80nM, K+


title: RBNS, RHAU53, Synthesized construct, 80nM, Li+


title: RBNS, RHAU53, Synthesized construct, 20nM, Li+


title: 6DT1 shSmarcd1 #4 rep3 [RNA-seq spheroids]

data_processing:
fastq files were uploaded to PartekFlow. Unaligned reads were filtered and aligned using STAR 2.7.8a alignment rool.
Gene and transcript counts were then normalized and a batch removal was perfromed.
Gene specific analysis was performed in order to compare changes in gene and transcript expression between Smarcd1 KD or OE and their respective controls.
Gene set enrichment analysis was performed to compare gene expression pathways altered between Smarcd1 KD or OE and their respective controls.
Assembly: Reads were mapped to mm39
Supplementary files format and content: gene expression data, text file

tag: protocol


title: skeletal muscle_contusion_60min_rep3

type: RNA

city: Shanghai

first: laimeng

last: song

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

institute: University of Shanghai for Science and Technology

description:
Gene expression in bruised mouse skeletal muscle after 1 hour
inj_3

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 12.6 (Agilent technologies, Santa Clara, CA, US).

data_processing: Rstudio was used to analyze the gene expression differences between the two groups based on the sequenced data, select miR-with significant expression, and search for targeted mRNA for functional enrichment analysis.

source_name: skeletal muscle,1day,2.5Gy,replicate 1

label_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

extract_protocol: RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit

value: mice skeletal muscle

tag: group

value: contusion


title: Smarcd1_OverExpression_2 RNA-Seq on plastic


title: 6DT1 shScr rep3 [RNA-seq spheroids]


title: sgUSP22_input

data_processing:
Reads were aligned to the human genome (UCSC hg38) and Drosophila melanogaster genome (UCSC dm3) using Bowtie2 (v2.4.5).
Dupulicates were removed by Sambamba (v1.0).
Mapped reads with high confidence were sorted, indexed, and transformed to bam format using SAMtools (v1.6).
Spike-in normalized bigwig files were generated using the deepTools (v3.5.4)
Peak was called by MACS2 (v2.2.9.1).
Assembly: hg38 and dm3
Supplementary files format and content: bigWig files

growth_protocol: HepG2 cells were cultured in Dulbecco's modified Eagle’s medium supplemented with 10% fetal bovine serum at 37℃ in a humidified atmosphere with 5% CO2. Drosophila Schneider 2 cells (S2 cells) were cultured in SFX-Insect medium supplemented with 10% fetal bovine serum at 27℃.

extract_protocol:
HepG2 cells were cross-linked with 1% formaldehyde for 10 minutes and quenched with 0.125 M glycine. Cells were then resuspended in SDS buffer. The resulting cell pellets were resuspended in ice-cold immunoprecipitation (IP) buffer, and subjected to sonication. Drosophila Schneider 2 cells (S2 cells) were prepared and processed in the same manner. Depending on the DNA concentration of each sample, chromatin from HepG2 cells was mixed with S2 cell chromatin at a ratio of 5:1. Subsequently, the chromatin was incubated overnight at 4°C with H2BK120ub antibodies. Protein A/G beads were then added at 4℃ for 4 hours. After thorough washes, samples were incubated in de-cross-linking buffer at 65°C for 6 hours, and DNA was extracted.
The DNA fragments were repaired and dA-tailed, after which they were ligated to sequencing adaptors. The final DNA library was obtained by size selection and PCR amplification.
Spike-in ChIP-seq

value: human hepatocellular carcinoma cell

value: HepG2 cells were infected with lentiviruses expressing cas9 and USP22 sgRNA to establish USP22 knockout cells, followed by treatment with Sorafenib for 24 hours.


title: sgUSP22_H2BK120ub_ChIP

tag: antibody


title: polII-E14-16h-Spt6KD-rep2

city: Wuhan

first: Shaobo

last: Liang

state: Hubei Sheng

address: BaYi Road, LUOJIA HILL

institute: Wuhan University

description: ChIP-seq

data_processing:
Reads trimmed by trim_galore were mapped to genome using bowtie2 (Cut&Tag and ChIP) or STAR (RNA-seq)
Redundant reads were deduplicated by picard
Peaks determintion was performed through Macs2 callpeak command. Deeptools bamCoverage converted BAM files into bigwig files
IDR was used to combine peaks of different replicates
FeatureCounts counted the read number on  gene level for each sample
Assembly: dm6, Ecoli
Supplementary files format and content: Cut&Tag and ChIP-seq bigwig file and narrowPeak file
Supplementary files format and content: gene read count for RNA-seq

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
cut&tag：Cells were immobilized on coA beads, antibodies were bound in antibody buffer  (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin, 0.01% NP-40, 2 mM EDTA),  and activate Tn5-PA transposase activity in tagmentation buffer  (10 mM MgCl2, 20 mM HEPES at pH 7.5, 300 mM NaCl, 0.5 mM spermidine, 1× protease inhibitors, 0.05% digitonin) , and cells were lysed to extract library fragments by add  1.5 μl 0.5 M EDTA, 0.5 μl 10% SDS and 1 μl 20 mg/mL proteinase K (sigma).                                                                            pol2 chip-seq：Cells were fixed with 1% paraformaldehyde for 10 min, and the chromosomes were fragmented using an ultrasonic crusher after lysis of the cells.                                                                                RNA-seq: RNA was extracted using trizol. 200 ng of total RNA was used to construct sequencing libraries.
cut&tag: 1×Agencourt AMPure XP beads (Beckman Coulter, A63881) were used to purify the tagementated DNA and eluted in 10 μl 0.1% Tween-20. The eluent was mixed with 10 U Bst 2.0 WarmStart DNA polymerase (NEB, M0538) in 1× Q5 polymerase reaction buffer, incubated at 65 °C for 30 minutes and stopped by incubation at 80 °C for 20 minutes. The universal i5 primer, barcoded i7 primer and Phanta EVO Super-Fidelity DNA Polymerase (Vazyme, P503) were added to amplify the R-loop CUT&Tag library. The libraries were size-selected with 0.56-0.85* Sera-Mag carboxylate-modified magnetic beads and eluted in 20 ul RNase-free water.                                                              pol2 chip-seq:  5ng DNA was used for dsDNA library construction according to manufacturer’s instructions (Rapid Plus DNA Lib Prep Kit for Illumina V2, ABclonal, RK20255).   The library was amplified for 13 cycles on the thermocycler.                                      RNA-seq:RNA libraries for Rna-Seq was prepared using MGIEasy RNA library Prep kit following manufacturer‘s protocols.
cut&tag
pol2 chip-seq
RNA-seq

