title: P5 d1 lin-CD34+ cells

description: P5 d1 lin-CD34+ cells

value: 1 day after transplantation


title: 2C_input

status: Public on Mar 18 2023

type: SRA

city: Jinan

first: Zenghui

last: Sun

address: 44 Wenhua West Road, Lixia District

country: China

institute: Shandong university

library_source: transcriptomic

data_processing:
Briefly, Paired-end reads were harvested from Illumina Novaseq 6000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4). Acetylated sites on RNAs (peaks) were identified by MACS software. Differentially acetylated sites were identified by diffReps.
These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
GO and Pathway enrichment analysis were performed by the differentially acetylated protein coding genes,.

molecule: polyA RNA

organism: Homo sapiens

source_name: kidney

growth_protocol: ccRCC and paracancer tissues were preserved in liquid nitrogen

extract_protocol:
Total RNA was rRNA depleted with Ribo-zero (Illumina) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions
The ac4C-IP-Seq service was provided by CloudSeq Inc. (Shanghai, China). Total RNA was rRNA depleted with Ribo-zero (Illumina) and then subjected to immunoprecipitation with the GenSeqTM ac4C-IP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction. RNA libraries for IP and input samples were then constructed with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a Novaseq 6000 platform (Illumina)

tag: tissue

value: kidney

tag: disease state

value: ccRCC tissue

tag: rip antibody


title: asynchronous mESCs_ARID1A_rep3

city: Memphis

first: Zhexin

last: Zhu

address: 262 Danny Thomas Pl

country: USA

institute: St Jude Children's Research Hospital

description:
asynchronous mESCs_CUT&RUN_ARID1A_2041752
asynchronous mESCs_CUT&RUN_ARID1A_2041752

library_source: genomic

data_processing:
Library strategy: CUT&RUN-seq
Basecalls performed using CASAVA version 1.4
Reads were aligned to mouse genome assembly mm10 by BWA(0.7.17） by internal automatically mapping pipeline.
Properly paired uniquely mapped reads were obtained using samtools (V1.10, with parameters “-q 10 -F 1804”)
We only kept CUT&RUN fragments with length shorter than 2000 bp for further analysis.
Stringent peaks for each replicate were called by MACS2 (V 2.1.1.20160309, with default parameters using IgG (for CUT&RUN) and filtered with fold enrichment cutoff: 5 and p-value threshold: 1e-9.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files of normalized read counts.
Supplementary_files_format_and_content: narrowPeak from MACS2

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic stem cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes.

extract_protocol:
https://doi.org/10.1038/nprot.2018.015
KAPA Hyper Prep Kit (KK8504)

treatment_protocol: For mitotic synchronization, mESCs were treated with 100 ng/ml nocodazole for 6 hours, and then mitotic cells were collected by gently shake-off. For mitotic release, mitotic cells were washed out three times by fresh mESC culture medium to remove residual nocodazole and then cultured in mESC medium for the indicated time.

tag: cell type

value: mouse embryonic stem cells

tag: strain

tag: treatment

value: untreatment

tag: antibody

value: ARID1A (SIGMA, HPA005456-100UL)


title: 1C_input


title: P3 d30 lin-CD34+ cells

city: Tianjin

first: Tao

last: Cheng

address: 288 Nanjing Road

institute: Institute of Hematology and Blood Diseases Hospital

description: P3 d30 lin-CD34+ cells

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were first truncated and processed by fastp to filter out low-quality reads (more than 15 “N” or more than 50% bases with quality value ≤ 5). Then, the template switch oligo (TSO) sequence, the polyA tail sequence and short reads were discarded for each separated single cell using Cutadapt. The clean reads were aligend and quantified by STARsolo (version 2.7.9a) with human reference genome GRCh38/hg38.
processed data provided as .tsv (UMI matrix of single cells)

molecule: total RNA

source_name: bone marrow

extract_protocol: BM samples were incubated on ice for no more than 10 min to lyse red blood cells. The single-cell suspensions were prepared for FACS. BM cells were stained with conjugated anti-human lineage cocktail (CD3, CD14, CD16, CD19, CD20, CD56), CD34 and CD38 antibody for 30 min at 4 °C. Cells were washed twice with sorting buffer (PBS supplemented with 2% FBS) and filtered through a 70-μm cell strainer. Finally, single-cell suspensions were added with DAPI and loaded onto a BD FACS Aria III cell instrument to sort Lin-CD34+ cells. Live Lin-CD34+ cells were sorted into every single well of 96-well plates containing cell lysis buffer and preserved at −80 °C before preparation for Single-Cell Tagged Reverse Transcription RNA sequencing (STRT-seq).

value: bone marrow

value: lin-CD34+ cells

tag: patient id

tag: group or_sampling_time

value: 30 days after transplantation

tag: Sex

value: Male

tag: age

tag: sample type

value: fresh bone marrow


title: P2 after d180 lin-CD34+ cells

description: P2 after d180 lin-CD34+ cells

value: one year after transplantation


title: asynchronous mESCs_ARID1A_rep2

description:
asynchronous mESCs_CUT&RUN_ARID1A_2035536
asynchronous mESCs_CUT&RUN_ARID1A_2035536


title: asynchronous mESCs_ESRRB_rep1

description:
asynchronous mESCs_CUT&RUN_ESRRB_2029017
asynchronous mESCs_CUT&RUN_ESRRB_2029017

value: ESRRB (R&D Systems, PP-H6705-00)


title: P2 d30 lin-CD34+ cells

description: P2 d30 lin-CD34+ cells


title: P1 d14 lin-CD34+ cells

description: P1 d14 lin-CD34+ cells

value: 14 days after transplantation

value: Female


title: P1 d30 lin-CD34+ cells

description: P1 d30 lin-CD34+ cells


title: Smarce1-MD30_240min_rep2

description: nascent RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Total stranded RNA sequencing data were mapped to mouse genome assembly mm10 using an internal AutoMapper pipeline. Briefly, the raw reads were trimmed with trim galore (V0.60) and mapped to mouse genome mm10 using STAR V2.7.1a.
Then the read counts were computed using RSEM(V1.3.0) based on GENCODE vM23.
RPM (Reads Per Million) was applied to normalize read counts in bigwig tracks
Genome_build: mm10
Supplementary_files_format_and_content: read counts from RSEM

extract_protocol:
Click-iT® Nascent RNA Capture Kit (https://www.thermofisher.com/order/catalog/product/C10365)
KAPA Hyper Prep Kit (KK8504)

value: cells were released from mitosis for 240 min


title: 2N_IP

value: Paracancer tissue

value: GenSeqTM ac4C-IP Kit


title: 3N_IP

value: kidney


title: 1N_IP


title: Skin tumor, BA.7

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: .csv matrix of raw counts

source_name: Skin tumor

extract_protocol:
Tissues were stored in RNAlater until further processing. Tissues were homogenized in RLT buffer from the RNeasy Mini Kit (Qiagen) containing beta- mercaptoethanol. RNA was extracted using Qiagen RNeasy RNA extraction kit following manufacturer's instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina)
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index)

value: Skin tumor

tag: genotype

value: Lgr5CreER P53 fl/+ P53 R172H/+ TGFBR2 fl/fl

value: Tumor


title: Skin tumor, BA.6

value: Lgr5CreER P53 fl/+ P53 R172H/+ TGFBR2 fl/fl Rosa-tom/+


title: Smarce1-MD30_240min_rep1

description: nascent RNA

value: mouse embryonic stem cells


title: Smarce1-MD09_240min_rep2

description: nascent RNA


title: 4N_input


title: Skin tumor, BA.3


title: Skin tumor, BA.2


title: Smarce1-MD09_240min_rep1

description: nascent RNA


title: Skin tumor, BA.4


title: Smarce1-MD(R42A)_A10_240min_rep2

description: nascent RNA


title: Skin tumor, B.1

value: Lgr5CreER P53 fl/+ P53 R172H/+ TGFBR2 fl/fl Notch1 fl/fl Rosa-tom/+


title: Smarce1-MD(R42A)_A10_240min_rep1

description: nascent RNA


title: Skin tumor, WT SI Tissue Rep 7

value: Lgr5CreER P53 fl/+ P53 R172H/+ TGFBR2 fl/fl Notch1 fl/fl


title: 2N_input


title: Skin tumor, BA.1


title: Skin tumor, WT SI Tissue Rep 6


title: 4N_IP


title: 1N_input


title: P1 d60 lin-CD34+ cells

description: P1 d60 lin-CD34+ cells

value: bone marrow

value: lin-CD34+ cells

value: 60 days after transplantation


title: asynchronous mESCs_ARID1A_rep1

description:
asynchronous mESCs_CUT&RUN_ARID1A_2029013
asynchronous mESCs_CUT&RUN_ARID1A_2029013

value: untreatment

value: ARID1A (SIGMA, HPA005456-100UL)


title: Skin tumor, WT SI Tissue Rep 5


title: Skin tumor, WT SI Tissue Rep 3


title: Smarce1-MD(R42A)_A04_240min_rep2

description: nascent RNA


title: Skin tumor, BA.5


title: N2 TNC

description: N2 TNC

data_processing:
Raw sequencing reads were first processed by fastp to filter out low-quality reads (more than 15 “N” or more than 50% bases with quality value ≤ 5). The clean reads were aligned and qualified using Cell Ranger Single-Cell Software Suite (version 3.0.2) with reference genome GRCh38/hg38.
processed data provided as .tsv (UMI matrix of single cells)

source_name: bone marrow and peripheral blood

extract_protocol: Collected samples were incubated on ice for no more than 10 min to lyse red blood cells. Then, cells were resuspended in 3 ml cold DPBS (Gibco). cell viabilities higher than 85% were used for preparation. If cell viability is lower than 85%, Dead Cell Removal Kit (Miltenyi Biotec) was applied to suspensions to improve cell viability. these total nucleated cells after lysis in 0.04% BSA with high viability were processed for single-cell sequencing using the Chromium Single Cell 3’ Regent Kits v2 or the Chromium Single Cell 3’ Regent Kits v3 following the manufacturer’s instructions.

value: bone marrow and peripheral blood

value: total nucleated cells

value: health control

value: Male

value: fresh bone marrow and peripheral blood


title: Skin tumor, WT SI Tissue Rep 2

value: Skin tumor


title: Smarce1-MD(R42A)_A04_240min_rep1

description: nascent RNA

value: cells were released from mitosis for 240 min


title: 3N_input

value: kidney

value: Paracancer tissue


title: Smarce1-MD30_180min_rep2

description: nascent RNA

value: mouse embryonic stem cells

value: cells were released from mitosis for 180 min


title: N1 TNC

description: N1 TNC


title: Smarce1-MD30_180min_rep1

description: nascent RNA


title: Smarce1-MD09_180min_rep2

description: nascent RNA


title: D9 TNC

description: D9 TNC

source_name: G-CSF mobilized peripheral blood

value: G-CSF mobilized peripheral blood

value: Donor

value: Female

value: fresh G-CSF mobilized peripheral blood


title: Skin tumor, Apc Kras flox SI Tissue Rep 6

value: Lgr5CreER P53 fl/+ P53 R172H/+ TGFBR2 fl/fl Notch1 fl/fl

value: Tumor


title: Skin tumor, WT SI Tissue Rep 4


title: Skin tumor, Apc Kras flox SI Tissue Rep 5

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/fl


title: Smarce1-MD09_180min_rep1

description: nascent RNA


title: D10 TNC

description: D10 TNC

value: total nucleated cells


title: D8 TNC

description: D8 TNC


title: Skin tumor, Apc Kras flox SI Tissue Rep 4

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/+ Rosa-tom/+


title: D7 TNC

description: D7 TNC


title: Smarce1-MD(R42A)_A10_180min_rep2

description: nascent RNA


title: N3 TNC

description: N3 TNC

value: bone marrow and peripheral blood

value: health control


title: Skin tumor, Apc Kras flox SI Tissue Rep 3

value: Skin tumor


title: Smarce1-MD(R42A)_A10_180min_rep1

description: nascent RNA


title: D6 TNC

description: D6 TNC

value: Male


title: Skin tumor, Apc Kras flox SI Tissue Rep 2


title: Skin tumor, WT SI Tissue Rep 1

value: Lgr5CreER P53 fl/+ P53 R172H/+ TGFBR2 fl/fl Notch1 fl/fl Rosa-tom/Rosa-tom


title: Smarce1-MD(R42A)_A04_180min_rep2

description: nascent RNA


title: D5 TNC

description: D5 TNC


title: Skin tumor, Apc Kras flox SI Tissue Rep 1

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/fl Rosa-tom/+


title: Skin tumor, Apc flox SI Tissue Rep 19


title: D3 TNC

description: D3 TNC


title: Smarce1-MD30_90min_rep2

description: nascent RNA

value: mouse embryonic stem cells

value: cells were released from mitosis for 90 min


title: Smarce1-MD30_90min_rep1

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 18


title: 10138T

type: RNA

city: Seoul

first: Yong-Min

last: Huh

address: 50 Shinchon-ro

country: South Korea

institute: Yonsei University

hyb_protocol: HumanHT-12 v3.0 Expression BeadChip array (Illumina) was used.

