title: Day6_Ctrl_Rep3


title: RPI11 17s

status: Public on Sep 07 2021

type: SRA

city: Stanford

first: D.

middle: Blaine

last: Marchant

state: California

address: Gilbert Biological Sciences Building, 371 Serra Mall

department: Biology

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Unique molecular identifiers (UMIs) and sample barcodes were extracted from the first read of each read pair using a custom R script. The second read of each read pair were aligned to the AGPv4 genome assembly using HiSat2.
The number of UMIs for each gene and each sample were counted.
Genome_build: AgpV4
Supplementary_files_format_and_content: BeyondProto.UMI.matrix.csv: Comma-separated text file containing transcript counts for each gene and cell sample.

molecule: polyA RNA

organism: Zea mays

source_name: isolated maize anther cell

growth_protocol: Maize (Zea mays) inbred line W23 bz2 was grown in a greenhouse at Stanford, CA with a 14-h day / 10-h night light cycle.

extract_protocol:
Maize anthers were dissected, fixed in Farmer's Solution and digested in protoplasting enzymes. Isolated cells were sorted via BioSorter (Union Biometrica) or Hana (Namocell).
Library protocol based on CEL-Seq2 with modifications similar to Nelms & Walbot 2019.

tag: tissue

value: anther

tag: inbred line


title: P7895

city: Gainesville

first: Mackenzie

middle: J

last: Dickson

state: Florida

address: 2250 Shealy Drive

department: Animal Science

institute: University of Florida

data_processing:
Original data files from high-throughput sequencing were transformed into sequenced raw reads by CASAVA base recognition
Reads were filtered to remove adaptors, reads with more than 10% uncertain nucleotides, and reads with more than 50% low quality reads.
After data filtering, paired-end clean reads of each sample were aligned to the latest bovine reference genome (ARS-UCD1.2) using HISAT2 v2.1.
Quantification was performed using FeatureCounts v1.5.0.
Differential expression analysis between pregnant and non-pregnant cows was performed using the DESeq2 R package v2_1.6.3.
Genome_build: Bovine genome ARS-UCD1.2

molecule: total RNA

organism: Bos taurus

source_name: Endometrium

extract_protocol:
Intercaruncular endometrium from uterus was collected post-mortem and snap frozen in liquid nitrogen. RNA was isolated using Qiagen Rneasy mini kit with on-column Dnase treatment.
Library preparation conducted by Novogene Inc and used NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: All cows previously received intrauterine infusion of pathogenic bacteria (E.coli and T.pyogenes). 146 days after bacteria infusion, cows were slaughtered, and uteri flushed with sterile PBS. Cows were classified as pregnant or non-pregnant based on conceptus recovery and concetration of interferon-tau in uterine fluid.

tag: pregnancy status

value: Pregnant


title: N8040

value: Non-pregnant


title: Day6_Rab9_Rep1

city: Washington DC

first: Xiujie

last: Sun

state: DC

address: 2300 I ST NW, Room 433

institute: The George Washington University

data_processing:
Basecalls performed using Illuminal CASAVA software.
Reads were aligned to mm10 genome assembly using Tophat.
Differentially expressed genes were detected by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads counts for each Sample

organism: Mus musculus

source_name: E0771 mammary tumor

extract_protocol:
RNA was harvested using Trizol reagent. About 500 ng RNA was used for the construction of sequencing libraries.
RNA libraries were prepared following the Illumina TruSeq stranded mRNA-seq sample preparation guide.

tag: strain

value: E0771 mammary tumor

tag: treatment

value: hDDR1 ECD antibody treatment


title: P8283


title: RPI11 22s


title: N7643


title: RPI11 19s


title: Day6_Rab9_Rep2


title: Day6_Rab9_Rep3


title: RPI11 21s


title: P7703


title: RPI28 13s


title: N7264


title: Day6_Ctrl_Rep2

value: IgG treatment


title: RPI11 15s


title: RPI11 18s


title: N7389


title: RPI11 28s


title: RPI11 20s


title: RPI11 12s


title: 200c-IP-20-R2

city: GuangZhou

first: Yan

last: Li

state: GuangDong

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: School of Life Science

country: China

institute: Sun Yat-sen University

description:
cell lysate
IP sample: denaturate 20 minutes

data_processing:
library strategy: Tn5 assisted MeRIP-seq
Reads aligned to genome (hg19) using HISAT (version 2.1.0) with default parameters, converted to BAM file using SamTools, then sorted BAM file using SamTools.
m6A enriched region were detected by exomePeak2 R package, processed across 2 replicates.RNA-Seq data(no IP, input RNA) in the same condition was used as input information
Transcripts reads count were detected by featurecounts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cell line was cultured with Dulbecco’s modified Eagle’s medium (DMEM; Corning, cat. no. 10-017-CV) supplemented with 10% (v/v) fetal bovine serum (FBS; Gibco) and tested to be mycoplasma negative.

extract_protocol:
Total RNA extraction, TRIzol reagent (Thermo Fisher Scientific, catalog no. 15596026) was used to cell suspension following the standard protocol. Cell lysate, the cells were resuspended in 3μL 0.2% (vol/vol) Triton X-100 (Sigma-Aldrich, cat. no. T9284) lysis buffer with 0.2 μL of Recombinant ribonuclease inhibitor. The lysate was incubated at 72 °C for 3 min and immediately put back on ice. Blood sample, red blood cells was removed by Red Blood Cell Lysis Buffer (Roche, cat. no. 11814389001). The total RNA was extracted using TRIzol reagent.
For library preparation, all reactions were performed in one tube and followed the protocol of TruePrep® RNA Library Prep Kit for Illumina (Vazyme, cat. no. TR501-01) with some modifications. The m6A MeRIP experiments were performed following the recommendations from the EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610) with some modifications.

treatment_protocol: IP sample was divided into two equal parts and then denatured in the condition of 95°C/10 min or 95°C/20min

tag: cell line

tag: cell type

value: embryonic kidney cells

tag: tissue source

value: kidney

tag: sample type

value: RNA IP against m6A

tag: denaturation time

value: 20 minutes


title: RPI11 10s


title: RPI11 16s


title: 200c-IP-20-R1


title: RNAseq_T131_3M

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

country: Germany

institute: LMU Munich

data_processing:
Paired end RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include reads per gene for each sample

source_name: ES cells

growth_protocol: Feeder-independent ES cells were cultured on 10cm gelatin-coated plates with ES cell medium containing Serum and LIF

extract_protocol:
Total RNA was extracted using Trizol and the RNA Clean & Concentrator -25 Kit (Zymo research , R1017) including the on-column DNAse step, ribosomal RNA was depleted with the NEBNext rRNA Depletion Kit (NEB, E6350)
Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420S)

tag: genotype

value: Morc3 rescue

value: mouse embryonic stem cells (ESCs)


title: T31820: Stimulated PBMC 72 h

city: Cleveland

first: Konstantin

middle: S

last: Leskov

state: OH

address: 2109 Adelbert Rd., WRT205

department: Molecular Biology and Microbiology

institute: Case Western Reserve University

description: CD3/CD28 Dynabeads

data_processing:
Dropseq Tools 1.0
STAR-2.5.1b
picard-tools-1.93
samtools-1.8
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: txt, digital gene expression matrix

source_name: PBMC

growth_protocol: RPMI

extract_protocol:
Drop-seq
Illumina Nextera XT

treatment_protocol: CD3/CD28 Dynabeads

value: Primary T-cells

value: Memory T-cells


title: U31620: Unstimulated PBMC


title: D4_CW4

description:
5_WT_D4_S20
Day4_Ctrl_Rep4

source_name: E0771 DDR1 WT

value: E0771 DDR1 WT


title: 200c-input-R2

description:
cell lysate
Input sample

value: no IP (input RNA)

value: no


title: D4_CK4

description:
20_KO_D4_S24
Day4_KO_Rep4

source_name: E0771 DDR1 KO

value: E0771 DDR1 KO


title: 200c-IP-10-R2

description:
cell lysate
IP sample: denaturate 10 minutes

value: 10 minutes


title: Day6_Ctrl_Rep1


title: 200c-IP-10-R1


title: D4_CK3

description:
19_KO_D4_S23
Day4_KO_Rep3


title: T31620: Stimulated PBMC 24 h

description: CD3/CD28 Dynabeads


title: ChIP_H3K9me3_T185_5

description: Standard ChIP protocol

library_source: genomic

data_processing:
Reads were mapped to the mouse genome (mm10) using bowtie2 (Langmead et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