value: embryo

tag: time

tag: chip antiobdy

value: Anti-RNA polymerase II  CTD repeat YSPTSPS (phospho S5) antibody(Abcam,#ab5408)


title: skeletal muscle_No contusions_60min_rep4

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in mouse skeletal muscle with no bruising after 1 hour
ct_4

source_name: skeletal muscle,7day,1.5Gy,replicate 1

value: healthy


title: skeletal muscle_contusion_60min_rep1

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in bruised mouse skeletal muscle after 1 hour
inj_1

source_name: skeletal muscle,1day,1Gy,replicate 1


title: skeletal muscle_contusion_60min_rep4

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in bruised mouse skeletal muscle after 1 hour
inj_4

source_name: skeletal muscle,1day,3Gy,replicate 1


title: skeletal muscle_contusion_60min_rep2

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in bruised mouse skeletal muscle after 1 hour
inj_2

source_name: skeletal muscle,1day,3.5Gy,replicate 1


title: Smarcd1_OverExpression_1 RNA-Seq on plastic

value: mammary

value: mammary cancer


title: RBNS, RHAU53, Synthesized construct, 0.5pmol, input

value: N/A (synthetic construct)

value: No


title: control_input

value: HepG2 cells were infected with lentiviruses expressing cas9 and control sgRNA to establish control cells, followed by treatment with Sorafenib for 24 hours.


title: polII-E14-16h-Spt6KD-rep1

description: ChIP-seq


title: polII-E14-16h-Ctrl-rep2

description: ChIP-seq

value: Ctrl


title: EZIMR90_48hrs_Samples1-6

city: Madison

first: Ryan

middle: Scott

last: Anderson

state: WI

address: 2015 Linden Drive

department: Department of Surgical Sciences

institute: University of Wisconsin-Madison School of Veterinary Medicine

description: mix7 contains 6 samples (EZIMR90_A1, EZIMR90_A2, EZIMR90_Y1, EZIMR90_Y2, EZIMR90_CTRL-01, EZIMR90_CTRL-2); demultiplex using barcodes provded in sample_barcodes.txt.gz

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (version 0.6.10).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Reads were sorted and indexed using SAMtools (version 1.10)
Gene count was obtaind by featureCounts(ver.2.0.6) and UMI duplication was removed by using UMI tools (ver.1.1.4).
Assembly: GRCh38
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

source_name: Cell Line

growth_protocol: The colonies were maintained in  expansion medium consisting of Stemline medium (S-3194, Sigma-Aldrich), 100 ng/ml human fibroblast growth factor-2 (FGF-2; WiCell), 100 ng/ml human epidermal growth factor (EGF; Millipore, Billerica, MA), 5 ng/ml heparin sulfate (Sigma-Aldrich), and penicillin/streptomycin/amphotericin B (PSA, 1%v/v; Life Technologies). They were kept at 37C and 5% CO2.

extract_protocol:
Total RNA was isolated from plated down EZ sphere cells that were maintained in the serum-supplemented medium (aged, young, or serum-free) for 48 hours using Direct-zol RNA Kit (Zymo Research, Irvine, CA, USA)
Libraries were prepared by BRB-Seq (Alpern D, et al. 2019) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

treatment_protocol: The expansion medium was supplemented with no serum, aged serum, or young serum from Fischer 344 × Brown Norway F1-hybrid rats at day 0.

value: Cell Line

value: Stem cell

value: myogenic differentiation,  serum supplementation


title: skeletal muscle_No contusions_60min_rep3

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in mouse skeletal muscle with no bruising after 1 hour
ct_3

source_name: skeletal muscle,7day,1Gy,replicate 1


title: EZH9_48hrs_Samples1-6

description: mix8 contains 6 samples (EZH9_A1, EZH9_A2, EZH9_Y1, EZH9_Y2, EZH9_CTRL-01, EZH9_CTRL-02); demultiplex using barcodes provded in sample_barcodes.txt.gz

value: WT


title: 6DT1 Empty Vector 2.5 rep3 [RNA-seq spheroids]

source_name: mammary

value: wildtype


title: 6DT1 shSmarcd1 #6 rep3 [RNA-seq spheroids]

value: knockdown


title: polII-E14-16h-Ctrl-rep1

description: ChIP-seq


title: Rloop-E14-16h-Spt6KD-rep2

description: Cut&Tag


title: 6DT1 shSmarcd1 #6 rep2 [RNA-seq spheroids]


title: HepG2 HNF1A KD, biological replicate 2

data_processing:
Reads were aligned to GRCh38 (for human cells) or GRCm38 (for mouse cells) and counted in gencode v38 (human) or M10 (mouse) genes with STAR 2.5.4a
Assembly: mm10/hg38
Supplementary files format and content: File contains raw read counts per gene.

source_name: liver

value: liver

value: liver cancer


title: Rloop-E14-16h-Ctrl-rep2

description: Cut&Tag

value: embryo


title: Rloop-E14-16h-Spt6KD-rep1

description: Cut&Tag


title: 6DT1 shSmarcd1 #4 rep2 [RNA-seq spheroids]


title: Rloop-E14-16h-Ctrl-rep1

description: Cut&Tag


title: 6DT1 Smarcd1 Over Epxression 2 rep3 [RNA-seq spheroids]

value: over expression


title: 6DT1 shScr rep2 [RNA-seq spheroids]


title: HepG2 HNF1A KD, biological replicate 1


title: 6DT1 Smarcd1 Over Epxression 2 rep2 [RNA-seq spheroids]


title: skeletal muscle_No contusions_60min_rep2

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in mouse skeletal muscle with no bruising after 1 hour
ct_2

source_name: skeletal muscle,7day,0Gy,replicate 1

value: mice skeletal muscle

value: healthy


title: Rloop-L3-stages-rep2

description: Cut&Tag

source_name: larva

value: larva


title: Rloop-L3-stages-rep1

description: Cut&Tag


title: Rloop-E8-10h-stages-rep2

description: Cut&Tag


title: Rloop-E20-22h-stages-rep1

description: Cut&Tag


title: HepG2 MTF1 KD, biological replicate 2


title: Rloop-E20-22h-stages-rep2

description: Cut&Tag


title: 6DT1 shSmarcd1 #6 rep1 [RNA-seq spheroids]