scan_protocol: Standard Illumina scanning protocol

data_processing: R limma package, neqc function (quantile normalization)

label: biotin

source_name: Human gastric cancer

label_protocol: Illumina TotalPrep™ RNA Amplification Kit was used for synthesis of labeled cRNA.

extract_protocol: RecoverAll™ total nucleic acid isolation kit (Ambion) or the mirVana RNA Isolation Labeling Kit (Ambion) were used. Quality control was performed with NanoDrop 2000 (Thermo Fischer Scientific) and RNA Nano 6000 chip (Agilent).

value: gastric cancer


title: 10137T


title: 10128T


title: 10126T


title: 10139T


title: Skin tumor, Apc flox SI Tissue Rep 17

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/+


title: D2 TNC

description: D2 TNC

value: G-CSF mobilized peripheral blood

value: Donor

value: Female


title: Smarce1-MD09_90min_rep2

description: nascent RNA


title: 10141T


title: D1 TNC

description: D1 TNC

value: fresh bone marrow and G-CSF mobilized peripheral blood


title: 31T


title: P10 d90 TNC

description: P10 d90 TNC

value: 90 days after transplantation

value: fresh bone marrow and peripheral blood


title: Smarce1-MD(R42A)_A04_180min_rep1

description: nascent RNA

value: cells were released from mitosis for 180 min


title: Smarce1-MD(R42A)_A10_90min_rep2

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 15

value: Tumor


title: Smarce1-MD09_90min_rep1

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 16

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/fl


title: D4 TNC

description: D4 TNC

value: total nucleated cells

value: fresh G-CSF mobilized peripheral blood


title: P10 d60 TNC

description: P10 d60 TNC

value: bone marrow and peripheral blood

value: 60 days after transplantation

value: Male


title: Skin tumor, Apc flox SI Tissue Rep 14

value: Skin tumor

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/+ Rosa-tom/+


title: 27T

value: gastric cancer


title: Smarce1-MD(R42A)_A10_90min_rep1

description: nascent RNA

value: mouse embryonic stem cells

value: cells were released from mitosis for 90 min


title: 11T


title: P10 d30 TNC

description: P10 d30 TNC

source_name: peripheral blood

value: peripheral blood

value: 30 days after transplantation

value: fresh peripheral blood


title: 29T


title: Skin tumor, Apc flox SI Tissue Rep 13

value: Lgr5CreER Kras G12D/+ TGFBR2 fl/+


title: 28T


title: 34T


title: 26T


title: Smarce1-MD(R42A)_A04_90min_rep2

description: nascent RNA


title: Smarce1-MD(R42A)_A04_90min_rep1

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 12

value: Lgr5Cre Braf V600E/+ Alk5/Alk5


title: P10 d21 TNC

description: P10 d21 TNC

value: 21 days after transplantation


title: P9 d90 TNC

description: P9 d90 TNC

value: 90 days after transplantation

value: fresh bone marrow and peripheral blood


title: Smarce1-MD30_45min_rep2

description: nascent RNA

value: cells were released from mitosis for 45 min


title: Smarce1-MD30_45min_rep1

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 11

value: Tumor


title: P10 d14 TNC

description: P10 d14 TNC

value: bone marrow and peripheral blood

value: total nucleated cells

value: 14 days after transplantation


title: P10 d1 TNC

description: P10 d1 TNC

value: bone marrow

value: 1 day after transplantation

value: Male

value: fresh bone marrow


title: Smarce1-MD09_45min_rep2

description: nascent RNA

value: mouse embryonic stem cells


title: Skin tumor, Apc flox SI Tissue Rep 10

value: Skin tumor


title: 25T

value: gastric cancer


title: P9 d60 TNC

description: P9 d60 TNC

value: 60 days after transplantation


title: Skin tumor, Apc flox SI Tissue Rep 8

value: Lgr5Cre Braf V600E/+ Alk5/Alk5


title: P9 d30 TNC

description: P9 d30 TNC

value: 30 days after transplantation


title: Smarce1-MD09_45min_rep1

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 7


title: P9 d21 TNC

description: P9 d21 TNC

value: peripheral blood

value: 21 days after transplantation

value: fresh peripheral blood


title: Smarce1-MD(R42A)_A10_45min_rep2

description: nascent RNA

value: cells were released from mitosis for 45 min


title: Skin tumor, Apc flox SI Tissue Rep 6

value: Tumor


title: 23T


title: 22T


title: 21T


title: 20T


title: 24T


title: 19T


title: 66T


title: Smarce1-MD(R42A)_A10_45min_rep1

description: nascent RNA


title: P9 d14 TNC

description: P9 d14 TNC

value: bone marrow and peripheral blood

value: total nucleated cells

value: fresh bone marrow and peripheral blood


title: Skin tumor, Apc flox SI Tissue Rep 9


title: Skin tumor, Apc flox SI Tissue Rep 5


title: 64T


title: Smarce1-MD(R42A)_A04_45min_rep1

description: nascent RNA


title: P8 d90 TNC

description: P8 d90 TNC

value: 90 days after transplantation


title: P9 d1 TNC

description: P9 d1 TNC

value: bone marrow

value: 1 day after transplantation

value: Male


title: Skin tumor, Apc flox SI Tissue Rep 4

value: Skin tumor


title: Smarce1-MD(R42A)_A04_45min_rep2

description: nascent RNA

value: mouse embryonic stem cells


title: Skin tumor, Apc flox SI Tissue Rep 3

value: Lgr5CreER Braf V600E/+ Alk5/+ RFP/+


title: P8 d60 TNC

description: P8 d60 TNC

value: 60 days after transplantation


title: P8 d30 TNC

description: P8 d30 TNC

value: 30 days after transplantation


title: Smarce1-MD30_0min_rep1

description: nascent RNA

value: nocodazole treatment for 6 hours


title: Smarce1-MD30_0min_rep2

description: nascent RNA


title: Smarce1-MD09_0min_rep2

description: nascent RNA


title: P8 d21 TNC

description: P8 d21 TNC

value: peripheral blood

value: 21 days after transplantation


title: P8 d1 TNC

description: P8 d1 TNC

value: fresh bone marrow


title: P8 d14 TNC

description: P8 d14 TNC

value: 14 days after transplantation


title: Smarce1-MD(R42A)_A10_0min_rep2

description: nascent RNA


title: Smarce1-MD09_0min_rep1

description: nascent RNA


title: Skin tumor, Apc flox SI Tissue Rep 2

value: Lgr5CreER Alk5/+ BrafV600E/+

value: Tumor


title: P7 after d180 TNC

description: P7 after d180 TNC

value: bone marrow and peripheral blood

value: total nucleated cells

value: one year after transplantation

value: Female

value: fresh bone marrow and peripheral blood


title: 57T

value: gastric cancer


title: Skin tumor, Apc flox SI Tissue Rep 1

value: Skin tumor

value: Lgr5Cre Braf V600E/+


title: Smarce1-MD(R42A)_A04_0min_rep2

description: nascent RNA

value: mouse embryonic stem cells


title: 59T


title: P7 d90 TNC

description: P7 d90 TNC

value: 90 days after transplantation


title: 58T


title: Smarce1-MD(R42A)_A04_0min_rep1

description: nascent RNA

value: nocodazole treatment for 6 hours


title: 61T


title: P7 d60 TNC

description: P7 d60 TNC

value: peripheral blood

value: 60 days after transplantation

value: fresh peripheral blood


title: P7 d30 TNC

description: P7 d30 TNC

value: 30 days after transplantation


title: 55T


title: Smarce1-MD30_asyn_rep2

description: nascent RNA

value: untreated


title: 56T


title: Smarce1-MD30_asyn_rep1

description: nascent RNA


title: MCF7-sgGT3-INCPR3

city: Houston

first: Yiwen

last: Chen

state: TX

address: 1400 Pressler Street,  Unit 1410

department: Bioinformatics & Comp Biology

institute: UT MD Anderson Cancer Center

description:
processed data file: GT3_INCPKonckout_differ_genes.csv
processed data file: GT3INCP_KO_RNASEQ_counts.txt

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l MCF7.sgrna.library --control-sgrna MCF7.sgrna.library.negctrl --norm-method control -n MCF7.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome with hisat2(v2.1.0). The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2).
genome build/assembly: human hg38 genome
processed data files format and content: RNASeq: Deseq2 normalized read count and differential expression result in csv file, CRISPR screen: read count and differential expression result in text file.

source_name: breast

growth_protocol: MCF7 cells were cultured in RPMI-1640 (Hyclone #SH30027.1). All culture medium were supplemented with 10% FBS (Gibco #10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI). All cell lines were cultured in an incubator (Thermo, HEARCELL VIOS 160i) with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini kit (QIAGEN, #74104) and was treated with DNase I (QIAGEN #79254). RPFs without ribosomal RNA were run on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised. The RPF RNAs were eluted and precipitated followed. The genomic DNAs were extracted by using QIAamp DNA Mini Kit (QIAGEN).
RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer’s instructions.  Sample preparation for ribosome profiling was conducted according to the manufacturer’s specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina). ChIP-seq libraries were prepared from 10 ng of ChIP DNA using the TruSeq ChIP Library Preparation Kit, according to the manufacturer’s instructions.