molecule: genomic DNA

growth_protocol: Feeder-independent ES cells were cultured on 10cm and 15cm gelatin-coated plates with ES cell medium containing Serum and LIF

extract_protocol:
For the standard ChIP protocol 25 million ES cells were cross-linked in 7-8mL pre-tempered ES medium containing 1% formaldehyde (Pierce 28906) for 10min at 22°C. Fixation was stopped by addition of 0.125M final concentration of glycine, followed by two washing steps with RT PBS containing 10% Serum. Fixed cells were resuspended in 10mL ice cold buffer LB1 (50mM Hepes-KOH pH 7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.50% NP-40, 0.25% Triton X-100, 1x Roche complete protease inhibitors (Roche, 04693159001)), rocked at 4°C for 10min and after centrifugation resuspended in 10mL ice cold buffer LB2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 1x protease inhibitors), rocked at 4°C for 5min and centrifuged again. The pelleted nuclei were resuspended in 1mL ice cold shearing buffer (10mM Tris-HCl pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, 0.1% SDS, 1x protease inhibitors). Buffer compositions for LB1, LB2 and shearing buffer are based on Boyer et al., 2005. Exactly 1mL was transferred to a 1mL milliTUBE with AFA fiber (Covaris 520130) and sonicated using a Covaris S220 device for a time of 15-20min and the following settings: Peak power 140 Watt, Duty factor 20%, Cycles per burst 200, Temperature of bath 4°C. The sheared samples were added to a 1.5mL tube with 110µL of 10% Triton X-100 (final concentration 1%) and centrifuged at 14000 rpm for 15 minutes at 4°C. The soluble chromatin containing supernatant was divided in 110µL aliquots (equivalent to 2-2.5Mio cells) and for IP diluted with 890µL complete Buffer A (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-Deoxycholate, 140 mM NaCl, 1x protease inhibitors). Per IP 30µL of Protein G Dynabeads (Invitrogen, 10004D) were used. For FLAG ChIP-seq experiments 1-2µL of anti -FLAG M2 antibody (Sigma-Aldrich, F3165) were used per IP and 4-5 IPs (equivalent to 10-12 million cells) were pooled to obtain enough material for library preparation. For H3K9me3 ChIP-seq experiments 1µL of anti-H3K9me3 (Active Motif, 39161) was used per IP. Beads were incubated with the corresponding antibody in complete Buffer A for 1.5h prior to IP, followed by two washes with Buffer A (without protease inhibitors). Diluted Chromatin was added to the pre-bound beads and incubated for 4h on a rotating wheel with 30 rpm at 4°C. After IP beads were washed 5 times with Buffer A and 1 time with Buffer C (10 mM Tris-HCl pH 8.0, 10 mM EDTA). Beads were resuspended in 100µL elution buffer (10 mM Tris HCl pH 8.0, 300 mM NaCl, 5 mM EDTA, 0.5% SDS), RNA was degraded by 2μl RNase A (10mg/mL) for 30min at 37°C, proteins were digested with 2μl Proteinase K (10 mg/mL) at 55°C for 1h and crosslink reversal of immunoprecipitated DNA was carried out overnight at 65°C. DNA was purified using the Agencourt AMPure XP beads (Beckman Coulter, A63882). The Low input protocol is adapted from Dahl and Collas, 2008. It used 2Mio cells lysed in 100µL Buffer-B (50mM Tris-HCl, pH 8.0, 10mM EDTA, 1%SDS, 1x protease inhibitors) and sonicated in a microtube (Covaris; 520045) using the Covaris S220 device with the settings: Peak power 105 Watt, duty factor 2%, cycles per burst 200, Temperature of bath 4°C. The supernatant after centrifugation was diluted with 900µl complete Buffer A and 150µL (corresponding to approximately 300.000 cells) were used per IP with 10µL Protein G Dynabeads and 1µL of anti-H3K9me3 antibody as described above.
Ultra II DNA Library prep kit for Illumina (NEB E7645S)

value: Morc3_dNx3FLAG rescue

tag: antibody

value: anti-H3K9me3 (Active Motif, 39161)


title: 200c-input-R1

description:
cell lysate
Input sample


title: RNAseq_T131_3D


title: RPI11 14s

value: anther


title: D4_CK5

description:
40_KO_D4_S25
Day4_KO_Rep5

value: E0771 mammary tumor


title: 500c-IP-20-R2

value: embryonic kidney cells


title: ChIP_H3K9me3_T143_5

description: Standard ChIP protocol

value: Morc3_W419A rescue


title: RNAseq_wt26p46

value: wild type


title: ChIP_H3K9me3_T181_7J

description: Standard ChIP protocol

value: Morc3_5KR_SUMOx3FLAG rescue


title: D4_CK2

description:
18_KO_D4_S22
Day4_KO_Rep2


title: D4_CW2

description:
3_WT_D4_S18
Day4_Ctrl_Rep2


title: 500c-IP-10-R2

value: kidney

value: RNA IP against m6A


title: 3-6

description:
x3_6
WT_vs_KO_result_DEseq_all_withNormData.txt

data_processing:
Basecalls performed using Illumina CASAVA software.
Reads were aligned to mm10 genome assembly using Tophat.
Differentially expressed genes were detected by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

source_name: mammary tumor cells

value: murine breast cancer cell line


title: D4_CW3

description:
4_WT_D4_S19
Day4_Ctrl_Rep3


title: D4_CK1

description:
16_KO_D4_S21
Day4_KO_Rep1


title: 500c-IP-20-R1

value: 20 minutes


title: Ctrl

description:
Ctrl
WT_vs_KO_result_DEseq_all_withNormData.txt

value: E0771 DDR1 WT


title: ChIP_H3K9me3_T131_3C_r2

description: Standard ChIP protocol

value: Morc3 rescue

value: mouse embryonic stem cells (ESCs)


title: ChIP_H3K9me3_KO27_2_r2

description: Standard ChIP protocol

value: Morc3 knock out


title: ChIP_H3K9me3_WT26_r3

description: Standard ChIP protocol


title: ChIP_H3K27ac_T131_3C

description: Standard ChIP protocol

value: H3K27ac (Diagenode, pAB-174-050)


title: ChIP_H3K9me3_T141_5

description: Standard ChIP protocol

value: Morc3_E35A rescue


title: 1000c-IP-20-R2


title: 3-7

description:
x3_7
WT_vs_KO_result_DEseq_all_withNormData.txt

value: E0771 DDR1 KO


title: D4_CW1

description:
1_WT_D4_S17
Day4_Ctrl_Rep1


title: 500c-IP-10-R1

value: 10 minutes


title: ChIP_H3K9me3_T142_5

description: Standard ChIP protocol

value: Morc3_G101A rescue

value: anti-H3K9me3 (Active Motif, 39161)


title: EV

description:
EV
WT_vs_KO_result_DEseq_all_withNormData.txt


title: 1000c-IP-10-R2

value: embryonic kidney cells


title: 500c-input-R1

description:
cell lysate
Input sample

value: no IP (input RNA)

value: no


title: E0771-P

description:
E0771_P
WT_vs_KO_result_DEseq_all_withNormData.txt


title: 500c-input-R2

description:
cell lysate
Input sample

value: kidney


title: ChIP_H3K27ac_WT26

description: Standard ChIP protocol

value: wild type


title: 1000c-input-R2

description:
cell lysate
Input sample


title: RK1

description: RW_vs_RK_result_DEseq_all_withNormData.txt


title: RK5


title: 1000c-IP-20-R1

value: RNA IP against m6A


title: RK4


title: 1000c-input-R1

description:
cell lysate
Input sample


title: ChIP_FLAG_T185_5

description: Standard ChIP protocol

value: Morc3_dNx3FLAG rescue

value: anti-FLAG M2 (Sigma-Aldrich, F1804)