value: mammary

value: mammary cancer


title: HepG2 NRF1 KD, biological replicate 2


title: Rloop-E8-10h-stages-rep1

description: Cut&Tag


title: HepG2 MTF1 KD, biological replicate 1


title: skeletal muscle_No contusions_60min_rep1

address: 五角镇街道佳木斯路2号复旦大学科技园2号楼216

description:
Gene expression in mouse skeletal muscle with no bruising after 1 hour
ct_1

source_name: skeletal muscle,7day,2Gy,replicate 1


title: Rloop-E2-4h-stages-rep1

description: Cut&Tag


title: 6DT1 Empty Vector 2.5 rep2 [RNA-seq spheroids]


title: control_H2BK120ub_ChIP

value: human hepatocellular carcinoma cell

value: HepG2 cells were infected with lentiviruses expressing cas9 and control sgRNA to establish control cells, followed by treatment with Sorafenib for 24 hours.


title: Rloop-0DMF-E14-16h-rep2

description: Cut&Tag


title: Rloop-0DMF-E14-16h-rep1

description: Cut&Tag


title: 6DT1 shSmarcd1 #4 rep1 [RNA-seq spheroids]


title: HepG2, biological replicate 3


title: 6DT1 shScr rep1 [RNA-seq spheroids]


title: 10% DMF-E10-14h-with-RNaseA

description: Cut&Tag

value: 10%DMF+RNase A


title: 10% DMF-E10-14h-without-RNaseA

description: Cut&Tag


title: HepG2, biological replicate 2


title: HepG2 NRF1 KD, biological replicate 1


title: 5% DMF-E10-14h-without-RNaseA

description: Cut&Tag


title: 6DT1 Smarcd1 Over Epxression 2 rep1 [RNA-seq spheroids]


title: Rloop-E2-4h-stages-rep2

description: Cut&Tag


title: 5% DMF-E10-14h-with-RNaseA

description: Cut&Tag

value: 5%DMF+RNase A


title: 6DT1 Empty Vector 2.5 rep1 [RNA-seq spheroids]


title: 2.5% DMF-E10-14h-with-RNaseA

description: Cut&Tag

value: 2.5%DMF+RNase A


title: 2.5% DMF-E10-14h-without-RNaseA

description: Cut&Tag


title: 0% DMF-E10-14h-without-Rnase

description: Cut&Tag


title: evoCDA, replicate 3, CD19 negative, pooled, gRNA

description: pooled, gRNA

data_processing:
After sequencing, the sequencing core facility performed the primary demultiplexing based on the P7 index. Subsequently, our laboratory conducted a secondary demultiplexing step using the P5 index, which is located internally within the read.
For each demultiplexed FASTQ, “raw” guide mapping was performed using CRISPR-SURF Count in base-editing mode. To identify significant regions based on the mapped guide RNA counts, we ran CRISPR-SURF Deconvolution on both the ABE8e and evoCDA datasets.
The paired-end FASTQs were also quality controlled with FastQC and MultiQC to ensure sufficient sequencing quality of our samples. Next, the paired-end FASTQs were passed into CRISPResso2 for read merging, alignment, and quantification of the edited alleles. The CRISPResso2 allele frequency tables were encoded into a feature indicator matrix containing columns for all possible REF>ALT variants across the amplicon and rows for all unique alleles. The matrices are then modeled by Millipede, a PyTorch-based Bayesian variable selection model, to generate beta coefficients and posterior inclusion probabilities for each feature (per-nucleotide).
The encoding matrix from CRISPR-Millipede, along with a design matrix describing the conditions of each sample (replicate and sorting population), was also passed into into pyDESeq2, a statistical package used to calculate differential expression of alleles between the CD19 positive and CD19 negative populations. The log fold change and adjusted p-value were plotted for the alleles observed across the cellular populations.
Assembly: N/A
Supplementary files format and content: "encoding" tsv file, produced by encoding the CRISPresso2 allele frequency tables into a feature indicator matrix, fed into CRISPR-Millipede
Supplementary files format and content: "hit_table" csv file, table of scores for hits modeled by CRISPR-Millipede

extract_protocol:
Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen).
For sgRNA count, the sgRNA cassette was PCR amplified from genomic DNA using primers carrying partial Illumina adaptor. PCR products were then re-amplified using primers carrying sample-specific barcode combinations. The endogenous CD19 enhancer sequence was PCR-amplified and barcoded using a similar strategy.
Distributions of edits within a 346 bp fragment of the CD19 enhancer were obtained by targeted amplicon sequencing using MiSeq at PE250 and PE300 configuration. Guide RNAs were enumerated by NGS as previously reported (Seruggia et al. Mol Cell 2019).

value: B cell precursor leukemia

value: CD19 enhancer pertubation

value: CD19 negative

value: Cytosine base editing


title: Smarcd1_KD6_3

description:
ATAC-seq
Sample_15_S15

data_processing:
fastq files were uploaded to PartekFlow. Unaligned reads were filtered and aligned using STAR 2.7.8a alignment rool.
Gene and transcript counts were then normalized and a batch removal was perfromed.
Gene specific analysis was performed in order to compare changes in gene expression between Smarcd1 KD or OE and their respective controls.
Gene set enrichment analysis was performed to compare gene expression pathways altered between Smarcd1 KD or OE and their respective controls.
Assembly: Reads were mapped to mm39
Supplementary files format and content: ATAC seq peaks, text file

value: knockdown


title: evoCDA, replicate 3, CD19 positive, pooled, gRNA

description: pooled, gRNA

value: CD19 positive


title: znf598 knockout, 6 hpf, rep3

data_processing:
Basecalling with Illumina Casava 1.8 software
Analyzed using Galaxy on public server
3' adapter trimming with Fastp
Alignment to genome with STAR v2.7.8a with --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 options
Read quantitation using featureCounts v3.36.0
Assembly: GRCz11
Supplementary files format and content: text files (tab-separated values) contain two columns: 1. gene id; 2. read counts

source_name: Whole embryo

extract_protocol:
Total RNA was extracted using TRI Reagent (Molecular Research Center) and treated with DNase I.
Library preparation using Ribo-Zero Gold rRNA Removal Kit followed by TruSeq Stranded Total RNA Library Prep Kit (Illumina)

value: Whole embryo

value: znf598 knockout mutant


title: HepG2, biological replicate 1

extract_protocol:
1x10^6 cells were resuspended in 600 uL RLT buffer (Qiagen). RNA was extracted using RNeasy plus kit (Qiagen).
Libraries were prepared using Illumina stranded RNA Library kit following manufacturer's instructions.