treatment_protocol: Sample preparation for ribosome profiling: MCF7 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minute and the cells were lysed by using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 µL of lysates were taken and 15 µL of RNase I (100 U/ µL, Thermo Fisher Scientific) were added, and the mixtures were incubated for 45min at room temperature followed by adding 15 µL SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery was done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were run on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised. The RPF RNAs were eluted and precipitated followed by library construction according to the manufacturer’s protocol. Sample preparation for ORF CRISPR/Cas9 screen: The MCF7 cells transduced with lentiCas9-EGFP (addgene, #63592) were sorted on a FACSAria cell sorter (BD Biosciences) and the cells with high EGFP expression were collected. These MCF7 cells with high expression of SpCas9 were plated into ten 10-cm dishes and infected with lentiviruses containing the sgRNA library at an MOI of 0.2~0.3. Following puromycin (2 μg/ml) selection for 4 days, 3.5 ×107 cells were split into three replicates. For each replicate, 8× 106 were harvested to extract genomic DNAs (Day 0, D0), using QIAamp DNA Mini Kit (QIAGEN), and 3.7×106 cells (~500×coverage for each sgRNA per replicate) were passed every 3 days and cultured for 21 days. At day 21 (D21), 8× 106 cells were harvested for each replicate to extract genomic DNA. The next-generation-sequencing (NGS)-ready sgRNA libraries were prepared by two rounds of PCR with the KAPA HiFi HotStart ReadyMix (Roche # KK2602).  Samples preparation for ChIP-seq: MCF7 cells stably expressing Flag-tagged GT3-INCP were first crosslinked with 1% formaldehyde (methanol-free, 16% Thermo Scientific, #28908) at room temperature for 10 minutes and then quenched with 0.125M Glycine (final concentration) for 5 minutes. After washing with cold PBS for three times, the cells were harvested using a silicon scraper. Cell pellets were resuspended in 5mL lysis buffer 1(50 mM Hepes-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100) and rocked at 4 degree for 5 minutes, followed by centrifugation at 2000 g for 4 minutes at 4°C. The cell pellets were then incubated with 5 mL LB2 buffer (10 mM Tris-HCl, pH=8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) at 4°C for 5 minutes with gently rocking. Nuclei were pelleted down by centrifugation of the cells at 2000 g for 5 min and were resuspended in 1 mL LB3 buffer (10 mM Tris-HCl, pH=8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine). All lysis buffer contained protease inhibitors (Roche #04693112001). Chromatin was sonicated to around 200 bp DNA fragments, using a Diagenode Bioruptor (three rounds of 5 cycles, 30” on 30” off). Lysates were cleared by addition of Triton X-100 to a final concentration of 1% and centrifugation at 2000 g for 10 minutes at 4°C. A total of 50 μl lysates were saved from each sample for input and stored at – 80°C until use. To prepare antibody-bound beads, 30 μl of magnetic beads (Invitrogen, Dynabeads) were washed three times with blocking buffer (1× PBS, 0.5% BSA) and incubated overnight with 4 μg of the anti-Flag M2(Sigma) antibodies at 4°C. For each ChIP, 900 uL sonicated lysate from 2×107 cells was incubated with the antibody-bound beads overnight at 4°C. Beads were washed 6 times with RIPA wash buffer (50 mM Hepes-KOH, pH= 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate) and 1 time with TBS (20 Mm Tris-HCL, PH 7.6, 150Mm NaCl) for 5 minutes each time at room temperature with gently rocking. All washing buffers contain the protease inhibitors. The beads were eluted twice with 50 ul elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) for 10 minutes at 65°C with rocking. Crosslinking was reversed by adding 6 uL 5M NaCl to the eluates and incubated at 65°C overnight. RNAs were degraded by incubation with 1μl of 10 mg/ml RNase at 37°C for 30 minutes and proteins were digested by incubation with 2 μl of 20 mg/ml of Proteinase K(Thermo Fisher) at 56°C for 2 hours. DNAs were then purified using QIAquik PCR purification kit (QIAGEN, #28106).

value: breast

tag: cell line

value: Breast invasive carcinoma


title: 16T


title: P7 d21 TNC

description: P7 d21 TNC

value: total nucleated cells

value: 21 days after transplantation


title: Smarce1-MD(R42A)_A10_0min_rep1

description: nascent RNA


title: Smarce1-MD09_asyn_rep2

description: nascent RNA


title: 52T


title: 15T


title: 71T


title: 2T


title: 72T


title: 70T


title: MCF7-sgGT3-INCPR1


title: Smarce1-MD09_asyn_rep1

description: nascent RNA


title: P7 d1 TNC

description: P7 d1 TNC

value: bone marrow

value: 1 day after transplantation

value: Female

value: fresh bone marrow


title: Smarce1-MD(R42A)_A10_asyn_rep2

description: nascent RNA


title: P6 d60 TNC

description: P6 d60 TNC

value: bone marrow and peripheral blood

value: fresh bone marrow and peripheral blood


title: Smarce1-MD(R42A)_A10_asyn_rep1

description: nascent RNA

value: mouse embryonic stem cells


title: P7 d14 TNC

description: P7 d14 TNC

value: 14 days after transplantation


title: MCF7-sgNCR3


title: P6 d90 TNC

description: P6 d90 TNC

value: 90 days after transplantation


title: Smarce1-MD(R42A)_A04_asyn_rep2

description: nascent RNA


title: MCF7-sgNCR2


title: MCF7-sgGT3-INCPR2


title: Smarce1-MD(R42A)_A04_asyn_rep1

description: nascent RNA


title: MCF7-sgNCR1


title: 69T

value: gastric cancer


title: NS_Smarce1-MD30_rep2

data_processing:
Total stranded RNA sequencing data were mapped to mouse genome assembly mm10 using an internal AutoMapper pipeline.
Briefly, the raw reads were trimmed with trim galore (V0.60) and mapped to mouse genome mm10 using STAR V2.7.1a. Then the read counts were computed using RSEM (V1.3.0) based on GENCODE vM23.
Counts were further normalized and differentially expressed genes were calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: read counts from RSEM

source_name: neural cells

growth_protocol: mESCs were cultured in Knockout DMEM supplemented with 15% ES-qualified FBS, 1% NEAA, 1% GlutaMAX, 0.5 mM beta-mercaptoethanol, and 10 ng/ml mLIF on 0.1% gelatin-coated tissue culture dishes. For direct neural differentiation, mESCs were cultured in RHA-B media for 6 days.

extract_protocol:
TRIzol (https://www.thermofisher.com/order/catalog/product/15596026)
KAPA Hyper Prep Kit (KK8504)

value: mESCs derived neural cells

value: RHB-A (TAKARA#Y40001)


title: MCF7-MCF7-GT3-INCP Input1

description: processed data file: Flag-GT3-INCP.IP1_2.pooled_peaks.narrowPeak

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l MCF7.sgrna.library --control-sgrna MCF7.sgrna.library.negctrl --norm-method control -n MCF7.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the ChIP-seq data: The ChIP-seq reads were first trimmed by Trim Galore (v0.6.5), a wrapper around two tools: cutadapt v2.8 and FastQC v0.11.5, and were then mapped to the human genome (GRCh38), using Bowtie2 (v2.4.1). The resulting sorted BAM files were converted into bedGraph and bigWig formats using BEDTools (v2.24.0) and UCSC bedGraphToBigWig (v4). The ChIP-seq peaks were identified by MACS2 (v2.1.2) with the parameters “macs2 callpeak -t ChIP.bam -c INPUT.bam -g hs --outdir output -n NAME 2> NAME.callpeak.log”. BETA (v1.0.7) was used to annotate the peaks that are associated with genes of interest.
genome build/assembly: human hg38 genome

tag: chip antibody

value: none (input)


title: 68T


title: MCF7-MCF7-GT3-INCP Input2

value: breast


title: P6 d21 TNC

description: P6 d21 TNC

value: peripheral blood

value: fresh peripheral blood


title: 37T


title: 36T


title: P6 d30 TNC

description: P6 d30 TNC

value: total nucleated cells

value: 30 days after transplantation


title: P6 d1 TNC

description: P6 d1 TNC

value: bone marrow

value: 1 day after transplantation


title: MCF7-Flag-GT3-INCP IP2

value: Breast invasive carcinoma

value: anti-Flag M2(Sigma)


title: 60T


title: NS_Smarce1-MD30_rep1

treatment_protocol: For direct neural differentiation, mESCs were cultured in RHA-B media for 6 days.


title: NS_Smarce1-MD09_rep2


title: P5 after d180 TNC

description: P5 after d180 TNC

value: bone marrow and peripheral blood

value: half a year after transplantation

value: Female

value: fresh bone marrow and peripheral blood


title: MCF7-Flag-GT3-INCP IP1


title: NS_Smarce1-MD09_rep1


title: P5 d90 TNC

description: P5 d90 TNC

value: 90 days after transplantation


title: P6 d14 TNC

description: P6 d14 TNC

value: 14 days after transplantation


title: NS_Smarce1-MD(R42A)_A10_rep1

value: mESCs derived neural cells

value: RHB-A (TAKARA#Y40001)


title: MCF7 RPF R2

data_processing:
Library strategy: Ribo-Seq
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l MCF7.sgrna.library --control-sgrna MCF7.sgrna.library.negctrl --norm-method control -n MCF7.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome with hisat2(v2.1.0). The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2).
For the Ribo-seq data: The ribosome-protected RNA fragments (RPF) reads were trimmed and the low-quality reads were filtered by Sickle (http://github.com/ucdavis-bioinformatics/sickle). The RPF reads after filtering were mapped to human rRNA sequences using bowtie and allowing for two mismatches. The reads that were not mapped to human rRNA sequences were then mapped to the human genome (GRCh38) with transcriptome annotations GENECODE v22 and v25, NCBI refseq, MiTranscriptome and lincRNA transcript annotations generated by Dr. John Rinn’s group, using STAR with parameters “--outFilterMismatchNmax 2 –outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1 --alignEndsType EndToEnd”. Quality control was performed using Ribo-TISH quality module with all the uniquely mapped RPF reads in the annotated ORFs. The RPFs were grouped by their lengths and each aligned RPF read was represented by its 5′ end before estimation of the P-site offset. The metagene RPF count profile near the start/stop codon was constructed by summing the RPF count between -40 and +20 bp of the first base of the start/stop codon across all annotated protein-coding genes. The P-site offset was estimated based on the distribution of the 5′ end of the metagene RPF counts near the annotated start codons. The RPF count between the 15 bp upstream of the first base of the start codon and the 12 bp upstream of the first base of the stop codon were used to calculate the RPF count distributions across three reading frames. The fraction of the RPF counts in the dominant frame (fd) was calculated as the ratio between the maximum RPF count among all three reading frames and the sum of the RPF counts from all reading frames. The cryptic ORFs were predicted with Ribo-TISH predict module with regular riboseq data longest mode.
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: Deseq2 normalized read count and differential expression result in csv file, CRISPR screen: read count and differential expression result in text file.

source_name: Breast invasive carcinoma

growth_protocol: MCF7 cells were cultured in RPMI- 1640 (Hyclone #SH30027.1). All culture medium were supplemented with 10% FBS (Gibco #10437-028) and 1% penicillin/streptomycin (Corning # 30-002-CI). All cell lines were cultured in an incubator (Thermo, HEARCELL VIOS 160i) with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini kit (QIAGEN, #74104) and was treated with DNase I (QIAGEN #79254). RPFs without ribosomal RNA were run on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised. The RPF RNAs were eluted and precipitated followed. The genomic DNAs were extracted by using QIAamp DNA Mini Kit (QIAGEN).
RNA-seq libraries were prepared from 2 μg of total RNA, using TruSeq Stranded mRNA Library Prep kit (Illumina # 20020594), according to the manufacturer’s instructions.  Sample preparation for ribosome profiling was conducted according to the manufacturer’s specifications for the TruSeq Ribo Profile (Mammalian) Library Prep Kit (Illumina).

treatment_protocol:
MCF7 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minutes and the cells were lyszed by using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 μl of lysate were taken and 15 ul of RNase I (100 U/μl, Thermo Fisher Scientific) were added and the mixtures were incubated for 45min at room temperature followed by adding 15 μl SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery were done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were ran on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised.
Sample preparation for ribosome profiling: MCF7 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minute and the cells were lysed by using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 µL of lysates were taken and 15 µL of RNase I (100 U/ µL, Thermo Fisher Scientific) were added, and the mixtures were incubated for 45min at room temperature followed by adding 15 µL SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery was done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were run on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised. The RPF RNAs were eluted and precipitated followed by library construction according to the manufacturer’s protocol. Sample preparation for ORF CRISPR/Cas9 screen: The MCF7 cells transduced with lentiCas9-EGFP (addgene, #63592) were sorted on a FACSAria cell sorter (BD Biosciences) and the cells with high EGFP expression were collected. These MCF7 cells with high expression of SpCas9 were plated into ten 10-cm dishes and infected with lentiviruses containing the sgRNA library at an MOI of 0.2~0.3. Following puromycin (2 μg/ml) selection for 4 days, 3.5 ×107 cells were split into three replicates. For each replicate, 8× 106 were harvested to extract genomic DNAs (Day 0, D0), using QIAamp DNA Mini Kit (QIAGEN), and 3.7×106 cells (~500×coverage for each sgRNA per replicate) were passed every 3 days and cultured for 21 days. At day 21 (D21), 8× 106 cells were harvested for each replicate to extract genomic DNA. The next-generation-sequencing (NGS)-ready sgRNA libraries were prepared by two rounds of PCR with the KAPA HiFi HotStart ReadyMix (Roche # KK2602).