title: 1000c-IP-10-R1


title: RK3


title: ChIP_FLAG_T181_7J

description: Standard ChIP protocol

value: Morc3_5KR_SUMOx3FLAG rescue


title: ChIP_H3.3_T185_5

description: Standard ChIP protocol

value: mouse embryonic stem cells (ESCs)

value: Histone H3.3 (Millipore, 09-838)


title: RW4

value: E0771 DDR1 WT


title: ChIP_H3.3_T181_7J

description: Standard ChIP protocol


title: RW5


title: 2000c-IP-20-R2

value: 20 minutes


title: RW3


title: ChIP_H3.3_T143_5

description: Standard ChIP protocol

value: Morc3_W419A rescue


title: 2000c-IP-20-R1


title: 2000c-IP-10-R1

value: 10 minutes


title: RW2


title: ChIP_H3.3_T142_5

description: Standard ChIP protocol

value: Morc3_G101A rescue


title: 2000c-IP-10-R2


title: RW1


title: 2000c-input-R2

description:
cell lysate
Input sample


title: 2000c-input-R1

description:
cell lysate
Input sample


title: ChIP_H3K27ac_KO27_2

description: Standard ChIP protocol

value: Morc3 knock out

value: H3K27ac (Diagenode, pAB-174-050)


title: Mtb (phosphate enriched) rep2

city: Kolkata

first: Manikuntala

last: Kundu

state: West Bengal

address: 93/1, Acharya Prafulla Chandra Road

country: India

institute: Bose Institute

data_processing:
Libraries were sequenced at Genotypic Technology Pvt. Ltd., on an Illumina Hiseq XTen platform by a 150bp paired-end reads.
DESeq software was used to carry out the transcriptomic analysis.
Genome_build: Mycobacterium tuberculosis H37Rv genome, accession: NC_000962
Supplementary_files_format_and_content: GT_SO_7951_Expression_Matrix.xlsx: Expression values in RC_matrix sheet indicate raw read count of genes generated by HTSeq; in the RPM_matrix sheet, reads are normalized to the total reads (i.e. reads per million) for each sample.

organism: Mycobacterium tuberculosis

source_name: Mtb phosphate enriched

growth_protocol: Mtb was grown to log phase in Middle Brook 7H9 medium containing 10% ADC.

extract_protocol:
RNA was extracted by homogenising in a Mini bead beater and purified with the Qiagen RNeasy kit.
~2.0 µg of total RNA was taken for rRNA depletion using Ribo-Zero rRNA Removal Kit (Bacteria). ~30 ng of Qubit quantified ribodepleted RNA was taken for fragmentation and priming. The fragmented and primed mRNA was further subjected to first strand synthesis in the presence of Actinomycin D (Gibco, Life Technologies, CA, USA) followed by second strand synthesis. The double stranded cDNA was purified using JetSeq magnetic beads (Bio, # 68031). The purified cDNA was end-repaired, adenylated and ligated to Illumina multiplex barcode adapters as per NEBNext® Ultra™ Directional RNA Library Prep Kit protocol. The adapter ligated cDNA were purified JetSeq beads and were subjected to 15cycles of Indexing-PCR (37 ˚C for 15mins followed by denaturation at 98˚C for 30 sec, cycling (98˚C for 10sec, 65˚C for 75sec) and 65˚C for 5mins) to enrich the adapter-ligated fragments. The final PCR products (sequencing library) were purified with JetSeq beads, followed by libraries quality control check. The Illumina-compatible sequencing libraries were initially quantified by Qubit fluorometer (Thermo Fisher Scientific, MA, USA) and its fragment size distribution were analyzed on Agilent TapeStation.
Transcriptomic profiling was done using Illumina-compatible NEBNext® Ultra™ Directional RNA Library Prep Kit ((NEB, #E7420S) ) at Genotypic Technology Pvt. Ltd., Bangalore, India.

treatment_protocol: Log phase cells were harvested and resuspended in either phosphate enriched or phosphate limited medium and grown for 72 hours under shaking at 37◦C.

tag: condition

value: phosphate enriched


title: ChIP_H3.3_T131_3C

description: Standard ChIP protocol

value: Morc3 rescue


title: Mtb (phosphate limited) rep2

source_name: Mtb phosphate limited

value: phosphate limited


title: Mtb (phosphate enriched) rep1


title: ChIP_H3.3_T141_5

description: Standard ChIP protocol

value: Morc3_E35A rescue


title: ChIP_H3.3_KO27_2_r2

description: Standard ChIP protocol


title: Mtb (phosphate limited) rep1


title: 60ng_input-R1

description: Input sample

value: embryonic kidney cells

value: kidney

value: no IP (input RNA)

value: no


title: ChIP_H3.3_WT26_r2

description: Standard ChIP protocol

value: wild type

value: mouse embryonic stem cells (ESCs)


title: 60ng_10min-R2

description: IP sample: denaturate 10 minutes

value: RNA IP against m6A


title: ChIP_H3.3_KO27_2_r1

description: Standard ChIP protocol

value: Histone H3.3 (Millipore, 09-838)


title: 60ng_20min-R1

description: IP sample: denaturate 20 minutes

value: 20 minutes


title: 60ng_10min-R1

description: IP sample: denaturate 10 minutes

value: 10 minutes


title: ATAC_T185_5_r2

data_processing:
Reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from Homer tag directories using makeBigWig.pl

extract_protocol:
The OmniATAC transposition reaction was performed with 50 000 cells as previously described (Corces, Trevino et al. 2017) using the Tagment DNA TDE1 Enzyme (Illumina, 20034197). DNA was purified using the PCR clean-up MinElute kit (Qiagen, 28006).
The transposed DNA was subsequently amplified in 50µl reactions with custom primers as previously described (Buenrostro et al., 2013). Libraries were purified and size selected for fragments less than 600bp using the Agencourt AMPure XP beads (Beckman Coulter, A63882).

value: Morc3_dN rescue


title: ChIP_H3.3_WT26_r1

description: Standard ChIP protocol


title: ChIP_H3K4me3_KO27_2

description: Low cell ChIP protocol

value: Morc3 knock out

value: anti-H3K4me3 (Diagenode, CS-003-100)


title: 100ng_IP-20min

description: IP sample: denaturate 20 minutes


title: ChIP_H3K4me3_WT26

description: Low cell ChIP protocol


title: RK2

value: E0771 DDR1 KO


title: 100ng_input

description: Input sample


title: ATAC_T181_7J_r2

value: Morc3_5KR_SUMO rescue


title: WT_Ikaros_frozen_rep2

city: Burlington

first: Princess

last: Rodriguez

state: Vermont

address: 89 Beaumont Avenue

department: Microbiology and Molecular Genetics

institute: University of Vermont

data_processing:
Library strategy: CUT&RUN
File processing was carried out using CUT&RUNTools (Zhu et al., 2019)
Trimmomatic-0.36 was used to trim TruSeq adapters
Bowtie 2 2.2.9 was used with "--dovetail" option indicated
Picard 2.8.0 MarkDuplicates was used to mark PCR duplicates
MACS2 was used to callpeaks with options " -f BAMPE  -q 0.01 -B --SPMR" indicated
Genome_build: mm10
Supplementary_files_format_and_content: peak files

source_name: Spleen

extract_protocol:
Spleens were harvested from C57BL/6 mice and B cells were isolataed by MACS. Cells were used immediated for CUT&RUN (fresh) or cell pellets were resuspended in 90%FBS/10% DMSO and frozen overnight.
Libraries were prepared using the NEBnext Ultra II DNA Library Prep Kit (Illumina)

value: wildtype

value: splenic B cells

tag: cell state

value: frozen

tag: target

value: Ikaros


title: 200ng_IP-10min

description: IP sample: denaturate 10 minutes

value: embryonic kidney cells

value: kidney


title: 60ng_20min-R2

description: IP sample: denaturate 20 minutes


title: 200ng_IP-20min

description: IP sample: denaturate 20 minutes


title: WT_Ikaros_fresh_rep1

value: fresh


title: 60ng_input-R2

description: Input sample

value: no IP (input RNA)

value: no


title: WT_IgG_frozen

value: IgG


title: 500ng_IP-20min

description: IP sample: denaturate 20 minutes

value: RNA IP against m6A

value: 20 minutes


title: ATAC_T181_7J_r1

value: mouse embryonic stem cells (ESCs)


title: WT_Ikaros_frozen_rep1


title: 500ng_IP-10min

description: IP sample: denaturate 10 minutes

value: 10 minutes


title: 200ng_input

description: Input sample


title: WT_IgG_fresh


title: 100ng_IP-10min

description: IP sample: denaturate 10 minutes


title: Corpus callosum, cuprizone diet, biological rep 4

type: RNA

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Probes were hybridised to the GeneChip MouseGene 1.0 ST arrays at 45°C for 16 hours. Hybridised arrays were then washed and stained on a Fluidics Station 450 using the Fluidics Station Program FS450_0007.