value: liver

value: liver cancer


title: Smarcd1_KD4_3

description:
ATAC-seq
Sample_14_S14

value: mammary


title: 0% DMF-E10-14h-with-Rnase

description: Cut&Tag

value: embryo

value: 0%DMF+RNase A


title: S2-cell-without-RNaseA

description: Cut&Tag

source_name: S2 cells

value: S2 cells

value: germ cells


title: S2-cell-with-RNaseA

description: Cut&Tag

value: 10%DMF+RNase A


title: Ctrl_KDScr_3

description:
ATAC-seq
Sample_13_S13

value: mammary cancer

value: wildtype


title: evoCDA, replicate 3, presort, pooled, gRNA

description: pooled, gRNA

value: B cell precursor leukemia

value: CD19 enhancer pertubation

value: presort


title: evoCDA, replicate 2, CD19 negative, pooled, gRNA

description: pooled, gRNA

value: CD19 negative

value: Cytosine base editing


title: znf598 knockout, 6 hpf, rep2

value: Whole embryo


title: Smarcd1_KD6_2

description:
ATAC-seq
Sample_12_S12

value: knockdown


title: znf598 knockout, 6 hpf, rep1

value: znf598 knockout mutant


title: znf598 knockout, 1 hpf, rep3


title: evoCDA, replicate 2, CD19 positive, pooled, gRNA

description: pooled, gRNA

value: CD19 positive


title: znf598 knockout, 1 hpf, rep2


title: Smarcd1_KD4_2

description:
ATAC-seq
Sample_11_S11

value: mammary


title: znf598 knockout, 1 hpf, rep1


title: Smarcd1_KD6_1

description:
ATAC-seq
Sample_9_S9


title: evoCDA, replicate 1, CD19 negative, pooled, gRNA

description: pooled, gRNA


title: Wild type, 6 hpf, rep3

value: Wild type AB strain


title: Wild type, 1 hpf, rep3


title: RBNS, RHAU53, Synthesized construct, 20nM, K+

value: N/A (synthetic construct)

value: K+


title: ABE8e, replicate 3, CD19 negative, pooled, gRNA

description: pooled, gRNA

value: Adenine base editing


title: evoCDA, replicate 1, presort, pooled, gRNA

description: pooled, gRNA


title: Wild type, 6 hpf, rep2


title: Smarcd1_KD4_1

description:
ATAC-seq
Sample_8_S8


title: Wild type, 6 hpf, rep1


title: Wild type, 1 hpf, rep2


title: evoCDA, replicate 2, presort, pooled, gRNA

description: pooled, gRNA


title: Ctrl_ EmptyVector 3

description:
ATAC-seq
Sample_5_S5


title: MANF overexpression rep 3

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

institute: Medical University of South Carolina

data_processing:
RNA-seq data was processed using the TrimGalore toolkit1 which employs Cutadapt2 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis.
Reads were mapped to the WBcel235r95 version of the C elegans genome and transcriptome3 using the STAR RNA-seq alignment tool4. Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool5.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq26 Bioconductor7 package with the R statistical programming environment8.
The false discovery rate was calculated to control for multiple hypothesis testing.
Assembly: WBCel235r95
Supplementary files format and content: count file (text file) includes raw counts for each sample
Supplementary files format and content: Differential expression includes fpkm normalized counts and pairwise comparisons

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Worms were maintained on K-agar plates seeded with OP50 at 20C.

extract_protocol:
For each group, 250-500 worms were collected and washed 3x with K-medium before flash-freezing in 1 ml Qiagen RLT buffer containing B-ME. Samples were then thawed and disrupted with a bullet blender (bead beater) at power 8 for 30 second intervals with 90 second rests on ice between. Worm lysates were then diluted with 70% ethanol and loaded onto RNeasy columns. RNA was isolated using the manufacturer protocol (Qiagen) including the optional DNaseI on-column digestion. RNA was quantified by Nanodrop and sent to the Duke Genomic Sequencing Core.
RNA libraries for RNA-seq were prepared by the Duke Genomic Sequencing Core.

treatment_protocol: Beginning at L4 stage, worms were transferred 4X per day to new plates for 6 days (through reproductive adulthood)

value: Whole worm

value: day 8 worm


title: Ctrl_KDScr_2

description:
ATAC-seq
Sample_10_S10

value: mammary cancer

value: wildtype


title: MANF deletion rep 3


title: Smarcd1_OverExpression_3

description:
ATAC-seq
Sample_6_S6

value: over expression


title: Wild type, 1 hpf, rep1


title: ABE8e, replicate 3, CD19 positive, pooled, gRNA

description: pooled, gRNA

value: B cell precursor leukemia

value: CD19 enhancer pertubation


title: evoCDA, replicate 1, CD19 positive, pooled, gRNA

description: pooled, gRNA

value: Cytosine base editing


title: Smarcd1_OverExpression_2

description:
ATAC-seq
Sample_4_S4


title: m6A_KD1_2

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

data_processing:
The sequencing data were aligned to hg19 by STAR alignment using the default setting in Galaxy plateform
The m6A peak calling was performed by Peakachu  with maximum insert size=200 and peak with fold-enrichment>4, adjusted p-value<0.001and baseMean>20 were defined as significant m6A peaks.
The significant m6A peaks identified from Scr, DAP3 sh1 and DAP3 sh2 samples were pooled (overlapping peaks were merged) as putative m6A peaks used for the downstream analysis.
Assembly: hg19
Supplementary files format and content: The processed data file contains the peaks identified by MeRIP
Library strategy: MeRIP-seq