title: MCF7 RPF R3


title: NS_Smarce1-MD(R42A)_A10_rep2


title: MCF7 RPF R1


title: P5 d30 TNC

description: P5 d30 TNC


title: P5 d60 TNC

description: P5 d60 TNC

value: 60 days after transplantation


title: MCF7-Day 21 R2

treatment_protocol:
The MCF7 cells transduced with lentiCas9-EGFP (addgene, #63592) were sorted on a FACSAria cell sorter (BD Biosciences) and the cells with high EGFP expression were collected. These MCF7 cells with high expression of SpCas9 were plated into ten 10-cm dishes and infected with lentiviruses containing the sgRNA library at an MOI of 0.2~0.3. Following puromycin (2 μg/ml) selection for 4 days, 3.5 ×107 cells were split into three replicates. For each replicate, 8× 106 were harvested to extract genomic DNAs (Day 0, D0), using QIAamp DNA Mini Kit (QIAGEN), and 3.7×106 cells (~500×coverage for each sgRNA per replicate) were passed every 3 days and cultured for 21 days. At day 21 (D21), 8× 106 cells were harvested for each replicate to extract genomic DNA.
Sample preparation for ribosome profiling: MCF7 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minute and the cells were lysed by using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 µL of lysates were taken and 15 µL of RNase I (100 U/ µL, Thermo Fisher Scientific) were added, and the mixtures were incubated for 45min at room temperature followed by adding 15 µL SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery was done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were run on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised. The RPF RNAs were eluted and precipitated followed by library construction according to the manufacturer’s protocol. Sample preparation for ORF CRISPR/Cas9 screen: The MCF7 cells transduced with lentiCas9-EGFP (addgene, #63592) were sorted on a FACSAria cell sorter (BD Biosciences) and the cells with high EGFP expression were collected. These MCF7 cells with high expression of SpCas9 were plated into ten 10-cm dishes and infected with lentiviruses containing the sgRNA library at an MOI of 0.2~0.3. Following puromycin (2 μg/ml) selection for 4 days, 3.5 ×107 cells were split into three replicates. For each replicate, 8× 106 were harvested to extract genomic DNAs (Day 0, D0), using QIAamp DNA Mini Kit (QIAGEN), and 3.7×106 cells (~500×coverage for each sgRNA per replicate) were passed every 3 days and cultured for 21 days. At day 21 (D21), 8× 106 cells were harvested for each replicate to extract genomic DNA. The next-generation-sequencing (NGS)-ready sgRNA libraries were prepared by two rounds of PCR with the KAPA HiFi HotStart ReadyMix (Roche # KK2602).


title: 32T

value: gastric cancer


title: 30T


title: 35T


title: MCF7-Day 21 R1


title: NS_Smarce1-MD(R42A)_A04_rep1


title: MCF7-Day 21 R3


title: NS_Smarce1-MD(R42A)_A04_rep2


title: P4 d70 TNC

description: P4 d70 TNC

value: peripheral blood

value: 70 days after transplantation

value: fresh peripheral blood


title: P5 d14 TNC

description: P5 d14 TNC

value: total nucleated cells


title: 49T


title: Smarce1-MD(R42A)_A02_r3

value: mouse embryonic stem cells

value: untreatment


title: Smarce1-MD_45_r3


title: 63T


title: Smarce1-MD(R42A)_A01_r3


title: Smarce1-MD_47_r3


title: 33T


title: MCF7-Day 0 R3


title: 46T


title: P4 d21 TNC

description: P4 d21 TNC

value: 21 days after transplantation


title: MCF7-Day 0 R1


title: K562 sgRNA sequencing: inf2_p3_50

city: San Francisco

first: Xuewen

state: CA

address: 1650 Owens Street

institute: Gladstone Institutes

data_processing:
Raw sequencing reads were aligned and quantified using the MAGeCK algorithm.
Data were analyzed using a maximum likelihood estimate (MAGeCK-MLE) to compute the gene essentiality under perturbation and control condition.
Assembly: Brunello Human CRISPR Knockout Pooled Library (Addgene, #73179-LV)
Supplementary files format and content: Txt files for sgRNA counts and normalized counts.
Supplementary files format and content: CSV file for gene essentiality under control and perturbation condtions.

extract_protocol:
Genomic DNA was extracted from cell pellets with the Blood and Cell Culture DNA Maxi Kit (Qiagen, 13323). The sgRNAs were amplified by PCR.
Brunello Human CRISPR Knockout Pooled Library (Addgene, #73179-LV)

treatment_protocol: 50% oxygen vs 21% oxygen

value: lymphoblast cells

value: WT

value: 50% oxygen, passage 3


title: K562 sgRNA sequencing: inf2_p5_50

value: 50% oxygen, passage 5


title: K562 sgRNA sequencing: inf2_p5_21

value: 21% oxygen, passage 5


title: P4 d30 TNC

description: P4 d30 TNC

value: bone marrow and peripheral blood

value: 30 days after transplantation

value: Female

value: fresh bone marrow and peripheral blood


title: 38T

value: gastric cancer


title: 41T


title: P5 d21 TNC

description: P5 d21 TNC

value: peripheral blood


title: 40T


title: siGATA3#3

data_processing:
For the screen data: MAGeCK (v0.5.9.4) was used to calculate the read count of individual sgRNAs in different samples with the following parameters: “mageck count -l MCF7.sgrna.library --control-sgrna MCF7.sgrna.library.negctrl --norm-method control -n MCF7.sgrna.count --sample-label D0,D21 --fastq files.fq”. DESeq2 was used to identify the differentially expressed sgRNAs between D0 and D21. The read counts were normalized by the mapped negative control sgRNAs using ratio median normalization, and the normalization factors were applied to all sgRNAs. The cryptic ORFs with at least 2 significantly depleted sgRNAs (log2Fold-Change <= -log2(1.5) and p < 0.05),
For the RNA-seq data: The RNA-seq reads were first trimmed for adaptor sequence and masked for low-complexity and low-quality sequence and were then mapped to the human genome (GRCh38) and GENCODE V22 transcriptome with hisat2(v2.1.0). The gene-level raw read-counts were calculated using htseq-count function of HTSeq (0.11.0), based on the aligned and sorted bam files. The normalization of read counts and differential gene expression analysis were performed, using DESeq2(1.22.2).
For the Ribo-seq data: The ribosome-protected RNA fragments (RPF) reads were trimmed and the low-quality reads were filtered by Sickle (http://github.com/ucdavis-bioinformatics/sickle). The RPF reads after filtering were mapped to human rRNA sequences using bowtie and allowing for two mismatches. The reads that were not mapped to human rRNA sequences were then mapped to the human genome (GRCh38) with transcriptome annotations GENECODE v22 and v25, NCBI refseq, MiTranscriptome and lincRNA transcript annotations generated by Dr. John Rinn’s group, using STAR with parameters “--outFilterMismatchNmax 2 –outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMax 20000 --outMultimapperOrder Random --outSAMmultNmax 1 --alignEndsType EndToEnd”. Quality control was performed using Ribo-TISH quality module with all the uniquely mapped RPF reads in the annotated ORFs. The RPFs were grouped by their lengths and each aligned RPF read was represented by its 5′ end before estimation of the P-site offset. The metagene RPF count profile near the start/stop codon was constructed by summing the RPF count between -40 and +20 bp of the first base of the start/stop codon across all annotated protein-coding genes. The P-site offset was estimated based on the distribution of the 5′ end of the metagene RPF counts near the annotated start codons. The RPF count between the 15 bp upstream of the first base of the start codon and the 12 bp upstream of the first base of the stop codon were used to calculate the RPF count distributions across three reading frames. The fraction of the RPF counts in the dominant frame (fd) was calculated as the ratio between the maximum RPF count among all three reading frames and the sum of the RPF counts from all reading frames. The cryptic ORFs were predicted with Ribo-TISH predict module with regular riboseq data longest mode.
Genome_build: human hg38 genome
Supplementary_files_format_and_content: RNASeq: Deseq2 normalized read count and differential expression result in csv file, CRISPR screen: read count and differential expression result in text file.

treatment_protocol: Sample preparation for ribosome profiling: MCF7 cells were treated with CHX (Sigma-Aldrich, final concentration 0.1mg/ml) for 1 minute and the cells were lysed by using Mammalian Lysis Buffer (including CHX at a concentration of 0.1mg/ml). Then 600 µL of lysates were taken and 15 µL of RNase I (100 U/ µL, Thermo Fisher Scientific) were added, and the mixtures were incubated for 45min at room temperature followed by adding 15 µL SUPERaseIn RNase inhibitor (Thermo Fisher Scientific) to stop the reaction. Ribosome recovery was done by illustra MicroSpin S-400 HR Columns (GE Healthcare) and the Ribosomal Protected Fragments (PFFs) were purified by RNA Clean & Concentrator (Zymo Research). Ribosomal RNA was subtracted using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat, Illumina). RPFs without ribosomal RNA were run on a 15% Urea denaturing-PAGE gel, and the gel slides from 28nt~30nt were excised. The RPF RNAs were eluted and precipitated followed by library construction according to the manufacturer’s protocol. Sample preparation for ORF CRISPR/Cas9 screen: The MCF7 cells transduced with lentiCas9-EGFP (addgene, #63592) were sorted on a FACSAria cell sorter (BD Biosciences) and the cells with high EGFP expression were collected. These MCF7 cells with high expression of SpCas9 were plated into ten 10-cm dishes and infected with lentiviruses containing the sgRNA library at an MOI of 0.2~0.3. Following puromycin (2 μg/ml) selection for 4 days, 3.5 ×107 cells were split into three replicates. For each replicate, 8× 106 were harvested to extract genomic DNAs (Day 0, D0), using QIAamp DNA Mini Kit (QIAGEN), and 3.7×106 cells (~500×coverage for each sgRNA per replicate) were passed every 3 days and cultured for 21 days. At day 21 (D21), 8× 106 cells were harvested for each replicate to extract genomic DNA. The next-generation-sequencing (NGS)-ready sgRNA libraries were prepared by two rounds of PCR with the KAPA HiFi HotStart ReadyMix (Roche # KK2602).