scan_protocol: Arrays were scanned on a GeneChip® Scanner 3000 7G

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with robust multiarray average algorithm (Affymetrix): RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

label: biotin

source_name: Corpus callosum, cuprizone diet

label_protocol: Samples for the GeneChip Mouse Gene 1.0 ST arrays were prepared and hybridized to the arrays according to the Ambion whole-transcript expression and the Affymetrix whole-transcript terminal labelling and control kit manuals. Briefly, for each sample, 150 ng of total RNA was reverse-transcribed into cDNA using a random hexamer oligonucleotide tagged with a T7 promoter sequence. After second strand synthesis, double-stranded cDNA was used as a template for amplification with T7 RNA polymerase to obtain antisense cRNA. Random hexamers were then used to reverse-transcribe the cRNA into single-stranded sense strand cDNA. The cDNA was then fragmented by uracil DNA glycosylase and apurinic/apyrimidic endonuclease 1. Fragment size was checked using the Agilent 2100 Bioanalyzer (fragment size between 50–200 bp). Fragmented sense cDNA was biotin-labelled !

growth_protocol: Mouse corpus callosum samples dissected after 1 week cuprizone intoxication or control samples

extract_protocol: mice were anaesthetized with ketamine (100 mg·kg−1 i.p.) and xylazine (10 mg·kg−1 i.p.), and transcardially perfused with ice-cold PBS, tissues were manually dissected after transcardial PBS perfusion, immediately frozen in liquid nitrogen, and kept at -80C until further processing. RNA was isolated using the RNeasy Kits from QIAGEN

treatment_protocol: 8 week-old C57BL/6 male mice (19 g - 20 g) were purchased from Janvier Labs (Le Genest-Saint-Isle, France), cuprizone intoxication (0.25%) for one week

value: wild-type

tag: Sex

value: male

tag: age

value: 8 weeks

value: cuprizone diet

value: corpus callosum


title: WT_H3K4me3_frozen_rep2

value: wildtype

value: splenic B cells

value: frozen


title: WT_H3K4me3_fresh_rep1


title: RNAseq_T131_3C

data_processing:
Paired end RNA-seq reads were mapped to the mouse genome (mm10) using STAR (Dobin et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: STAR output; reads per gene for each sample

value: Morc3 rescue


title: RNAseq_WT26_p56

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74106) including the on-column DNAse step, ribosomal RNA was depleted using the RNARibo-Zero rRNA Removal Kit (Illumina, MRZH11124)
Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420S)

value: wild type


title: Corpus callosum, cuprizone diet, biological rep 3

tag: tissue


title: RNAseq_WT26_p43


title: RNAseq_KO27_3

value: Morc3 knock out


title: RNAseq_WT26_p42


title: 500ng_input

description: Input sample

value: embryonic kidney cells

value: kidney

value: no IP (input RNA)

value: no


title: WT_H3K4me3_frozen_rep1


title: Corpus callosum, normal diet, biological rep 1

source_name: Corpus callosum, normal diet

value: normal diet


title: Corpus callosum, cuprizone diet, biological rep 1


title: Corpus callosum, normal diet, biological rep 4


title: Corpus callosum, cuprizone diet, biological rep 2


title: Corpus callosum, normal diet, biological rep 3


title: Septum3

city: Tokyo

first: Shogo

last: Ito

email: itoshogo@keio.jp, itopap122@icloud.com

address: 35 Shinanomachi Shinjuku-ku

department: Cardiology

country: Japan

institute: Keio University School of Medicine

hyb_protocol: 0.6 ug /1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul /55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul /55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Ver. 2.0 (G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k /4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um /5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Low Input Quick Amp Labeling kit, One-Color (Agilent) (5190-2305) according to the manufacturer's instructions, followed by RNeasy mini kit (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop 2000c Spectrophotometer.

extract_protocol: Mice were anesthetized deeply and sacrificed by decapitation. Sternotomy was performed and cold PBS was perfused into RV and LV, hearts were extirpated and froze by liquid nitrogen immediately. Frozen heart tissue was broken into powder using Cryopress (CP-100W, Microtec–Nichion Co. Ltd, Funabashi, Japan). These products were dissolved in Trizol reagent (Invitrogen) and m-RNA was extracted.Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).


title: RNAseq_KO27_2

value: mouse embryonic stem cells (ESCs)


title: LV3


title: RV4


title: RNAseq_KO27_1


title: 37: human high stress monocyte RNA-seq

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

data_processing:
Quality control was assessed using FastQC (version 0.11.7). Reads were trimmed using trimmomatic (version 0.36). Reads were mapped to human reference genome hg19 using STAR (version 2.6.1d). Genomic features were assigned using featureCounts (version v1.6.3).
genome build: hg19
processed data files format and content: rawcounts.txt files contain comma separated raw counts

source_name: whole blood

extract_protocol: Whole blood was collected into PAXgene Blood RNA tubes (PreAnalytiX GmbH BD Biosciences, Mississauga, ON, Canada), and RNA was isolated. The quality and yield of the isolated RNA was determined with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) and sequenced single end on the Illumina HiSeq4000 platform.

value: 65 years

tag: group

value: high stress

value: monocytes


title: 36: human high stress monocyte RNA-seq

value: 62 years


title: RV3


title: Septum1


title: Corpus callosum, normal diet, biological rep 2

value: wild-type

value: male

value: 8 weeks

value: corpus callosum


title: 38: human high stress monocyte RNA-seq

value: 56 years


title: Dorsal Starchy Endosperm rep3,7DAF

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

hyb_protocol: standard Agilent protocol

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner, and background of the Cy3 raw signals was corrected using the Feature Exraction (ver. 10.5.1.1, Agilent Technologies).

data_processing: The raw data was processed using the R package limma (Ritchie et al., 2015)

organism: Oryza sativa

source_name: Endosperm

label_protocol: Total RNA (2.5 ng) was amplified to obtain complementary RNA (cRNA) using a Quick Amp Labeling kit and labelled using One-color (Agilent technologies) cyanine-3 (Cy3)-CTP, according to the modified manufacturer’s instruction.

growth_protocol: 26/20oC for day/night starting at 6:00AM and 7:00PM during ripening

extract_protocol: Picopure RNA isolation kit (Molecular Devices)

treatment_protocol: Control temperature at 26/20oC

value: Dorsal Starchy Endosperm

tag: developmental stage


title: Septum2

tag: strain


title: ChIP_FLAG_T148_3_r2

description:
Standard ChIP protocol
GS1071_T148.3_Morc3_G101A_FLAG_rep2_ChIP_CCGTCC

value: Morc3_G101A_3xFLAG rescue

value: anti-FLAG M2 (Sigma-Aldrich, F1804)


title: ChIP_FLAG_T149_3_r2

description:
Standard ChIP protocol
GS1072_T149.3_Morc3_W419A_FLAG_rep2_ChIP_ATTCCT

value: Morc3_W419A_3xFLAG rescue


title: 34: human high stress monocyte RNA-seq

value: 70 years


title: Lateral Starchy Endosperm rep3,7DAF

value: Lateral Starchy Endosperm


title: RV2


title: SMARCA4_23_KO_ATAC_rep2

city: Cambridge

first: Carla

last: Concepcion

state: MA

address: 500 Main Street, 76-431

department: Koch Institute

institute: MIT

description: SMARCA4 ATACseq

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using bowtie v1.0.1 and BAMs were processed with Picard MarkDuplicates (v1.77) to compress duplicates. BAMs for all samples were merged with Samtools merge (v0.1.13) and peaks were called on the merged BAM using macs2 (v2.1.1). Reads per peak per sample were quantified using BEDTools multicov (v2.26.0).
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes raw read counts per peak