source_name: human esophageal squamous carcinoma cells

growth_protocol: RPMI medium 10% FBS

extract_protocol:
total RNA harvest by Trizol method
RNA was fragmented to around 200nt and purified using RNeasy Mini Kit (Qiagen). Dynabeads™ protein G beads (Invitrogen) were washed twice by IP buffer (150 mM NaCl, 10 mM Tris-HCl [pH 7.5], 0.1% IGEPAL CA-630 in nuclease-free H2O), resuspended in 500 μl of IP buffer with 5μg anti-m6A antibody at 4oC for 4 hours. Following 2 washes in IP buffer, the beads was resuspended in 500μl of the IP reaction mixture containing 10μg fragmented total RNA, 100μl of 5×IP buffer, and 5μl of SUPERase·In™ RNase Inhibitor (Invitrogen) and incubated for 2 hours at 4 oC. A low/high salt-washing method was used: the RNA reaction mixture was washed twice in 1ml IP buffer, twice in 1ml low-salt IP buffer (50 mM NaCl, 10 mM Tris-HCl [pH 7.5], 0.1% IGEPAL CA-630 in nuclease-free H2O), and twice in 1ml high-salt IP buffer (500 mM NaCl, 10 mM Tris-HCl [pH 7.5], 0.1% IGEPAL CA-630 in nuclease-free H2O) for 5 minutes each at 4 oC. After extensive washing, the m6A-enriched fragmented RNA was eluted from the beads in 350 μl of RLT buffer supplied in RNeasy Mini Kit (Qiagen) for 10 minutes at room temperature. A magnetic separation rack was used to pull beads to the side of the tube. Supernatant was collected to a new tube and 350μl 70% ethanol was added to it. RNA was purified following the manufacturer's protocol. Equal volume of m6A-enriched fragmented RNA from control and knockdown samples was used for library construction using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) and sequenced using Hiseq X platform.

treatment_protocol: shScr control or two shDAP3 knockdown


title: N2 rep 3

value: wild-type


title: m6A_KD1_1

value: human esophageal squamous carcinoma cells


title: m6A_Scr_2

value: shScr


title: ABE8e, replicate 3, presort, pooled, gRNA

first: Eric

last: Che

description: pooled, gRNA

value: presort


title: m6A_KD2_1


title: Ctrl_KDScr_1

description:
ATAC-seq
Sample_7_S7

value: mammary


title: m6A_KD2_2


title: m6A_Scr_1


title: MANF overexpression rep 2


title: Ctrl_ EmptyVector 2

description:
ATAC-seq
Sample_3_S3


title: ABE8e, replicate 2, presort, pooled, gRNA

description: pooled, gRNA


title: ABE8e, replicate 2, CD19 positive, pooled, gRNA

description: pooled, gRNA

value: CD19 positive


title: N2 rep 2


title: Input_KD2_2


title: ABE8e, replicate 1, CD19 negative, pooled, gRNA

description: pooled, gRNA

value: CD19 negative


title: ABE8e, replicate 1, CD19 positive, pooled, gRNA

description: pooled, gRNA


title: MANF overexpression rep 1


title: Input_KD1_1


title: Input_KD1_2


title: Smarcd1_OverExpression_1

description:
ATAC-seq
Sample_2_S2


title: Input2_MP13249

city: Dallas

first: Kenneth

middle: S

last: Chen

state: TX

address: 5323 Harry Hines Blvd

department: Pediatrics

institute: UT Southwestern

description: input RNA

data_processing:
input and immunoprecipitated RNA was analyzed by sequencing on the Illumina NovaSeq 6000 platform.
Chimeric and non-chimeric eCLIP sequences were compared to input in each sample using the CLIPper algorithm (v2.0)
Assembly: mm10
Supplementary files format and content: ago2: non-chimeric reads
Supplementary files format and content: mir_targets: chimeric reads

source_name: tumor

extract_protocol:
Frozen tumor fragments from two IPRb1 mice were shipped to Eclipsebio for miR-eCLIP sequencing, which entails sequencing of both chimeric eCLIP RNA and total RNA.   For chimeric eCLIP, samples were lysed in lysis buffer, sonicated, and digested with RNase I. AGO2-RNA complexes were immunoprecipitated with primary AGO2 antibody overnight and using magnetic beads pre-coupled to secondary antibody. Cleaved mRNA 5’-ends were phosphorylated with T4 PNK and ligated with T4 RNA Ligase I. Samples were then dephosphorylated with alkaline phosphatase and T4 PNK, and an RNA adapter was ligated to the 3′ ends of the mRNA fragments. Samples were then treated with Proteinase K to isolate RNA, column-purified, and reverse transcribed.    Total RNA was isolated using the Qiagen miRNeasy Mini Kit. Poly(A) selected RNA was heat fragmented and then treated with alkaline phosphatase and T4 PNK. An RNA adapter was then ligated to 3′-ends of mRNA fragments, column purified, and reverse transcribed.
Following reverse transcription, a 5’ Illumina DNA adapter was ligated and PCR amplified with barcoded Illumina compatible primers. Libraries were quantified using Agilent TapeStation and sequenced on the Illumina HiSeq or NovaSeq platform.

value: tumor


title: IP1_MP18167

description: miR-eCLIP RNA


title: IP2_MP13249

description: miR-eCLIP RNA


title: N2 rep 1


title: ABE8e, replicate 1, presort, pooled, gRNA

address: 531 Newbury St

description: pooled, gRNA

value: Adenine base editing


title: Input_Scr_2


title: TvEV4

city: Los Angeles

first: Joshua

middle: Andrew

last: Kochanowsky

state: California

address: 619 Charles E Young Dr E

department: Microbiology, Immunology and Molecular Genetics

institute: University of California Los Angeles

data_processing:
fastq files were aligned to version 110 of Homo sapiens reference genome (https://ftp.ensembl.org/pub/release-110/gtf/homo_sapiens) available on EnsemblDB using kallisto
Adundance.tsv files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (>1 log2FC and 5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Assembly: hg38
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

growth_protocol: BPH-1 cells were Human benign prostate hyperplasia 1 (BPH-1) epithelial cells were cultured at 37 degrees Celsius with 5% CO2 in RPMI 1640, L-glutamine, and HEPES media (Gibco) supplemented with 10 U/ml penicillin, 10 μg/ml streptomycin, and 10% fetal bovine serum (FBS; Gibco).

extract_protocol:
Direct-zolTM RNA Miniprep Kit (Zymo Research; Cat. #R2071) according to the manufacturer’s instructions
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: BPH-1 cells were treated with TvEVs isolated from T. vaginalis strain B7RC2 (50ug/mL) or mock treated for 6 hours prior to RNA isolation.