tag: sirna


title: P4 d14 TNC

description: P4 d14 TNC

value: 14 days after transplantation


title: P4 d1 TNC

description: P4 d1 TNC

value: bone marrow

value: 1 day after transplantation

value: fresh bone marrow


title: K562 sgRNA sequencing: inf2_p3_21

value: 21% oxygen, passage 3


title: Smarce1-MD_45_r2

value: mouse embryonic stem cells

value: untreatment


title: Smarce1-MD_47_r2


title: K562 sgRNA sequencing: inf1_p5_50

value: lymphoblast cells

value: WT


title: siGATA3#1


title: P3 d30 TNC

description: P3 d30 TNC

value: total nucleated cells

value: Male


title: P3 after d180 TNC

description: P3 after d180 TNC

value: bone marrow and peripheral blood

value: one year after transplantation


title: siGATA3#2


title: Smarce1-MD(R42A)_A01_r2


title: Smarce1-MD(R42A)_A02_r2


title: K562 sgRNA sequencing: inf2_p0

value: Passage 0


title: siNC2#2


title: P3 d90 TNC

description: P3 d90 TNC

value: 90 days after transplantation

value: fresh bone marrow and peripheral blood


title: siNC2#3


title: K562 sgRNA sequencing: inf1_p5_21

value: 21% oxygen, passage 5


title: Smarce1-MD_47_r1


title: P3 d21 TNC

description: P3 d21 TNC

value: peripheral blood

value: 21 days after transplantation

value: fresh peripheral blood


title: Smarce1-MD_45_r1


title: K562 sgRNA sequencing: inf1_p3_21


title: siNC2#1


title: P3 d14 TNC

description: P3 d14 TNC

value: 14 days after transplantation


title: siLNC00992#3


title: K562 sgRNA sequencing: inf1_p3_50

value: 50% oxygen, passage 3


title: Smarce1-MD(R42A)_A02_r1

value: mouse embryonic stem cells


title: K562 sgRNA sequencing: inf1_p0


title: P2 after d180 TNC

description: P2 after d180 TNC


title: Smarce1-MD(R42A)_A01_r1

value: untreatment


title: P2 d90 TNC

description: P2 d90 TNC


title: siLINC00992#2


title: Smarce1-MD_30_r3


title: Mn_treated_3

city: Nanning

first: Qifeng

address: No. 10, Hua-dong Rd

institute: Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine

data_processing:
The resulting sequencing reads were processed according to the standard quality control criteria: (1) reads containing N; (2) reads containing more than four bases with a quality score < 10; (3) reads containing more than six bases with a quality score < 13; (4) reads with 5’ primer contaminants or without 3’ primer; (5) reads without the insert tag; (6) reads with ploy A; and (7) reads shorter than 15 nucleotides and longer than 44 nucleotides.
Trimmomatic (Bolger et al., 2014) was used to remove the adaptor sequence and to eliminate low quality reads.
The remaining clean reads were aligned to sequences in miRBase 22 (Kozomara et al., 2019)
24-33 bp reads among remaining unmapped reads were aligned to the sequences in piRNA Cluster database (Rosenkranz, 2016), piRNA sequence from NCBI, and GtRNA database (Chan & Lowe, 2016)（for tRNA derived from piRNAs）
After filtered rRNA, all remaining unmapped reads were aligned to the sequence in tsRBase (Zuo et al., 2021).
SPORTS 1.1 (Shi et al., 2018) was used to align and annotated rsRNA with its pre-compiled annotation databases.
Assembly: rn6
Supplementary files format and content: processed data files is txt format, containning raw count of sequencing reads.

organism: Rattus norvegicus

source_name: Striatum

extract_protocol:
TRIzol reagent (1 ml; Invitrogen; 15596018) was added to a microtube with pulverized tissues or collected cells.
The RNA segment was separated by PAGE, then a 15- to 45-nucleotide stripe was selected and recycled. The adapters were obtained from the QIAseq® miRNA Library Kit (QIAGEN: 331505) and ligated sequentially.

value: Striatum

value: 200 mg/kg MnCl2·4H2O with physiological saline (10 ml/kg administration volume) route once a day, six days per week, for 8 weeks


title: Mn_treated_2


title: Smarce1-MD_09_r3


title: siNC#2


title: MMT_treated_3

value: 4 mg/kg MMT (about 1 mg Mn/kg) with corn oil via the intragastrical route once a day, six days per week, for 8 weeks


title: Smarce1-MD(R42A)_A04_r3


title: Mn_treated_1


title: Smarce1-MD(R42A)_A10_r3


title: P1 d30 TNC

description: P1 d30 TNC

value: bone marrow

value: total nucleated cells

value: 30 days after transplantation

value: Female

value: fresh bone marrow


title: P1 d14 TNC

description: P1 d14 TNC

value: bone marrow and peripheral blood

value: fresh bone marrow and peripheral blood


title: siLINC00992#1


title: siNC#1


title: MMT_treated_2


title: Smarce1-MD_30_r2


title: MMT_treated_1


title: control_3

value: corn oil (1 ml/kg administration volume), route once a day, six days per week, for 8 weeks


title: Smarce1-MD_09_r2


title: siNC#3


title: P2 d30 TNC

description: P2 d30 TNC

value: Male


title: Smarce1-MD(R42A)_A10_r2


title: control_2


title: P1 d1 TNC

description: P1 d1 TNC

value: 1 day after transplantation


title: control_1


title: Smarce1-MD(R42A)_A04_r2


title: Brain, psap knockout, 4 months-post-fertilization, replicate 4 [15628X8]

city: Salt Lake City

first: Tejia

last: Zhang

state: UT

address: 30 South 2000 East

department: Pharmacology and Toxicology

institute: University of Utah

data_processing:
Reference database was created from zebrafish Zv10 genome and gene feature files (Ensembl release 94) using STAR version 2.6.1b (splice junctions optimized for 150 bp reads).
Optical duplicates were removed using clumpify v38.34, reads were trimmed of adapters using cutadapt 1.16, alignment was performed with STAR (two pass mode), and genes were assigned using featureCounts version 1.6.3.
Output files (cutadapt, FastQC, Picard CollectRnaSeqMetrics, STAR, and featureCounts) were summarized using MultiQC to check for outliers.
Differential expression analysis was performed in DESeq2 version 1.22.2 (5% false discovery rate).
Assembly: Zv10
Supplementary files format and content: DESeq2-generated .xlsx file containing raw and normalized counts annotated by Ensembl gene ID, and fold changes/adjusted p-values annotated by gene name

organism: Danio rerio

source_name: Brain (3 per sample)

extract_protocol:
RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit (Qiagen) following manufacturer's instructions; 3 brains (4 months-post-fertilization) were pooled for each sample.
cDNA library was prepared using the TruSeq Stranded Total RNA Library Prep Ribo-Zero Gold Kit (Illumina) following manufacturer's instructions.

value: Brain (3 per sample)

value: TuAB

value: psap knockout

tag: time

value: 4 months-post-fertilization


title: Smarce1-MD_30_r1

value: mouse embryonic stem cells

value: untreatment


title: Smarce1-MD_09_r1


title: Brain, wildtype, 4 months-post-fertilization, replicate 4 [15628X7]

tag: tissue

value: wildtype


title: Brain, psap knockout, 4 months-post-fertilization, replicate 3 [15628X6]


title: Splenocytes_naïve_rep4

city: Suwon-si

first: Se Jin

last: Im

state: Gyeonggi-do

address: 2066, Seobu-ro, Jangan-gu

department: Department of Immunology

institute: Sungkyunkwan University School of Medicine

description: Gene expression data from naïve mouse CD8 T lymphocytes

hyb_protocol: RNA isolated from mouse TILs was hybridized to Affymetrix mouse 430 2.0 arrays (Emory University, Genomics Core Facility).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Raw data (CEL files) were normalized by RMA using Affy R package.

label: biotn

source_name: Splenocytes from naïve mouse

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

growth_protocol: Mouse skin melanoma B16F10-GP (5x10^5) cells suspended in 25% Matrigel Matrix (Corning)/RPMI were injected on the right flank (day 0).

extract_protocol: RNA from FACS sorted cells was purified by Allprep DNA/RNA micro kit (QIAGEN).

treatment_protocol: Tumors were harvested in RPMI media including 5% FCS when the tumors reached the size of about 1cm^2 area, cut into small pieces and digested for 1hour with Collagenase IV (150U/mL) and DNase (20µg/ml) at 37’C with shaking. Single cell suspension of TILs was isolated by 44%/67% Percoll gradient centrifugation. Cell sorting was performed on a FACS Aria II (BD Biosciences) for microarray analysis. From B16F10-GP bearing mice, stem-like (Tim-3-2B4- PD-1+) and exhausted (Tim-3+2B4+ PD-1+) CD8 T cells were isolated between day 17 and day 19 post inoculation.

value: 6-8 weeks old

value: Spleen

value: CD8 T lymphocytes


title: Brain, wildtype, 4 months-post-fertilization, replicate 3 [15628X5]


title: fetal ovaries, 15 μM NAPQI, 14.5dpc, rep3

city: Chongqing

first: Xinyi

last: Mu

address: 1 Yixueyuan Road, Yuzhong District, Chongqing, PR China

institute: Chongqing Medical University

data_processing:
FastQC v0.11.8
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC v0.11.8
Trimmed sequence reads were mapped to Mus_musculus.GRCm39.dna.toplevel.fa using HISAT2 v2.0.5
Read count extraction and normalization were performed using HTSeq(0.9.1)
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: fetal ovary

growth_protocol: The 14.5 dpc ovaries were isolated and placed in wells containing 1 ml serum-free DMEM/F12 medium, then cultured in a 37 ℃ humidified incubator for three days

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: 15 μM NAPQI or equal volumes of ethyl acetate were added to cultures of 14.5 dpc ovaries for three days

value: fetal ovary

value: WT

value: ovary culture with 15 μM NAPQI for 3-days


title: fetal ovaries, 15 μM NAPQI, 14.5dpc, rep2


title: TILs_Tm PD-1+ Tim-3-_rep3

description: Gene expression data from Tim-3- PD-1+ CD8 TILs

source_name: Tumor-infiltrating lymphocytes (TILs) from B16F10-GP bearing mice (day 17 and day 19 post inoculation)

value: B16F10-GP Tumor

value: CD8 TILs


title: TILs_Tm PD-1+ Tim-3-_rep2


title: fetal ovaries, 15 μM NAPQI, 14.5dpc, rep1


title: Brain, wildtype, 4 months-post-fertilization, replicate 2 [15628X3]


title: Splenocytes_naïve_rep3


title: TILs_Tm PD-1+ Tim-3+_rep3

description: Gene expression data from Tim-3+ PD-1+ CD8 TILs


title: ESC_WT rep2

first: Zhenzhen

last: Lin

address: No. 22, Qixiangtai Road

institute: Tianjin Medical University

data_processing:
Paired-end FASTQ files were controlled for quality, mapped to the reference genome (mm10) and converted into interaction matrices using HiC-Pro (V2.11.1) (Servant et al., 2015) using pipeline code available at https://github.com/nservant/HiC-Pro.
We used 200 kb bin sizes to generate raw and ICE (iterative correction and eigenvector decomposition) (Imakaev et al.,2012) normalized matrix. The valid pair ﬁles were transformed to .hic ﬁles which were ready for juicer (V1.9.8) for exploratory visualization.
Assembly: mm10
Supplementary files format and content: hicpro-validpairs

source_name: ESC

extract_protocol:
ESCs were cross-linked, nuclei-lysed, and chromatin-digested with Dpn II. After biotin ﬁlling, proximity ligation was carried out under dilute conditions to favor ligation of fragments in three-dimensional proximity. After reverse-crosslinking, DNA was precipitated using isopropanol and sheared to 100-400 bp fragments using Bioruptor Pico (Diageode) sonicator. Biotinylated DNA fragments were pulled down with MyOne Streptavidin T1 beads (ThermoFisher) to enrich for physically interacting sites, followed by end repair, dATP tailing and adaptor ligation.
Hi-C DNA was amplified with 8 to 12 PCR amplification cycles using The NEBNext Multiplex Oligos for Illumina (NEB). Then, Hi-C library DNA was purified with AMPure XP beads (Beckman Coulter) and fragments ranging from 300 bp to 500 bp were selected.

value: ESC

value: mouse embryonic stem cell


title: TILs_Tm PD-1+ Tim-3+_rep4


title: TILs_Tm PD-1+ Tim-3-_rep1


title: TILs_Tm PD-1+ Tim-3+_rep2


title: Smarce1-MD(R42A)_A10_r1


title: Brain, psap knockout, 4 months-post-fertilization, replicate 1 [15628X2]

value: Brain (3 per sample)


title: ESC_Terc-/- rep1

value: Terc-/-


title: fetal ovaries, Control, 14.5dpc, rep2

value: ovary culture with ethyl acetate for 3-days


title: Smarce1-MD(R42A)_A04_r1


title: ESC_WT rep1


title: ESC_Terc-/- rep2


title: Splenocytes_naïve_rep2


title: Brain, psap knockout, 4 months-post-fertilization, replicate 2 [15628X4]

value: TuAB

value: psap knockout

value: 4 months-post-fertilization


title: Brain, wildtype, 4 months-post-fertilization, replicate 1 [15628X1]

value: wildtype


title: fetal ovaries, Control, 14.5dpc, rep3


title: SUDHL5_PR_18h_bio replicate 2

status: Public on Mar 17 2023

city: Bethesda

first: David

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
SUD5_PR_18h_2
2x50 cycle

data_processing:
Align to the genome with Bowtie2.
An in-house algorithm for peak calling.
Assembly: hg19
Supplementary files format and content: The wig files contain peak information for visualization on the UCSC genome browser, as well as for implementing other downstream analysis.
Library strategy: CUT&RUN

growth_protocol: All cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
DNA was extracted using CUTANA Chic/CUT&RUN kit (Epicypher, SKU-14-1048).
Libraries were constructed using CUTANA CUT&RUN library prep kit (Epicypher, SKU-14-1001).