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, 23

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% fetal bovine serum and 1X penicillin-streptomycin.

extract_protocol:
Transposition and downstream steps were performed as described in: Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J., 2015. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr. Protoc. Mol. Biol. 109:21.29.1-21.29.9. doi: 10.1002/0471142727.mb2129s109
Library preparation was performed as described in: Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J., 2015. ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr. Protoc. Mol. Biol. 109:21.29.1-21.29.9. doi: 10.1002/0471142727.mb2129s109
(paired end 40mer reads)

treatment_protocol: No treatment

value: Lung Adenocarcinoma cell line 23

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: Lateral Starchy Endosperm rep1,7DAF


title: ChIP_FLAG_T146_5_r2

description:
Standard ChIP protocol
GS1070_T146.5_Morc3_E35A_FLAG_rep2_ChIP_CTTGTA

value: Morc3_E35A_3xFLAG rescue

value: mouse embryonic stem cells (ESCs)


title: LV2


title: Dorsal Starchy Endosperm rep2,7DAF


title: 35: human low stress monocyte RNA-seq

value: 74 years

value: low stress

value: monocytes


title: LV1


title: Dorsal Starchy Endosperm rep1,7DAF


title: SMARCA4_36_WT_ATAC_rep2

description: SMARCA4 ATACseq

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, 36

value: Lung Adenocarcinoma cell line 36

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: Lateral Starchy Endosperm rep2,7DAF


title: 33: human low stress monocyte RNA-seq

value: 68 years


title: Central Starchy Endosperm rep3,7DAF

value: Central Starchy Endosperm


title: RV1


title: SMARCA4_T2_WT_ATAC_rep2

description: SMARCA4 ATACseq

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, T2

value: Lung Adenocarcinoma cell line T2


title: ChIP_FLAG_T145_5_r2

description:
Standard ChIP protocol
GS1069_T145.5_Morc3_WT_FLAG_rep2_ChIP_GGCTAC

value: Morc3_3xFLAG rescue


title: Central Starchy Endosperm rep1,7DAF


title: Central Starchy Endosperm rep2,7DAF


title: ChIP_FLAG_T149_3_r1

description:
Standard ChIP protocol
GS1068_T149.3_Morc3_W419A_FLAG_rep1_ChIP_TAGCTT

value: anti-FLAG M2 (Sigma-Aldrich, F1804)


title: ChIP_FLAG_T148_3_r1

description:
Standard ChIP protocol
GS1067_T148.3_Morc3_G101A_FLAG_rep1_ChIP_GATCAG

value: Morc3_G101A_3xFLAG rescue


title: 27: human low stress monocyte RNA-seq

value: 64 years


title: SMARCA4_M_KO_ATAC_rep1

description: SMARCA4 ATACseq

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, M

value: Lung Adenocarcinoma cell line M


title: 28: human low stress monocyte RNA-seq

value: 49 years


title: PBRM1_23_KO_CnR

description: PBRM1 CUT&RUN

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using bowtie2 v2.2.6; BAMs were processed to remove duplicates using Picard MarkDuplicates v2.17.0; Alignments were sorted by read name using samtools v1.5 and converted to BED format using bedtools bamtobed and subsequently to bedgraph using bedtools genomecov (BEDTools v2.29.2). Peaks were called using SEACR v1.2 (Meers MP, Tenenbaum D, Henikoff S., 2019)    by selecting the top 0.5% of regions by area under the curve (AUC).
Genome_build: mm9
Supplementary_files_format_and_content: Tar gzipped archive of BED files with peak calls per Cut&Run sample

extract_protocol:
DNA was extracted using PCI and chloroform.
Libraries were constructed using NEB UltraII.
Cut&Run (paired end 25mer reads)

treatment_protocol: Cells were subjected to a published CUT&RUN protocol (Skene, Henikoff and Henikoff, Nature Protocols 2018).

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: SMARCA4_23_KO_ATAC_rep1

description: SMARCA4 ATACseq

value: Lung Adenocarcinoma cell line 23


title: SMARCA4_M_KO_ATAC_rep2

description: SMARCA4 ATACseq


title: 29: human high stress monocyte RNA-seq

value: 72 years

value: high stress


title: ChIP_FLAG_T145_5_r1

description:
Standard ChIP protocol
GS1065_T145.5_Morc3_WT_FLAG_rep1_ChIP_CAGATC

value: mouse embryonic stem cells (ESCs)


title: SMARCA4_36_WT_ATAC_rep1

description: SMARCA4 ATACseq


title: 31: human low stress monocyte RNA-seq

value: 66 years

value: low stress

value: monocytes


title: SMARCA4_T2_WT_ATAC_rep1

description: SMARCA4 ATACseq

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: ChIP_FLAG_WT26_r2

description:
Standard ChIP protocol
GS1023_WT26_FLAG_ChIP_GATCAG

value: wild type


title: ChIP_FLAG_K14E8_r3

description:
Standard ChIP protocol
GS1024_K14E8_Morc3_FLAG_ChIP_TAGCTT

value: Morc3 3xFLAG knock in


title: 26: human high stress monocyte RNA-seq

value: 63 years


title: Aleurone rep3,7DAF

value: Aleurone


title: Aleurone rep1,7DAF


title: ChIP_FLAG_WT26_r1

description:
Standard ChIP protocol
GS1021_WT26_FLAG_ChIP_CAGATC

value: anti-FLAG M2 (Sigma-Aldrich, F1804)


title: 24: human low stress monocyte RNA-seq

value: 64 years


title: Aleurone rep2,7DAF


title: 25: human low stress monocyte RNA-seq

value: 61 years


title: Lateral Starchy Endosperm rep3,12DAF

value: Lateral Starchy Endosperm

value: 12 DAF


title: Lateral Starchy Endosperm rep2,12DAF


title: PBRM1_36_WT_CnR

description: PBRM1 CUT&RUN


title: ChIP_FLAG_T146_5_r1

description:
Standard ChIP protocol
GS1066_T146.5_Morc3_E35A_FLAG_rep1_ChIP_ACTTGA

value: Morc3_E35A_3xFLAG rescue


title: Lateral Starchy Endosperm rep1,12DAF


title: ChIP_H3K9me3_T131_3M

description:
Standard ChIP protocol
GS999_H3K9me3_ChIP_T131_3M_TGACCA

value: Morc3 rescue

value: anti-H3K9me3 (Active Motif, 39161)


title: 23: human high stress monocyte RNA-seq

value: 52 years

value: high stress


title: BRD9_23_KO_CnR

description: BRD9 CUT&RUN

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: 20: human low stress monocyte RNA-seq

value: low stress

value: monocytes


title: ChIP_H3K9me3_T131_3D

description:
Standard ChIP protocol
GS998_H3K9me3_ChIP_T131_3D_TTAGGC

value: mouse embryonic stem cells (ESCs)


title: PBRM1_M_KO_CnR

description: PBRM1 CUT&RUN


title: ChIP_H3K9me3_T131_3C_r1

description:
Standard ChIP protocol
GS997_H3K9me3_ChIP_T131_3C_CGATGT


title: 21: human low stress monocyte RNA-seq

value: 50 years


title: BRD9_36_WT_CnR

description: BRD9 CUT&RUN

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: BRD9_M_KO_CnR

description: BRD9 CUT&RUN


title: Dorsal Starchy Endosperm rep3,12DAF

value: Dorsal Starchy Endosperm


title: PBRM1_T2_WT_CnR

description: PBRM1 CUT&RUN


title: ChIP_FLAG_K14E8_r1

description:
Standard ChIP protocol
GS319_K14E8_Morc3_FLAG_ChIP_GATCAG

value: Morc3 3xFLAG knock in

value: anti-FLAG M2 (Sigma-Aldrich, F1804)