value: prostate

value: Wild type

value: TvEV treated (50ug/mL)


title: Input1_MP18167

description: input RNA


title: Input_Scr_1


title: TvEV3


title: Ctrl_ EmptyVector 1

description:
ATAC-seq
Sample_1_S1

value: mammary cancer

value: wildtype


title: MANF deletion rep 2

value: Whole worm

value: day 8 worm


title: arid1b, 6 dpf, rep14

city: Worcester

first: Summer

last: Thyme

address: 364 Plantation St

institute: UMass Chan Medical School

data_processing:
Single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.

source_name: head with eyes, 2-5 heads combined

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: head with eyes, 2-5 heads combined

value: arid1b 195d50i wild types


title: ABE8e, replicate 2, CD19 negative, pooled, gRNA

city: Boston

institute: Harvard Medical School

description: pooled, gRNA

value: B cell precursor leukemia

value: CD19 enhancer pertubation


title: AAV_LUN_40w_rep4

first: Karyn

last: Esser

data_processing:
Alignment was performed by using HISAT2 software
Duplicated aligned reads were marked and removed using the Picardtools software
The gene expression count data were extracted using the HTseq software
Assembly: GRCm38 (mm10)
Supplementary files format and content: DESeq2 normalized counts are reported in normalized_counts_data.csv

source_name: Lung

extract_protocol:
Samples were homogenized in TRIzol reagent and RNA was isolated using Qiagen’s RNeasy mini kit
Poly-A selected RNA-seq libraries were prepared using Illumina mRNA Prep kit following manufacturer's protocols.

value: Lung

value: Male

value: 40 weeks

value: KO+AAV

value: ICBR


title: arid1b, 6 dpf, rep12


title: KO_LUN_40w_rep4

value: KO


title: Structure-seq, HEK293T, DHX36-KO, DMSO, Rep1

data_processing:
The adapters were first removed using Cutadapt v1.15 and the reads shorter than 20nt or with quality score lower than 30 were filtered out.
The remaining reads were mapped to human or mouse transcriptome reference using Bowtie2 v2.3.3.1.
Next, the mapped reads with more than 3 mismatches or mismatch at the first base were removed, RT stops were counted and reactivity scores were calculated using StructureFold2 package.
Assembly: hg38/mm10
Supplementary files format and content: comma-delimited text file includes SHAPE/DMS reactivity score of each transcript

extract_protocol:
poly(A)-selected RNAs
Each library was prepared with 500 ng poly(A)-selected RNAs after 2 rounds of selection (Thermo Fisher Scientific, AM1922). The poly(A) RNAs were fragmented to around 300 nt length at 95°C for 1 min and purified using RNA clean and concentrator (Zymo research, R1016). The fragmented RNA was then subjected to a 5' dephosphorylation reaction at 37°C for 30 min by adding rSAP (NEB, M0371L) and PNK enzyme (NEB, M0201S) in 1× T4 PNK buffer (NEB, B0201S). Next, the 3’adapter was ligated to the dephosphorylated RNA using T4 RNA ligase 2 KQ (NEB, M0373L) at 25°C for 1 h. Excess adapters were digested and removed by adding RecJf (NEB, M0331) and 5’ deadenylase (NEB, M0331) for 30 min at 30°C followed by column purification (Zymo research, R1016). The following reverse transcription (RT) was performed in 1 X RT buffer (20 mM Tris, pH 7.5, 4 mM MgCl2, 1 mM DTT, 0.5 mM dNTPs, 150 mM LiCl) with SuperScript III enzyme (Thermo Scientific, 18080093) at 42°C for 40 min. RNA was digested by 2M NaOH and the reaction was neutralized with 1M Tris-HCl (pH 7.5) followed by column purification (Zymo research, R1016). The 5’adapter (for C2C12 libraries) or dU adapter (for HEK293T libraries) was ligated to the cDNA with Quick T4 DNA ligase (NEB, M2200L) and incubated in 37°C overnight. For the C2C12 library, the ligated product was run on the 10% denaturing urea-TBE acrylamide gel (Thermo Scientific, EC68752BOX), and the 100–400 nt region was cut and dissolved in 1X TEN250 buffer (1X TE 7.4, 0.25 M NaCl) at 80°C for 30 min followed by column purification (Zymo research, R1016). For the HEK293T libraries, the ligated product was first purified by column (Zymo research, R1016), then USER II enzyme (NEB, M5509) was added to cleave the product followed by a second column purification (Zymo research, R1016). The purified product was used for PCR cycle test and amplification with different barcoded reverse primer. PCR products with 150–400 bp were then cut and purified with 2% agarose gel and column (Zymo research, D4008).

treatment_protocol: For HEK293T cells, the WT and DHX36-KO cells were harvested in 1X PBS buffer (Thermo Fisher Scientific, 10010049) and probed with NAI (50 mM in final) or 5% DMSO as negative control for 15 min at 37°C, 500 rpm. Then DTT (200mM in final) was added immediately to quench each probing reaction. After spinning down the cells (~ 500 g) for 3 min at room temperature, total RNAs were extracted and quantified using RNeasy Plus Mini Kit (Qiagen, 74136) and Nanodrop ND-1000 Spectrophotometer. For C2C12 cells, the proliferating WT or Dhx36-KO myoblasts were harvested in 1X PBS buffer and probed with DMS (20 mM in final) or 5% DMSO as negative control for 15 min at 37°C. Then DTT (200mM in final) was added immediately to quench each probing reaction. After spinning down the cells (~ 500 g) for 3 min at room temperature, total RNAs were extracted using RNeasy Plus Mini Kit (Qiagen, 74136).

value: DHX36 knockout

value: DMSO


title: Structure-seq, HEK293T, DHX36-KO, NAI, Rep1

value: NAI


title: AAV_LUN_40w_rep3


title: arid1b, 6 dpf, rep15


title: AAV_LUN_40w_rep2


title: MANF deletion rep 1


title: Structure-seq, HEK293T, WT, DMSO, Rep2

value: WT


title: Mock4

value: prostate

value: Wild type

value: Mock treated


title: Mock3


title: TvEV1

value: TvEV treated (50ug/mL)