treatment_protocol: All cells were grown at 1 x 10^6 cells/ml and either treated with vehicle (DMSO) or Prednisolone (10mM or 25nm) for 0h, 1h and 18h.

value: human DLBCL cell line

value: Cas9 engineered

value: Prednisolone (25nM) 18h


title: RAMOS_PR_2h_bio replicate 1

description:
RAMOS_PR_2h_1
2x50 cycle

source_name: RAMOS

value: RAMOS

value: human BL cell line

value: Prednisolone (10mM) 2h


title: RAMOS_PR_18h_bio replicate 1

description:
RAMOS_PR_18h_1
2x50 cycle

value: Prednisolone (10mM) 18h


title: SUDHL5_PR_2h_bio replicate 2

description:
SUD5_PR_2h_2
2x50 cycle

value: Prednisolone (25nM) 2h


title: SUDHL5_PR_2h_bio replicate 1

description:
SUD5_PR_2h_1
2x50 cycle


title: Splenocytes_naïve_rep1

value: 6-8 weeks old

value: Spleen

value: CD8 T lymphocytes


title: SUDHL5_PR_18h_bio replicate 1

description:
SUD5_PR_18h_1
2x50 cycle


title: SUDHL5_PR_0h_bio replicate 2

description:
SUD5_PR_0h_2
2x50 cycle


title: TILs_Tm PD-1+ Tim-3+_rep1

value: B16F10-GP Tumor

value: CD8 TILs


title: SUDHL5_PR_0h_bio replicate 1

description:
SUD5_PR_0h_1
2x50 cycle


title: FL318_PR_2h_bio replicate 2

description:
FL318_PR_2h_2
2x50 cycle


title: FL318_PR_0h_bio replicate 2

description:
FL318_PR_0h_2
2x50 cycle


title: FL318_PR_0h_bio replicate 1

description:
FL318_PR_0h_1
2x50 cycle


title: fetal ovaries, Control, 14.5dpc, rep1

value: fetal ovary

value: WT

value: ovary culture with ethyl acetate for 3-days


title: FL318_PR_18h_bio replicate 1

description:
FL318_PR_18h_1
2x50 cycle


title: RAMOS_PR_0h_bio replicate 1

description:
RAMOS_PR_0h_1
2x50 cycle


title: HBL1_PR_0h_bio replicate 2

description:
HBL1_PR_0h_2
2x50 cycle


title: HBL1_PR_18h_bio replicate 2

description:
HBL1_PR_18h_2
2x50 cycle


title: HBL1_PR_2h_bio replicate 2

description:
HBL1_PR_2h_2
2x50 cycle


title: HBL1_PR_18h_bio replicate 1

description:
HBL1_PR_18h_1
2x50 cycle


title: HBL1_PR_0h_bio replicate 1

description:
HBL1_PR_0h_1
2x50 cycle


title: HBL1_PR_2h_bio replicate 1

description:
HBL1_PR_2h_1
2x50 cycle


title: TMD8_CSKi_24h bio replicate2

description:
TMD8_CSKi_24h_R2
2x75 cycle
paired-end RNA-Seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2.
Raw read counts per gene were called with Htseq-Count.
FPKM and median shift.
Assembly: hg19
Supplementary files format and content: DLBCL_CSKi_RNAseq_Normalized_log2.txt

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini kit.
Libraries were generated using TruSeq stranded mRNA library prep (Illumina).

treatment_protocol: All cells were grown at 0.5 x 10^6 cells/ml and either treated in duplicates with vehicle (DMSO) or CSKi (500nm) for 1h, 3h, 6h, and 24h.


title: TMD8_CSKi_24h bio replicate1

description:
TMD8_CSKi_24h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_CSKi_6h bio replicate2

description:
TMD8_CSKi_6h_R2
2x75 cycle
paired-end RNA-Seq

value: CSKi (500nm)_6h


title: FL318_PR_18h_bio replicate 2

description:
FL318_PR_18h_2
2x50 cycle

value: human DLBCL cell line


title: TMD8_DMSO_6h bio replicate2

description:
TMD8_DMSO_6h_R2
2x75 cycle
paired-end RNA-Seq

value: Cas9 engineered


title: TMD8_CSKi_6h bio replicate1

description:
TMD8_CSKi_6h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_6h bio replicate1

description:
TMD8_DMSO_6h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_3h bio replicate2

description:
TMD8_DMSO_3h_R2
2x75 cycle
paired-end RNA-Seq


title: TMD8_CSKi_1h bio replicate2

description:
TMD8_CSKi_1h_R2
2x75 cycle
paired-end RNA-Seq

value: CSKi (500nm)_1h


title: FL318_PR_2h_bio replicate 1

description:
FL318_PR_2h_1
2x50 cycle


title: TMD8_CSKi_3h bio replicate1

description:
TMD8_CSKi_3h_R1
2x75 cycle
paired-end RNA-Seq

value: CSKi (500nm)_3h


title: TMD8_CSKi_1h bio replicate1

description:
TMD8_CSKi_1h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_1h bio replicate1

description:
TMD8_DMSO_1h_R1
2x75 cycle
paired-end RNA-Seq


title: DOHH2_CSKi_24h bio replicate2

description:
DOHH2_CSKi_24h_R2
2x75 cycle
paired-end RNA-Seq


title: P2 d21 TNC

description: P2 d21 TNC

value: peripheral blood

value: total nucleated cells

value: 21 days after transplantation

value: Male

value: fresh peripheral blood


title: DOHH2_CSKi_24h bio replicate1

description:
DOHH2_CSKi_24h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_1h bio replicate2

description:
TMD8_DMSO_1h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_DMSO_24h bio replicate2

description:
DOHH2_DMSO_24h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_DMSO_6h bio replicate2

description:
DOHH2_DMSO_6h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_CSKi_6h bio replicate1

description:
DOHH2_CSKi_6h_R1
2x75 cycle
paired-end RNA-Seq


title: DOHH2_CSKi_6h bio replicate2

description:
DOHH2_CSKi_6h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_CSKi_3h bio replicate2

description:
DOHH2_CSKi_3h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_CSKi_3h bio replicate1

description:
DOHH2_CSKi_3h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_24h bio replicate2

description:
TMD8_DMSO_24h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_DMSO_3h bio replicate2

description:
DOHH2_DMSO_3h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_DMSO_3h bio replicate1

description:
DOHH2_DMSO_3h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_24h bio replicate1

description:
TMD8_DMSO_24h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_DMSO_3h bio replicate1

description:
TMD8_DMSO_3h_R1
2x75 cycle
paired-end RNA-Seq


title: DOHH2_CSKi_1h bio replicate2

description:
DOHH2_CSKi_1h_R2
2x75 cycle
paired-end RNA-Seq


title: DOHH2_DMSO_1h bio replicate1

description:
DOHH2_DMSO_1h_R1
2x75 cycle
paired-end RNA-Seq


title: DOHH2_DMSO_1h bio replicate2

description:
DOHH2_DMSO_1h_R2
2x75 cycle
paired-end RNA-Seq


title: TMD8_24h_Prednisolone_Replicate 2

description:
tmd8_24h_r2
total mRNA
2x50 cycle
paired-end RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2.
Raw read counts per gene were called with Htseq-Count.
FPKM normalization and median shift.
Assembly: hg19
Supplementary files format and content: DLBCL_Prednisolone_RNAseq_FPKM_Normalized_Log2.txt

treatment_protocol: All cells were grown at 0.5 x 10^6 cells/ml and either treated in duplicates with vehicle (DMSO), prednisolone (25nm or 10µM) for 0h 6h and 24h.


title: DOHH2_CSKi_1h bio replicate1

description:
DOHH2_CSKi_1h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_6h_Prednisolone_Replicate 2

description:
tmd8_6h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: DOHH2_DMSO_24h bio replicate1

description:
DOHH2_DMSO_24h_R1
2x75 cycle
paired-end RNA-Seq


title: TMD8_0h_DMSO_Replicate 2

description:
tmd8_0h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: TMD8_24h_Prednisolone_Replicate 1

description:
tmd8_24h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: TMD8_6h_Prednisolone_Replicate 1

description:
tmd8_6h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: TMD8_CSKi_3h bio replicate2

description:
TMD8_CSKi_3h_R2
2x75 cycle
paired-end RNA-Seq


title: HBL1_6h_Prednisolone_Replicate 2

description:
hbl1_6h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: TMD8_0h_DMSO_Replicate 1

description:
tmd8_0h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: HBL1_24h_Prednisolone_Replicate 2

description:
hbl1_24h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: DOHH2_DMSO_6h bio replicate1

description:
DOHH2_DMSO_6h_R1
2x75 cycle
paired-end RNA-Seq


title: HBL1_24h_Prednisolone_Replicate 1

description:
hbl1_24h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: HBL1_0h_DMSO_Replicate 2

description:
hbl1_0h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: HBL1_0h_DMSO_Replicate 1

description:
hbl1_0h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: RAMOS_24h_Prednisolone_Replicate 2

description:
ramos_24h_r2
total mRNA
2x50 cycle
paired-end RNA-seq

value: RAMOS

value: human BL cell line


title: HBL1_6h_Prednisolone_Replicate 1

description:
hbl1_6h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: RAMOS_6h_Prednisolone_Replicate 2

description:
ramos_6h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: RAMOS_24h_Prednisolone_Replicate 1

description:
ramos_24h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: FL318_24h_Prednisolone_Replicate 2

description:
fl318_24h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: RAMOS_6h_Prednisolone_Replicate 1

description:
ramos_6h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: RAMOS_0h_DMSO_Replicate 1

description:
ramos_0h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: RAMOS_0h_DMSO_Replicate 2

description:
ramos_0h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: FL318_6h_Prednisolone_Replicate 2

description:
fl318_6h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: FL318_6h_Prednisolone_Replicate 1

description:
fl318_6h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: FL318_24h_Prednisolone_Replicate 1

description:
fl318_24h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: SUDHL5_6h_Prednisolone_Replicate 2

description:
sud5_6h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: SUDHL5_0h_DMSO_Replicate 2

description:
sud5_0h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: SUDHL5_24h_Prednisolone_Replicate 1

description:
sud5_24h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: FL318_0h_DMSO_Replicate 2

description:
fl318_0h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: HCT116 Iso-seq

first: Ashish

last: Lal

address: 37 Convent Drive, Room 6134

department: NCI

institute: NIH

description: PacBio IsoSeq

data_processing:
PacBio SMRTlink generated raw subreads were converted into HiFi circular consensus sequences (CCS)
PacBio IsoSeq v3 pipeline was used to demultiplex the barcodes and remove primers. Additional refine steps included trimming polyA tails and removing concatemers to generate Full Length Non-Concatemer (FLNC) reads.
Hierarchical clustering,  iterative clustering and merging steps were performed to obtain consensus isoforms and the full-length (FL) consensus sequences
The high-quality FL transcripts were mapped to the reference genome by using the minimap2
Isoform classification and quality control were done using SQANTI3 software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include SQUANT3 annotated isoforms for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for PacBio sequencing  were prepared using PacBio Iso-seq  Library Prep Kit following manufacturer's protocols.