title: 16: human high stress monocyte RNA-seq

value: 71 years


title: 17: human low stress monocyte RNA-seq

value: 56 years


title: ChIP_FLAG_K14E8_r2

description:
Standard ChIP protocol
GS320_K14E8_Morc3_FLAG_ChIP_TAGCTT


title: BRD9_T2_WT_CnR

description: BRD9 CUT&RUN


title: Dorsal Starchy Endosperm rep2,12DAF

value: 12 DAF


title: Dorsal Starchy Endosperm rep1,12DAF


title: ChIP_H3K9me3_WT26_r1

description:
Low cell ChIP protocol
GS312_H3K9me3_ChIP_WT26p43_GCCAAT

value: wild type


title: ChIP_H3K9me3_WT26_r2

description:
Low cell ChIP protocol
GS314_H3K9me3_ChIP_WT26p56_ACTTGA


title: SMARCC1_23_KO_CnR

description: SMARCC1 CUT&RUN


title: 14: human high stress monocyte RNA-seq

value: 60 years


title: Central Starchy Endosperm rep2,12DAF

value: Central Starchy Endosperm


title: ChIP_H3K9me3_KO27_3

description:
Low cell ChIP protocol
GS310_H3K9me3_ChIP_KO27_3_TGACCA

value: Morc3 knock out

value: anti-H3K9me3 (Active Motif, 39161)


title: 14_2_6766B

first: A

last: Bhutkar

address: 77 Massachusetts Avenue

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
RNAseq: Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.3.1 and bowtie v1.2.3 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: isolated cancer cells from lungs

growth_protocol: Lung tumors were initiated in KP, KPS-HET and KPS mice through intratracheal instillation of adenoviral Cre recombinase driven by the CCSP promoter

extract_protocol:
Moribund mice were sacrificed. Tumor-bearing lungs were enzymatically dissociated and cancer cells were isolated through FACS.
Libraries were constructed using Low Input polyA + Clontech SMARTseq

value: KrasLSL-G12D/+; Trp53fl/fl; Smarca4+/+; Rosa26LSL-TdTom

tag: infection

value: adenoviral Cre

value: mixed B6;129S2


title: 13: human high stress monocyte RNA-seq

value: 57 years

value: high stress

value: monocytes


title: 15_1_6764B


title: Central Starchy Endosperm rep3,12DAF


title: 10: human high stress monocyte RNA-seq

value: 77 years


title: Aleurone rep3,12DAF

value: Aleurone


title: 12_6627B


title: 12: human low stress monocyte RNA-seq

value: 70 years

value: low stress


title: 13_6616B

value: KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/fl; Rosa26LSL-TdTom


title: Aleurone rep1,12DAF

value: 12 DAF


title: ARID1A_2_M_KO_CnR

description: ARID1A CUT&RUN (CST antibody)

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: Aleurone rep2,12DAF


title: 4: human low stress monocyte RNA-seq

value: 74 years


title: ChIP_H3K9me3_KO27_2

description:
Low cell ChIP protocol
GS308_H3K9me3_ChIP_KO27_2_CGATGT

source_name: ES cells

tag: cell line

value: mouse embryonic stem cells (ESCs)


title: SMARCC1_T2_WT_CnR

description: SMARCC1 CUT&RUN

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: 11: human low stress monocyte RNA-seq

value: 66 years

tag: cell type


title: 8: human low stress monocyte RNA-seq

value: 75 years


title: ARID1A_2_T2_WT_CnR

description: ARID1A CUT&RUN (CST antibody)


title: 2: human high stress monocyte RNA-seq


title: ARID1A_2_36_WT_CnR

description: ARID1A CUT&RUN (CST antibody)


title: ChIP_Input_WT26

description:
Input
GS133_Input_WT26_ATCACG

value: wild type


title: ChIP_FLAG_K9G1

description:
Standard ChIP protocol
GS180_K9G1_Setdb1_FLAG_ChIP_CTTGTA

value: Setdb1 3xFLAG knock in

value: anti-FLAG M2 (Sigma-Aldrich, F1804)


title: ATAC_T141_5_r2

source_name: Morc3_E35A rescue_ESCs

value: Morc3_E35A rescue


title: ATAC_T143_5_r2

source_name: Morc3_W419A rescue_ESCs

value: Morc3_W419A rescue


title: Central Starchy Endosperm rep1,12DAF

value: Central Starchy Endosperm


title: ATAC_T131_3C_r3

source_name: Morc3 rescue_ESCs

value: Morc3 rescue


title: 6: human low stress monocyte RNA-seq

value: 62 years

value: monocytes


title: SMARCC1_36_WT_CnR

description: SMARCC1 CUT&RUN


title: 11_6762B

value: KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/+; Rosa26LSL-TdTom

value: adenoviral Cre

value: mixed B6;129S2


title: ARID1A_2_23_KO_CnR

description: ARID1A CUT&RUN (CST antibody)

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: 5_6768B


title: SMARCC1_M_KO_CnR

description: SMARCC1 CUT&RUN


title: ARID1A_1_23_KO_CnR

description: ARID1A CUT&RUN (Abcam antibody)


title: ATAC_KO27_2_r3

source_name: Morc3 knock out_ESCs

value: Morc3 knock out

value: mouse embryonic stem cells (ESCs)


title: 2_6900B

value: KrasLSL-G12D/+; Trp53fl/fl; Smarca4+/+; Rosa26LSL-TdTom


title: 10_1_6623B

value: KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/fl; Rosa26LSL-TdTom


title: 7_1_6933B


title: Alex-Mount-Sinai-WT-2

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing reads from hESC colonies were mapped to hg38 using HISAT2.
Counts of reads mapping to genes were obtained using featureCounts software of Subread package against Ensembl v90 annotation.
Differential expression analysis was carried out using the DESeq2 package. Principal component analysis (PCA) in DESeq2 package was utilized to identify outliers.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file with counts

source_name: hESCs

extract_protocol:
Total RNA from WT, PB2 KO and PB2 OE hESCs was isolated using a RNeasy Micro kit (Qiagen), following the recommended instructions for on-column DNase digestion. RNA quality and concentrations were measured using an Agilent Bioanalyzer (Agilent RNA 6000 Pico), and samples with RNA integrity number scores higher than 7 were used.
Poly(A) mRNA were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490S) and cDNA libraries for Illumina nextgeneration sequencing were prepared with NEBNext Ultra Directional RNA Library Prep Kit (NEBE7760S). Three independent samples for each condition were barcoded using NEBNext Index primers 7 (NEB, E7335S), pooled together as one sample, and run on an Illumina platform HiSeq2500 with onesided 75 base reads, with about 30 million reads per sample.

value: WT

value: hESCs


title: ARID1A_1_36_WT_CnR

description: ARID1A CUT&RUN (Abcam antibody)

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: ATAC_T142_5_r2

source_name: Morc3_G101A rescue_ESCs

value: Morc3_G101A rescue


title: Alex-Mount-Sinai-WT-3


title: ATAC_T143_5_r1

value: Morc3_W419A rescue


title: SMARCA4_36_WT_RNAseq

description:
SMARCA4 RNAseq
WT_36

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

extract_protocol:
Total RNA was isolated using Trizol per manufacturer's instruction. RNA quality and purity was assessed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing with the Illumina Neoprep library preparation system per manufacturer's instructions.
RNAseq (single end 50mer reads)

value: Lung Adenocarcinoma cell line 36


title: H3K4ME3_23_KO_CnR

description: H3K4ME3 CUT&RUN


title: ARID1A_1_M_KO_CnR

description: ARID1A CUT&RUN (Abcam antibody)


title: ATAC_T142_5_r1


title: Alex-Mount-Sinai-PB2OE-2

value: OE

value: PLXNB2 overexpression


title: Alex-Mount-Sinai-WT-1


title: ATAC_T131_3C_r2

value: Morc3 rescue


title: ATAC_T141_5_r1

value: Morc3_E35A rescue


title: ATAC_WT26_r3

source_name: wild type_ESCs

value: wild type


title: SMARCA4_23_KO_RNAseq

description:
SMARCA4 RNAseq
KO_23

value: Lung Adenocarcinoma cell line 23


title: Alex-Mount-Sinai-PB2KO-3

value: KO

value: PLXNB2 KO


title: ARID1A_1_T2_WT_CnR

description: ARID1A CUT&RUN (Abcam antibody)