title: AAV_LUN_40w_rep1


title: Input_KD2_1

value: human esophageal squamous carcinoma cells


title: Mock5


title: arid1b, 6 dpf, rep11

value: head with eyes, 2-5 heads combined

value: arid1b 195d50i wild types


title: arid1b, 6 dpf, rep9

value: arid1b 195d50i homozygotes


title: KO_LUN_40w_rep3

value: Lung

value: Male


title: Structure-seq, HEK293T, DHX36-KO, DMSO, Rep2


title: arid1b, 6 dpf, rep13


title: Mock2


title: KO_LUN_40w_rep2

value: 40 weeks


title: arid1b, 6 dpf, rep10


title: CDE N(3), input library

first: Julia

last: Weigand

data_processing:
NGS data were analyzed using a custom Python script. Briefly, it searches for each occurrence of a used partial random stem-loop and calculates its enrichment. The enrichment value "E" of a given random region is defined as follows E_loop=(freq_pulldown)/(freq_input)
Assembly: other
Supplementary files format and content: Excel files containing the sRBNS E-values generated by the sRBNS analysis pipeline. E represents the enrichment of a specific random region and is defined as the frequency of the random region in the reads of the pulldown divided by its frequency in the input reads.
Library strategy: RNA Bind-n-Seq

source_name: synthetic sequence library

extract_protocol:
For the sRBNS experiment, a Twin-Strep tagged coreROQ domain and different pre-structured RNA input pools were used. The three different RNA input pools [CDE pool N(3), CDE pool N(3-5), ADE pool N(6)] were generated by in vitro transcription. For the sRBNS experiment, we adapted the protocol from https://doi.org/10.1016/bs.mie.2015.02.007. The protein was equilibrated in binding buffer (25 mM Tris-HCl pH 7.5, 150 mM KCl, 3 mM MgCl2, 0.01% Tween, 500 µg/mL BSA, 1 mM DTT) at three different concentrations (10, 50, 500 nM) for 30 min at 4°C. Second, the folded RNA was added to a final concentration of 1 µM together with 40 U of ribonuclease inhibitor (moloX, Berlin) and incubated for 1 h at room temperature. Pulldown was performed by incubating the RNA pool/coreROQ mixture with 1 μL of washed MagStrep "type3" XT beads (IBA Lifesciences, Göttingen, Germany) for 1 h at 4°C. Unbound RNA was then removed by washing three times with wash buffer (25 mM Tris-HCl pH 8.0, 150 mM KCl, 60 μg/ml BSA, 0.5 mM EDTA, 0.01% Tween). The RNA/coreROQ complexes were then eluted twice with 25 µL of Elution Buffer (wash buffer containing 50 mM biotin). RNA was then extracted using the Zymo RNA Clean & Concentrator-5 Kit (Zymo Research, Freiburg, Germany) according to the manufacturer's instructions.
The RNA extracted after pulldown was transcribed into cDNA. The cDNA was then amplified by PCR, using primers to insert an index for each concentration and Illumina adapters. Deep sequencing was then performed at GENEWIZ (Leipzig, Germany).

value: synthetic sequence library


title: arid1b, 6 dpf, rep8


title: Mock1


title: Structure-seq, HEK293T, WT, NAI, Rep2


title: Structure-seq, HEK293T, WT, DMSO, Rep1


title: arid1b, 6 dpf, rep7


title: KO_LUN_40w_rep1

value: KO

value: ICBR


title: AAV_WFT_40w_rep4

source_name: White fat

value: White fat

value: KO+AAV


title: BPH-1, TvMh4

source_name: prostate

treatment_protocol: BPH-1 cells were infected with the indicated pathogens at an MOI of 1 or mock infected for 6 hours prior to RNA isolation.

tag: infection

value: T. vaginalis in symbiosis with M. hominis


title: arid1b, 6 dpf, rep5

value: arid1b 195d50i heterozygotes


title: Structure-seq, HEK293T, DHX36-KO, NAI, Rep2

tag: cell line

value: DHX36 knockout

value: NAI


title: 10477_480_P_S1

description:
10477_480_P
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv

data_processing:
Analysis was performed using mirDeep2 for alignment to both the genome and to a separate spike-in control fasta file
Assembly: mm10
Supplementary files format and content: raw counts

source_name: pineal

extract_protocol:
RNA was isolated using the miRNeasy kit (Qiagen). Small RNA sequencing was performed at DNA Link, using QIAseq miRNA Library QC Spike-ins (Qiagen cat. 331535) as a control.
NEBNext small RNA

value: pineal

value: control


title: BPH-1, TvMh5

value: prostate

value: Wild type


title: BPH-1, TvMh3


title: BPH-1, TvMh2


title: 10242_247_P_S0

description:
10242_247_P
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv


title: arid1b, 6 dpf, rep3

value: head with eyes, 2-5 heads combined


title: 10369_333_P_S0

description:
10369_333_P
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv


title: AAV_WFT_40w_rep2


title: 10166_T_S4

description:
10166_T
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv

value: tumor

value: IPDrosha


title: BPH-1, TvMh1


title: AAV_WFT_40w_rep3

value: Male

value: 40 weeks


title: AAV_WFT_40w_rep1


title: Structure-seq, HEK293T, WT, NAI, Rep1

value: WT


title: arid1b, 6 dpf, rep6

value: arid1b 195d50i homozygotes


title: 10166_B_S7

description:
10166_B
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv

source_name: normal brain

value: normal brain


title: KO_WFT_40w_rep4

value: White fat

value: KO

value: ICBR


title: arid1b, 6 dpf, rep2

value: arid1b 195d50i heterozygotes


title: 10047_T_S3

description:
10047_T
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv


title: KO_WFT_40w_rep3


title: arid1b, 6 dpf, rep1


title: arid1b, 6 dpf, rep4


title: BPH-1, Tv4

value: T. vaginalis


title: lymph node S8934_s66747 scRNAseq full transcriptome

city: Leiden

first: Cornelis

last: van Bergen

address: Albinusdreef 2

department: Hematology

institute: Leiden University Medical Center

description: 10X Genomics

data_processing:
BCR comma separated cellranger output files
cellranger VDJ analysis fasta output
cellranger VDJ analysis annotation output
GEX Tab-separated values files and matrix files
cellranger GEX count table output
Assembly: GRCh38-2020-A

source_name: lymph node

growth_protocol: Frozen cells were thawed, stained with CD19 and CD10, and purified by FACSariaII device prior to submission for 10X Genomics Chromium processing

extract_protocol:
cellranger-6.0.1
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 (K1B_GEX) and vdj_GRCh38_alts_ensembl-3.1.0 (K1B_BCR) as references

treatment_protocol: Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).