title: SUDHL5_24h_Prednisolone_Replicate 2

description:
sud5_24h_r2
total mRNA
2x50 cycle
paired-end RNA-seq


title: SUDHL5_6h_Prednisolone_Replicate 1

description:
sud5_6h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: P1 d60 TNC

description: P1 d60 TNC

data_processing:
Raw sequencing reads were first processed by fastp to filter out low-quality reads (more than 15 “N” or more than 50% bases with quality value ≤ 5). The clean reads were aligned and qualified using Cell Ranger Single-Cell Software Suite (version 3.0.2) with reference genome GRCh38/hg38.
processed data provided as .tsv (UMI matrix of single cells)

value: bone marrow and peripheral blood

value: 60 days after transplantation

value: Female

value: fresh bone marrow and peripheral blood


title: SUDHL5_0h_DMSO_Replicate 1

description:
sud5_0h_r1
total mRNA
2x50 cycle
paired-end RNA-seq


title: EGFP KD, high MNase, H3, rep 1

city: Pittsburgh

last: Klein

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
library strategy: MNase-ChIP-seq
Barcode adapter sequences removed
Paired-end fastq files were trimmed to 25 bp and mapped to the mm10 genome with bowtie2 (using the options -q -N 1 -X 1000 –no-unal)
Mapped reads were filtered for mapping quality (MAPQ ≥ 10) and unpaired reads using SAMtools
Filtered reads were converted to bigWig files and normalized to 1x coverage using deepTools bamCoverage (options -bs 5 --smoothLength 20 --normalizeUsing RPGC, --effectiveGenomeSize 2308125349 -e --centerReads)
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Replicate-averaged bigwig

growth_protocol: Murine embryonic stem cells were grown under feeder-free conditions in DMEM, supplemented with 10% Fetal Bovine Serum, 2 mM-Glutamine, 1X non-essential amino acids, 0.129mM 2-mercaptoethanol, and 1000U/mL Leukemia Inhibitory Factor (LIF). Cells were passaged every 48 hours using trypsin (Gibco) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened by PCR to confirm no mycoplasma presence.

extract_protocol:
Cells were crosslinked using formaldehyde, lysed in hypotonic buffer and incubated with MNase for five minutes. The reaction was quenched using EDTA and samples were pre-cleared with protein A beads (NEB) in complete immunoprecipitation buffer (20mM Tris-HCl pH[7.5], 1M NaCl, 2M EDTA, 0.1% Triton X-100 with fresh protease inhibitors added). Input samples were taken from cleared chromatin. Pre-coupled antibody-protein A beads were added to cleared chromatin and incubated overnight at 4°C with rotation. Antibodies used were IgG (Abcam: ab37415, lot: GR3208186-1) and H3 (Abcam: ab1791, lot: GR3428015-1). Bead-bound samples were washed twice with low salt wash (20mM Tris HCl pH [8.0], 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and then twice with high salt wash (20mM Tris HCl pH [8.0], 2mM EDTA, 500mM NaCl, 1% Triton X-100, 0.1% SDS). Samples were eluted at 65°C for 1.5 hours in elution buffer (100mM NaHCO3, 1% SDS) and cleaned using AMPureXP beads (Beckman Coulter). Cleaned DNA was used as a template for qPCR or for input into library builds.
Library preparation was performed using NEB Next II Ultra DNA kit with 14 cycles of PCR amplification.

treatment_protocol: EGFP KD cells were incubated with 3.5 µg esiRNAs, 25 µL Lipofectamine 3000 in serum-free medium for 18 hours, then medium was replaced and cells were incubated for 30 more hours. Cells were incubated at 37 degrees Celsius with 5% CO2 for the duration of treatment. After 48 hours of undisturbed growth on 10 cm plates, medium was aspirated and cells were washed with DPBS. DPBS was aspirated and fresh serum-free medium (Opti-MEM) was added, containing 3 µg of esiRNAs targeting EGFP (control), along with 30 µL Lipofectamine 3000. Cells were incubated in 5% CO2 incubators for 18 hours to allow esiRNA transfection, then medium was aspirated and replaced with fresh DMEM. 48 hours after the initial esiRNA addition, cells were harvested as follows.

value: Embryonic stem cells

value: EGFP knockdown


title: EGFP KD, low MNase, IgG, rep 1

value: IgG


title: WT, low MNase, H3, rep 1

description:
WT_5U_H3_rep1
WT_5U_H3_mean.bw


title: WT, high MNase, IgG, rep 2

description:
WT_30U_IgG_rep2
WT_30U_IgG_mean.bw


title: EGFP KD, low MNase, Input, rep 1


title: EGFP KD, low MNase, H3, rep 1


title: WT, high MNase, IgG, rep 1

description:
WT_30U_IgG_rep1
WT_30U_IgG_mean.bw


title: WT, low MNase, IgG, rep 2

description:
WT_5U_IgG_rep2
WT_5U_IgG_mean.bw


title: WT, low MNase, Input, rep 2

description:
WT_5U_Input_rep2
WT_5U_Input_mean.bw


title: WT, high MNase, H3, rep 2

description:
WT_30U_H3_rep2
WT_30U_H3_mean.bw


title: FL318_0h_DMSO_Replicate 1

description:
fl318_0h_r1
total mRNA
2x50 cycle
paired-end RNA-seq

value: human DLBCL cell line

value: Cas9 engineered


title: WT, low MNase, IgG, rep 1

description:
WT_5U_IgG_rep1
WT_5U_IgG_mean.bw


title: WT, low MNase, Input, rep 1

description:
WT_5U_Input_rep1
WT_5U_Input_mean.bw


title: WT, low MNase, H3, rep 2

description:
WT_5U_H3_rep2
WT_5U_H3_mean.bw


title: Y1_liver_Input_3

city: Baltimore

first: Supriyo

last: De

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Illumina sequencing reads (~50 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option separately to the GRCm38/mm10 genome assembly.
Sam output files were then filtered to keep alignments with a minimum mapping quality of 10 using samtools/1.9 and PCR duplicates removed with picard/2.23.7. Sambamba/0.7.1 was used to keep only uniquely aligned reads. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. Input reads were subtracted from MeDIP samples with bigwigCompare.
Peaks were called using peakranger/1.18 with the bcp option using H3 and input as background for H3K27me3 and IgG respectively from the same animal
Assembly: mm10
Supplementary files format and content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; scores represent the coverage on the genome location

source_name: liver

extract_protocol:
meDIP-seq was performed using the MagMeDIP-seq Package (Diagenode) following the manufacturer’s protocol with a mouse antibody against 5mC (Diagenode, 33D3 clone, C15200081). Briefly, 1.2 µg of genomic DNA was sonicated into ~200 bp fragments using the S220 focused ultrasonicator (Covaris). Prior to immunoprecipitation, samples were spiked with hydroxymethylated, methylated and unmethylated internal DNA controls. IP efficiency and success was verified by qPCR targeting internal DNA controls. The DNA amount was quantified by Qubit HS DNA kit and the fragment size was assessed on a 2100 BioAnalyzer using a DNA HS kit (Agilent).
Individual libraries for immunoprecipitated DNA and 10% input were dual indexed (NEBNext Multiplex Oligos, unique dual indices, New England Biolabs), PCR amplified and then pooled into equimolar amounts and further quantified using the NEBNext Library Quant Kit (New England Biolabs). The pooled library was subjected to 50 bp paired-end sequencing on the Illumina NextSeq 2000 platform.
MagMeDIP-seq

treatment_protocol: Old as treated group

value: liver

value: 18 weeks

tag: sex (m=male, f=female)

value: M

tag: medip antibody


title: Y4_liver_Input_3

value: 16 weeks


title: O4_liver_Input_3

value: 82 weeks


title: Y3_liver_Input_3

value: 13 weeks

value: F


title: Y2_liver_Input_3

value: 12 weeks


title: Splenocytes_naïve_rep5

description: Gene expression data from naïve mouse CD8 T lymphocytes

value: 6-8 weeks old

value: Spleen

tag: cell type

value: CD8 T lymphocytes


title: O2_liver_Input_3

tag: strain

value: 81 weeks


title: O3_liver_Input_3

value: 87 weeks


title: Y4_liver_5mC

value: 5mC (Diagenode, 33D3 clone, C15200081, Lot RD-004)


title: Y2_liver_5mC


title: Y3_liver_5mC


title: O1_liver_Input_3

value: 90 weeks


title: Y1_liver_5mC


title: O4_liver_5mC


title: O2_liver_5mC


title: Y4_liver_H3K27me3_2

data_processing:
Illumina sequencing reads (~50 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option separately to the GRCm38/mm10 and GRCh38/hg38 genome assemblies.
Sam output files were then filtered to keep alignments with a minimum mapping quality of 10 using samtools/1.9 and PCR duplicates removed with picard/2.23.7. Sambamba/0.7.1 was used to keep only uniquely aligned reads. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. H3 and input reads were subtracted from specific histone modification IPs or IgG respectively with bigwigCompare.
Peaks were called using peakranger/1.18 with the bcp option using H3 and input as background from the same animal
Assembly: mm10, hg38
Supplementary files format and content: bigwig files were generated using bamCoverage in deepTools/3.5/0; scores represent the coverage on the genome location
Supplementary files format and content: peak bed files

extract_protocol:
Crude nuclei preparations were made from ~100 mg frozen tissue by douncing in nuclei preparation buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20, 0.1% NP-40, 0.01% digitonin and 1 mM BSA, supplemented with protease inhibitors and 1 mM sodium butyrate). After centrifugation, the nuclei pellet was crosslinked with 1% formaldehyde in 2 ml PBS by constant rotation at room temperature for 10 min followed by quenching with 125 mM glycine and two PBS washes. The nuclei were lysed with nuclei lysis buffer (10 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium-deoxycholate, 0.5% N-lauroylsarcosine supplemented with protease inhibitors and 1mM sodium butyrate) and sheared to <500bp using a Covaris S220 Ultrasonicator. An aliquot of the sheared chromatin sample was removed to check sonication success and to quantify the amount of chromatin. The immunoprecipitation, wash and elution steps were performed as reported previously (Sen et al., 2019) except ~4% HeLa chromatin was spiked in to 2 µg mouse chromatin prior to immunoprecipitation (only for liver samples).
DNA (~5 ng) was used to prepare libraries with the NEBNext Ultra II library preparation kit with unique dual index primers (New England Biolabs). The library quality and quantity were verified by BioAnalyzer DNA 1000 (Agilent) run and qPCR with NEBNext Library Quant kit (New England Biolabs) respectively.