title: SMARCA4_T2_WT_RNAseq

description:
SMARCA4 RNAseq
WT_T2

value: Lung Adenocarcinoma cell line T2


title: Alex-Mount-Sinai-PB2KO-2


title: Riboseq.mouse.testis.4EGIControl.adult.rep1

city: Rochester

first: Xin

state: NY

address: 601 Elmwood Ave

department: Biochemistry and Biophysics

institute: University of Rochester

description: Ribo-seq

data_processing:
Analyses were performed using piPipes v1.4. All data from the ribosome profiling (Ribo-seq), RNA sequencing, were analyzed using the latest mouse genome release mm10 (GCA_000001635.7). Generally, one mismatch is allowed for genome mapping.
For RNA-seq reads, the expression per transcript was normalized to the top quartile of expressed transcripts per library calculated by Cuffdiff, and the tpm (transcripts per million) value was quantified using the Salmon software.
For Ribo-seq analysis, uniquely mapping reads between 26 nt and 32 nt were selected for further analysis. Libraries from harringtonine treatment were further normalized to the sum of reads mapping to mitochondrial coding sequences. Libraries from puromycin treatment were further normalized to the sum of reads mapping to the 5´-UTR of mRNAs.
Genome_build: Mouse: mm10 (GCA_000001635.7)
Supplementary_files_format_and_content: For Ribo-seq, processed data files are unique genome alignment results in BED13 format (https://github.com/bowhan/piPipes/wiki). RNAseq quantification results are .sf files output by Salmon software.

growth_protocol: Animals mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. Lizards were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560), and rRNAs were depleted from total RNAs with complementary DNA oligomers (IDT) and RNaseH (Invitrogen, Waltham, MA, USA)
1, Strand-specific RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol. 2, Ribo-seq: Testes samples were lysed, RNase T1 & A treated and loaded on sucrose gradients, and 80S monosomes were recovered for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and has been trimmed in the raw data.

treatment_protocol: The mice were anesthetized with Ketamine/Xylazine mixture (Ketamine 100 mg/kg; Xylazine 25 mg/kg) via intraperitoneal injection. After complete anesthesia, testes were exteriorized with a longitudinal incision around 1 cm at the center of abdomen. The tunica albuginea was penetrated using a sharp 26 G needle (BD, Franklin Lakes, NJ, USA, 30511) 1 mm from the vascular pedicle, and the needle was withdrawn to generate path for introducing a blunt end Hamilton needle (Hamilton, Reno, NV, USA, 7786-02). PBS containing 0.02% Fast Green FCF (Thermo Fisher Scientific, Waltham, MA, USA) with harringtonine (LKT labs, 0.5 μg/μl in a total volume of 10 μl) or puromycin dihydrochloride (Invitrogen, 2.5 μg/μl in a total volume of 10 μl) was slowly injected using a Hamilton microsyringe (1705RN) into one testis, and vehicle control without drug was injected into the other testis. The needle was held in place for 30 seconds before removal to prevent back flow of the solution. Successful completion of injection was indicated by testis filled with green solution. The testes were returned to the abdominal cavity after injection. The incisions were sutured. At the end point, the mice were euthanized by cervical dislocation, and the testes were collected.

value: wt

value: adult

value: whole testis

tag: molecule subtype

value: Ribosome footprints


title: RNAseq.mouse.testis.CBP80IP.adult

description: Strand-specific RNA-seq

value: rRNA depleted RNA


title: Alex-Mount-Sinai-PB2OE-1

value: hESCs


title: SMARCA4_M_KO_RNAseq

description:
SMARCA4 RNAseq
KO_M

value: Lung Adenocarcinoma cell line M

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: Alex-Mount-Sinai-PB2OE-3

value: OE


title: ATAC_WT26_r2

value: mouse embryonic stem cells (ESCs)


title: H3K4ME1_23_KO_CnR

description: H3K4ME1 CUT&RUN


title: TA 10 uM #2

first: Kaylie

last: Padgett-Pagliai

address: 2033 Mowry Road, Lab 325 CGRC

data_processing:
Raw sequences were modified to trim the Illumina sequencing adapter using Cutadapt.
Sequence processing using the Sickle tool to verify the quality of the samples prior to further analyses.
Sequences were mapped against the genome of L. crescens BT-1 using Bowtie2.
The mapped mRNA sequences were aligned using Samtools.
mRNA sequences were counted using the HTseq tool.
Genome_build: Liberibacter crescens BT-1 (NC_019907.1)
Supplementary_files_format_and_content: Processed data files are in the form of an Htseq .txt file with gene counts.
Supplementary_files_format_and_content: DESeq2_results.txt: Processed data file is in the form of an DESeq2 results file in a .txt file with differential expression data.

organism: Liberibacter crescens BT-1

source_name: L. crescens BT-1, TA

growth_protocol: L. crescens BT-1 cells were grown with 10 μM tolfenamic acid (in 0.05% dimethyl sulfoxide) while the control was grown with 0.05% DMSO. L. crescens BT-1 cells were collected at OD600= 0.3 (mid-exponential phase) by centrifugation at 8000 rpm, at 4 °C.

extract_protocol:
Total RNA was extracted with the RiboPure-Bacteria (Life Technologies) kit following the manufacturer’s protocol. The quality of isolated RNA samples was examined in an Agilent 2100 Bioanalyzer. The rRNA was depleted using the MICROBExpress Bacterial mRNA enrichment kit (Life Technologies) according to the manufacturer’s instructions.
Single end RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina) and followed by sequencing using a HiSeq2500 system. RNA sequencing was performed by the Genome Sciences Facility at Penn State University in Hershey, PA. The assays were performed in duplicates, and approximately 2million reads were obtained for each library.

tag: treatment

value: Tolfenamic acid


title: H3K4ME3_T2_WT_CnR

description: H3K4ME3 CUT&RUN

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: ATAC_KO27_2_r1

value: Morc3 knock out


title: TCL1_129

city: Luxembourg

first: Etienne

last: Moussay

address: 6 rue Nicolas-Ernest Barblé

department: Cancer Research

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
After initial QCs using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/), fastq files were processed using a local Snakemake workflow including the following main steps.
First, raw reads were trimmed from their UMI index, poly A and adapter sequences using a combination of dedicated scripts and cutadapt (v2.10).
Next, filtered reads were submitted for mapping (STAR v2.5.3a) on the Mouse Reference genome (GRCm38).
Collapsing of reads originating from the same fragment was achieved with umi_tools (v 1.0.0) and counting was perfomed with featureCounts (subread v2.0.0).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

source_name: B cells from leukemic (Eu-TCL1) mice

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained and sorted by FACS (Aria III). RNA was harvested using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols

tag: mouse status

value: leukemic

value: Spleen

value: B cells

tag: phenotype


title: Riboseq.mouse.testis.4EGI.adult.rep1

description: Ribo-seq

tag: genotype

tag: drug treatment


title: H3K4ME1_36_WT_CnR

description: H3K4ME1 CUT&RUN


title: ATAC_WT26_r1

value: wild type


title: ATAC_KO27_2_r2


title: TCAH5889

source_name: Eµ-TCL1 CD19Cre/WTAHRfl/fl Hif1afl/fl

extract_protocol:
Spleens were removed, gently dissociated on ice, and cells were antibody-stained (anti-CD5 and anti-CD19) and sorted by FACS (Aria III). RNA was harvested using NucleoZOL reagent and columns. QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina was used with 100 ng of total RNA for the construction of sequencing libraries. UMI were added to the protocol.
Libraries were prepared for sequencing using standard protocols

tag: strain/genotype

value: leukemic B cells


title: Alex-Mount-Sinai-PB2KO-1

value: KO

value: PLXNB2 KO


title: TCAH4722


title: WT_1G

source_name: B cells from WT (C57BL/6)