value: lymph node

value: tissue

tag: cell type

value: B cell

value: fresh


title: KO_WFT_40w_rep2

address: 1345 Center Drive M5-44

tag: genotype


title: 10047_B_S6

description:
10047_B
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv


title: KO_WFT_40w_rep1


title: BPH-1, Tv3

value: prostate

value: Wild type


title: BPH-1, Tv2


title: 10028_T_S0

description:
10028_T
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv

value: tumor

value: IPDrosha


title: 10028_B_S5

description:
10028_B
mirdeep2count-rawreads.csv
mirdeep2count-spikeinreads.csv


title: BPH-1, Tv1


title: AAV_HRT_40w_rep3

source_name: Heart

value: Heart

value: Male

value: 40 weeks

value: KO+AAV


title: BPH-1, Mh5

value: M. hominis


title: lymph node S8934_s66747 scRNAseq BCR enriched_kappa

description: 10X Genomics

tag: treatment


title: AAV_HRT_40w_rep4

tag: tissue


title: lymph node S8934_s66747 scRNAseq BCR enriched

description: 10X Genomics


title: lymph node S13530_s1336560 scRNAseq full transcriptome

description: 10X Genomics

data_processing:
BCR comma separated cellranger output files
Supplementary files format and content: all_contig.fasta - cellranger VDJ analysis fasta output
Supplementary files format and content: all_contig_annotations.csv - cellranger VDJ analysis annotation output
GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix - cellranger GEX count table output
Assembly: GRCh38-2020-A

extract_protocol:
cellranger-6.0.1
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references


title: Aged mouse Striatum, replicate 4

first: Kay

last: Linker

address: 10833 Le Conte Avenue, 53-263 CHS

department: Physiology

institute: UCLA

description: 10x Genomics

data_processing:
cellranger 4.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
scRNA-seq was performed to profile the striatum of C57BL6J mice at 18 months of age. The brain was immediately dissected out and was sectioned into 400 mm slices in ice-cold artificial cerebrospinal fluid (ACSF) oxygenated with 95% O2 and 5% CO2 and immediately transferred to an oxygenated recovery solution. The cortical, hippocampal, or striatal tissue was dissected out in ice-cold ACSF and cut into small pieces. The tissue was digested in ACSF containing 1 mg/ml pronase at 34 °C for 30 min. The digested tissue was dissociated in ice-cold oxygenated ACSF containing 1% fetal bovine serum. The dissociated cells were filtered through a 20 mm filter and washed with ice-cold ACSF. To remove myelin, the cell pellet was resuspended in PBS and processed with debris removal kit (Miltenyi Biotec). Isolated cells were diluted to 1000 cells/ml in 0.04% BSA/PBS and processed with 10X Genomics platform.  The library preparation and sequencing were performed following 10X Genomics Chromium protocols.
Single cell suspension from mouse brain tissues were prepared using 10x Genomics Chromium Single Cell 3’ Reagent Kits v2 and v3 (10X Genomics, Pleasanton, CA) according to manufacture’s protocol. Quantity and quality of cDNA were assessed by Agilent 2100 expert High Sensitivity DNA Assay. cDNA samples were sequenced on NovaSeq 6000 or NextSeq 500 platform at UCLA Technology Center for Genomics and Bioinformatics.

value: Brain

value: 18 months

value: Glia enriched


title: Aged mouse Striatum, replicate 3

description: 10x Genomics


title: BPH-1, Mh4


title: Aged mouse Striatum, replicate 2

description: 10x Genomics


title: BPH-1, Tv5

value: T. vaginalis


title: KO_HRT_40w_rep4

institute: University of Florida

value: KO

value: ICBR


title: TvEV2

value: TvEV treated (50ug/mL)


title: BPH-1, Mh2


title: lymph node S8934_s1336560 scRNAseq BCR enriched_kappa

description: 10X Genomics

value: lymph node

value: tissue

value: B cell

value: fresh


title: lymph node S8934_s1336560 scRNAseq BCR enriched

description: 10X Genomics


title: BPH-1, Mh3

value: prostate

value: Wild type


title: lymph node S8934_s66747 scRNAseq BCR enriched_gamma_reseq

description: 10X Genomics


title: BPH-1, Mh1


title: lymph node S13530_s1309520 scRNAseq full transcriptome

description:
GEX
10X Genomics

data_processing:
cellranger-6.0.1
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 using GRCh38-3.0.0 and vdj_GRCh38_alts_ensembl-3.1.0 as references
BCR comma separated cellranger output files
Supplementary files format and content: all_contig.fasta: cellranger VDJ analysis fasta output
Supplementary files format and content: all_contig_annotations.csv: cellranger VDJ analysis annotation output
GEX Tab-separated values files and matrix files
Supplementary files format and content: barcodes features matrix: cellranger GEX count table output
Assembly: GRCh38-2020-A
Supplementary files format and content: processed PacBio csv.gz: barcode and gene aligned with read genotype

extract_protocol:
Frozen cells were thawed, stained with CD19 and CD10, and purified by FACSariaII device prior to submission for 10X Genomics Chromium processing
Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics).


title: KO_HRT_40w_rep3

value: Heart

value: Male


title: KO_HRT_40w_rep2

value: 40 weeks


title: Control_iPSC [NCH80_3]

city: Memphis

first: Zhaohui

last: Xu

address: 262 Danny Thomas Place

department: Infectious Diseases

institute: St. Jude Children's Research Hospital

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequences were removed, then processed with miRge3.0
Assembly: human mirna database
Supplementary files format and content: tab-delimited text files include miRNA values for each Sample

extract_protocol:
Cell-free RNA from maternal blood plasma anCell-free RNA from maternal blood plasma and supernatant from proliferating iPSC-CMs were extracted using the miRNeasy Serum/Plasma Kit (Qiagen, cat. No 217184), following the manufacturer’s protocol. The samples were then sequenced using Lexogen's small RNA sequencing service.
Library Construction was prepared by Lexogen from extracted RNA samples

value: iPSC-Derived Cardiomyocytes NCH80

value: iPSC-Derived Cardiomyocytes

tag: molecule subtype

value: small RNA


title: Control_iPSC [NCH80_2]


title: lymph node S13530_s1309520 scRNAseq BCR enriched

description:
BCR
10X Genomics


title: BPH-1, Mock4

value: Mock


title: BPH-1, Mock3


title: Control_iPSC [NCH80_1]


title: AAV_LIV_40w_rep4

city: Gainesville

source_name: Liver

value: Liver

value: KO+AAV