title: O1_liver_5mC


title: O3_liver_H3K27me3_2

value: 80 weeks


title: O3_liver_5mC


title: O4_liver_H3K27me3_2


title: O2_liver_H3K27me3_2


title: O1_liver_H3K27me3_2


title: Y2_liver_H3K27me3_2


title: Y3_liver_H3K27me3_2


title: Y4_liver_H3_2

value: H3(Cell Signaling Technology,4620S, Lot14)


title: Y3_liver_H3_2

value: liver


title: O4_liver_H3_2


title: Y1_liver_H3_2

value: 14 weeks


title: O3_liver_H3_2


title: Y2_liver_H3_2

value: M


title: O1_liver_H3_2


title: Y4_liver_Input_2


title: O3_liver_Input_2


title: Y1_liver_Input_2


title: Y2_liver_Input_2


title: Y3_liver_Input_2


title: WT, high MNase, H3, rep 1

description:
WT_30U_H3_rep1
WT_30U_H3_mean.bw

value: Embryonic stem cells

tag: treatment


title: Y1_liver_H3K27me3_2


title: O2_liver_Input_2


title: O1_liver_Input_2


title: Y4_liver_PolII

value: Rpb1 NTD((Cell Signaling Technology,14958S, Lot5)


title: Y2_liver_PolII


title: O2_liver_H3_2


title: Y1_liver_PolII


title: MCF7-Day 0 R2


title: O4_liver_PolII


title: O2_liver_PolII


title: Y4_liver_H2AK119ub1

value: H2AK119ub1(Cell Signaling Technology,8240S, Lot9)


title: Y2_liver_H2AK119ub1


title: O3_liver_PolII

value: F


title: O4_liver_H2AK119ub1


title: O2_liver_H2AK119ub1


title: Y3_liver_H2AK119ub1

value: 12 weeks


title: Y4_liver_H3K36me3


title: Y1_liver_H2AK119ub1


title: O3_liver_H2AK119ub1


title: O1_liver_H2AK119ub1


title: O4_liver_Input_2


title: Y3_liver_PolII


title: Y1_liver_H3K36me3


title: O3_liver_H3K36me3


title: O1_liver_PolII


title: O2_liver_H3K36me3


title: Y4_liver_H3K9me3


title: Y3_liver_H3K9me3


title: O1_liver_H3K36me3


title: Y1_liver_H3K9me3


title: O2_liver_H3K9me3


title: O4_liver_H3K9me3


title: Y2_liver_H3K9me3


title: Y3_liver_H3K36me3


title: O3_liver_H3K9me3


title: Y3_liver_EZH2_IgG

data_processing:
Illumina sequencing reads (~50 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by the on-board DRAGEN informatics pipeline (Illumina DRAGEN FASTQ Generation – 3.7.4) on the NextSeq 2000.
The FASTQ files were trimmed to remove adapter sequences with trimgalore/0.6.6 and the qualities of the FASTQs checked by running FASTQC/0.11.9. The reads were aligned with bowtie/2-2.4.2 using the end-to-end option separately to the GRCm38/mm10 and GRCh38/hg38 genome assemblies.
Sam output files were then filtered to keep alignments with a minimum mapping quality of 10 using samtools/1.9 and PCR duplicates removed with picard/2.23.7. Sambamba/0.7.1 was used to keep only uniquely aligned reads. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were also removed from the analysis.
The bamCoverage option in deepTools/3.5.0 was used to generate RPKM normalized bigWig files. H3 and input reads were subtracted from H3K27me3 and IgG respectively with bigwigCompare.
Peaks were called using peakranger/1.18 with the bcp option using H3 and input as background for H3K27me3 and IgG respectively from the same animal
Assembly: mm10, hg38
Supplementary files format and content: bigwig files were generated using  bamCoverage in deepTools/3.5/0; Scores represent the coverage on the genome location

source_name: mouse liver

tag: age group

value: young


title: O4_liver_EZH2_IgG

value: old


title: Y2_liver_EZH2_IgG


title: O3_liver_EZH2_IgG


title: O2_liver_EZH2_IgG


title: Y4_liver_EZH2_Input


title: O1_liver_EZH2_IgG


title: O4_liver_EZH2_Input


title: Y2_liver_H3K36me3


title: Y1_liver_EZH2_IgG


title: O3_liver_EZH2_Input


title: Y1_liver_EZH2_Input


title: O2_liver_EZH2_Input


title: O1_liver_EZH2_Input


title: Y4_liver_EZH2_IgG


title: O1_liver_H3K9me3


title: Y4_liver_EZH2


title: O4_liver_H3K36me3


title: Y2_liver_EZH2


title: Y2_liver_EZH2_Input


title: O3_liver_EZH2


title: O2_liver_EZH2


title: Y3_reg_liver_Input

tag: time point

value: after regeneration


title: Y2_reg_liver_Input


title: Y1_reg_liver_Input


title: O1_liver_EZH2


title: Y3_liver_EZH2_Input


title: Y2_bef_liver_Input

value: before regeneration


title: O2_reg_liver_Input


title: Y3_bef_liver_Input


title: O1_reg_liver_Input


title: Y1_bef_liver_Input


title: O2_bef_liver_Input


title: O3_reg_liver_Input


title: O3_bef_liver_Input


title: Y3_reg_liver_H3


title: Y2_reg_liver_H3


title: O4_liver_EZH2


title: Y3_liver_EZH2


title: Y1_liver_EZH2


title: O2_reg_liver_H3


title: O3_reg_liver_H3


title: Y1_reg_liver_H3


title: Y3_bef_liver_H3


title: O1_reg_liver_H3


title: Y1_bef_liver_H3


title: O1_bef_liver_H3


title: Y2_reg_liver_H3K27me3


title: O3_bef_liver_H3


title: Y2_bef_liver_H3


title: O2_bef_liver_H3


title: Y1_reg_liver_H3K27me3


title: Y3_reg_liver_H3K27me3


title: O1_reg_liver_H3K27me3


title: O2_reg_liver_H3K27me3


title: O3_reg_liver_H3K27me3


title: O2_bef_liver_H3K27me3


title: O1_bef_liver_Input


title: O1_bef_liver_H3K27me3


title: Y1_bef_liver_H3K27me3


title: O3_bef_liver_H3K27me3


title: Y2_bef_liver_H3K27me3


title: Y3_bef_liver_H3K27me3


title: U87 NFKB2 KD TWEAK rep 3 [U87_RNAseq_NFKB2KD_TW3]

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using STAR
featureCounts was used to extract raw counts
Differential analysis was performed with DESeq2
Assembly: hg38
Supplementary files format and content: bigwig (files for each ChIP provided were merged from two biological replicates), narrowPeak

growth_protocol: U-87MG cells were seeded in DMEM + 10% FBS. After 24h, cells were starved in optimem for 8h then treated with 10ng/ml TWEAK for 48h. TWEAK was replenished after 24h.

extract_protocol:
RNA was extracted using Trizol and treated with Dnase.
RNA-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol through the polyA mRNA workflow

value: NFKB2 KD

value: TWEAK


title: U87 NFKB2 KD TWEAK rep 1 [U87_RNAseq_NFKB2KD_TW1]


title: U87 ETS1 KD TWEAK rep 2 [U87_RNAseq_ETS1KD_TW2]

value: ETS1 KD


title: U87 NFKB2 KD TWEAK rep 2 [U87_RNAseq_NFKB2KD_TW2]


title: U87 control TWEAK rep 2 [U87_RNAseq_Control_TW2]

value: control


title: U87 ETS1 KD TWEAK rep 3 [U87_RNAseq_ETS1KD_TW3]


title: U87 control TWEAK rep 3 [U87_RNAseq_Control_TW3]


title: U87 ETS1 KD TWEAK rep 1 [U87_RNAseq_ETS1KD_TW1]


title: U87 control UT rep 3 [U87_RNAseq_Control_UT3]

value: Untreated


title: U87 control UT rep 2 [U87_RNAseq_Control_UT2]


title: U87 ETS1 KD TWEAK rep 2 [U87_RNApol2_ETS1KD_TW2]

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using Bowtie2
Peaks were called using MACS2 with subtraction of input signal
bigwig files were generated using deepTools
Assembly: hg38
Supplementary files format and content: bigwig (files for each ChIP provided were merged from two biological replicates), narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Diagenode Bioruptor. DNA was sheared to 200-500bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol

value: RNA pol2


title: U87 control UT rep 1 [U87_RNAseq_Control_UT1]


title: U87 ETS1 KD TWEAK rep 1 [U87_RNApol2_ETS1KD_TW1]


title: U87 NFKB2 KD TWEAK rep 1 [U87_RNApol2_p52KD_TW1]


title: U87 control TWEAK rep 2 [U87_RNApol2_C_TW2]


title: U87 control UT rep 1 [U87_RNApol2_C_UT1]


title: U87 control TWEAK rep 1 [U87_RNApol2_C_TW1]


title: U87 NFKB2 KD TWEAK rep 2 [U87_RNApol2_p52KD_TW2]


title: U87 control UT rep 2 [U87_RNApol2_C_UT2]


title: E3LZ10.7, shHMGA1 2

first: LI

last: LUO

state: MD

address: 720 Rutland Ave, Ross Build

department: Hematology

institute: Johns Hopskins University

description:
E3LZ10.7_shHMGA_gene_count.txt
E3LZ10.7_shHMGA_gene_abundance.txt

data_processing:
raw reads were ‘cleaned’ using ‘Fastq quality trimmer by sliding window’ and aligned to the human reference genome (hg38) with TopHat using strand-specific parameters
Transcript abundance (fragments per kilobase/million reads, FPKM) and differential expression estimates were generated (Cuffdiff2.1.1)
Assembly: hg38
Supplementary files format and content: tab delimited text file containing raw counts
Supplementary files format and content: tab delimited text file containing relative abundance reported as Transcripts per Million (TPM)

growth_protocol: E3LZ10.7 cells were cultured in DMEM with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep kit.
RNA libraries for RNASeq was prepared using TrueSeq stranded mRNA kit (illumina) following manufacturer's protocol

treatment_protocol: Cells were transduced with shHMGA1 lentivirus and selected with 5.3ug/ml of puromycin for 7 days

value: Pancreatic cancer cells

value: HMGA1 knockdown

value: 7 days after lentivirus infection


title: U87_ETS1KD_guide2_TW_p52_rep2


title: E3LZ10.7, shHMGA1 1


title: E3LZ10.7, shControl 1

value: Control


title: U87_ETS1KD_guide1_TW_p52_rep1


title: U87 control TW ETS1 rep 2


title: U87_ETS1KD_guide2_TW_p52_rep1


title: U87 control TW ETS1 rep 1


title: U87_ETS1KD_guide1_TW_p52_rep2


title: E3LZ10.7, shControl 2


title: U87 control TWEAK rep 1 [U87_RNAseq_Control_TW1]


title: U87 control UT ETS1 rep 2


title: U87 control UT ETS1 rep 1


title: U87 ETS1 KD guide 1 input


title: U87 ETS1 KD guide 2 input


title: U87 control TW p52 rep 2


title: U87 control UT p52 rep 1


title: U87 control input


title: U87 control TW p52 rep 1


title: U87 control UT p52 rep 2


title: iPSC_MS337_228

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

data_processing:
All read data were processed with cutadapt v1.18 and mapped with Tophat2 v2.1.1/bowtie2 v2.3.4.1 as described previously (Nakamura et.al.).
Read counts per genes were calculated using HTseq v0.11.0.
For allelic expression analysis, read data were re-mapped using masked MacFas5.0 reference, as described above.
Mapped BAM files were processed with SNPsplit and masked MacFas5.0 reference to split into paternal and maternal allele
Read counts per genes were calculated using HTseq for both BAM, separately.
Assembly: macFas5.0 or GRCh38.p12
Supplementary files format and content: tab-delimited text files include read counts for each Sample

extract_protocol:
Total RNA extraction from 5000-20000 cells were carried out using Nucleospin RNA XS extraction kit (Takara, 740902).
cDNA synthesis was performed as described previously (Nakamura et al, 2015). Briefly, 0.2ng/µL of V1(dT)24 sequence was annealed to the 3’ end of the 1ng of total RNA by incubation at 70ºC for 90 seconds. Reverse transcription was performed by adding 133U/µL of SuperScript III (Invitrogen, 1089075) and serial incubation at 50ºC for 5 min and at 70ºC for 10 min. The residual primers were excised by treating with 0.5U/µL of Exonuclease I (Takara, 2650A) at 37ºC for 30 min followed by 80ºC for 25 min. Poly-A was added to the 3’ end of the cDNA by incubating at 37ºC 15 min and 70ºC for 10 min in the presence of 3mM dATPs (GE Healthcare, 28-4065-01) and 0.75U/µL terminal nucleotidyl transferase (TdT, Invitrogen, 10533-065). For cDNA amplification, the cDNA was applied to thermal cycling in the presence of 0.62 µM of V3(dT)24 and V1(dT)24, 0.05U/µL Ex Taq HS (Takara, RR006).

value: iPS cell

tag: tag

value: DDX4-tdTomato, TFAP2C-EGFP

value: wildtype