value: healthy


title: TCL1_214GD


title: H3K27AC_T2_WT_CnR

description: H3K27AC CUT&RUN


title: DMSO #2

source_name: L. crescens BT-1, DMSO

value: DMSO


title: H3K27AC_M_KO_CnR

description: H3K27AC CUT&RUN


title: ATAC_T131_3C_r1

value: Morc3 rescue


title: TCL1_96G


title: H3K4ME1_T2_WT_CnR

description: H3K4ME1 CUT&RUN


title: Ciprofloxacin library

city: Boston

first: Jacob

middle: Eric

last: Lazarus

address: 55 Fruit St

institute: Massachusetts General Hospital

description: Supplemental_table_3_Antibiotic_CON-ARTIST.xlsx

data_processing:
Reads were trimmed of transposon and adapter sequences in CLC Genomics Workbench
Reads were mapped to S marcescens genome using Bowtie, allowing for 1 mismatch
Data was processed using the ARTIST pipeline. Code available in Pritchard 2014 Plos Genetics 10(11):e1004782
Genome_build: SAMN18473280
Supplementary_files_format_and_content: matrix of ARTIST pipeline output

organism: Serratia marcescens subsp. marcescens ATCC 13880

source_name: S. marcescens strain ATCC 13880 with spontaneous streptomycin-resistant mutation

growth_protocol: libraries were created on LB - chloramphenicol/streptomycin plates at 37C

extract_protocol:
gDNA was isolated using Wizard Genomic DNA extraction kit
transposon-containing fragments were amplified with custom primers using PCR

treatment_protocol: for selection, libraries were grown for 6 hours in liquid LB culture at 37C in absence of drug or with antibiotic indicated above and and then plated on LB agar at 37 deg C

value: outgrowth for 6 hours in LB + ciprofloxacin 0.05 ug/mL


title: Cefepime library

value: outgrowth for 6 hours in LB + cefepime 0.025 ug/mL


title: H3K4ME1_M_KO_CnR

description: H3K4ME1 CUT&RUN

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: H3K4ME3_M_KO_CnR

description: H3K4ME3 CUT&RUN


title: C3a-3

hyb_protocol: 0.6 ug /1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul /55ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul /55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Ver. 2.0 (G4853B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 074036_D_F_20150914) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: NRVM cultured with C3a protein

growth_protocol: Hearts from 8–10 rats (1–2 day old neonatal Sprague-Dawley rat) were excised, the ventricles minced and tissue pieces dissociated in Ca2+/Mg2+ free Hank’s balanced salt solution that contains 0.1% trypsin and 12 μg/mL pancreatin. The dispersed cells were re-suspended in Ultraculture serum-free medium (Fisher Scientific) supplemented with 2 mM L-glutamine, 2 μg/L vitamin B12, 20 U/mL penicillin and 20 μg/mL streptomycin. After preplating, cells were re-suspended in the culture medium and counted. Cells were plated on collagen-coated cover glasses (diameter 15 mm) and incubated at 37 °C in a humidified atmosphere containing 5% CO2 humidified  containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: C3a recombinant protein (R&D systems) were administered into NRVMs and cultured under the same culture condition for 12h until just before cell lysate collection. Final concentration of C3a protein was 0.5μg/ml.

value: Neonatal rat ventricular myocytes (NRVMs)


title: TCH0255

source_name: Eµ-TCL1 CD19Cre/WTHif1ɑfl/fl

value: E{mu}-TCL1 CD19Cre/WTHif1{alpha}fl/fl


title: H3K27AC_36_WT_CnR

description: H3K27AC CUT&RUN

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, 36

value: KrasG12D/+; Trp53-/-; Smarca4+/+


title: WT_1D


title: TCAH0550


title: WT_138G


title: SMARCA2_M_KO_CnR

description: SMARCA2 CUT&RUN

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, M


title: TA 10 uM #1

value: Tolfenamic acid


title: TCH0332


title: H3K27AC_23_KO_CnR

description: H3K27AC CUT&RUN

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, 23


title: TCH4950


title: Cefoxitin library

value: outgrowth for 6 hours in LB + cefoxitin 4 ug/mL


title: SMARCA4_36_WT_CnR

description: SMARCA4 CUT&RUN


title: C3a-1


title: Control-2

source_name: NRVM cultured in control medium


title: TC4637

source_name: Eµ-TCL1 CD19Cre/WTAHRWT/WT Hif1aWT/WT

value: Spleen


title: SMARCA2_36_WT_CnR

description: SMARCA2 CUT&RUN


title: Control-3


title: SMARCA4_M_KO_CnR

description: SMARCA4 CUT&RUN


title: SMARCA2_23_KO_CnR

description: SMARCA2 CUT&RUN


title: SMARCA4_T2_WT_CnR

description: SMARCA4 CUT&RUN

source_name: Murine KP Lung Adenocarcinoma tumor-derived cell line, T2


title: DMSO #1


title: SMARCA2_T2_WT_CnR

description: SMARCA2 CUT&RUN


title: TCA2410

source_name: Eµ-TCL1 CD19Cre/WTAHRfl/fl

value: E{mu}-TCL1 CD19Cre/WTAHRfl/fl


title: C3a-2


title: 81-PBMC

city: Madison

first: Aleksandar

middle: K.

last: Stanic

state: WI

address: 202 S. Park St., Meriter Atrium B

department: Obstetrics and Gynecology

institute: University of Wisconsin - Madison

data_processing:
CellRanger v3.1 was applied to generate filtered gene count matrices for each sample.
We enriched the data for high-quality cells according to the following metrics (keeping cells with mean absolute deviation within [-3,3]): fraction of UMIs aligning to mitochondrial transcripts, fraction of housekeeping genes detected, number of RNA or surface features detected, and number of RNA (surface feature) UMIs.
We removed cells without VDJ sequencing data or that appeared to be CD4+CD8+/CD4-CD8- (manual gating).
Using Seurat v3.0, we normalized RNA values with log normalization and surface features with centered log ratio (CLR).
To identify MAIT cells, we first aligned the RNA-seq data sets using the Seurat v3.0 integration pipeline, then computed clusters with Seurat using resolution=0.5. A cluster of MAIT cells was identified according to surface feature expression CD161+ TCR-Va7.2+.
Genome_build: GRCh38 3.0
Supplementary_files_format_and_content: Supplementary files include antibody capture feature reference, Seurat v3.0 object (in RDS format), cell metadata, and count matrix files for all samples combined (separated for RNA and antibody capture, FB). Future users may need to run Seurat::UpdateSeuratObject to update the object for newer versions of Seurat.
Supplementary_files_format_and_content: feature_reference.csv: Feature barcode (antibody capture) reference file.
Supplementary_files_format_and_content: MAIT_cell_metadata.tsv.gz: Cell metadata including barcodes, sample, localization, QC metrics.
Supplementary_files_format_and_content: MAIT_FB_barcodes.tsv.gz: Antibody capture (feature barcoding) barcode file.
Supplementary_files_format_and_content: MAIT_FB_features.tsv.gz: Antibody capture (feature barcoding) feature file.
Supplementary_files_format_and_content: MAIT_FB_matrix.mtx.gz: Antibody capture counts, sparse matrix.
Supplementary_files_format_and_content: MAIT_object_seurat_v3.rds: RDS format Seurat v3.0 object.
Supplementary_files_format_and_content: MAIT_RNA_barcodes.tsv.gz: Gene expression barcode file.
Supplementary_files_format_and_content: MAIT_RNA_features.tsv.gz: Gene expression feature file.
Supplementary_files_format_and_content: MAIT_RNA_matrix.mtx.gz: Gene expression counts, sparse matrix.

source_name: MAIT cells from peripheral blood

growth_protocol: Sequenced cells in this study were isolated from tissues and not grown.

extract_protocol:
T cells from decidua basalis and matched PBMCs were enriched using the Dynabeads® Untouched™ Human T Cells Kit (Invitrogen). T cell enriched samples were then labeled with Zombie NIR™ Fixable Viability Kit (BioLegend). Subsequently, cells treated with TruStain FcX™ (BioLegend), then labeled with fluorochrome- and TotalSeq™-C oligonucleotide-conjugated antibodies. Samples were then sorted into PBS (Ca++/MG++ free, 1% non-acetylated BSA, 1 mL/mL RNase inhibitor) using the BD FACSAria in a 3 laser (488nm, 561nm, 405nm) configuration, collecting 100,000 live, CD3+ cells. Sorted cells were then processed using the Chromium Next GEM Chip K Single Cell A Chip Kit (10X Genomics).
According to manufacturer's protocol (10X Genomics Chromium, Single Cell Immune Profiling 5' v1.1 chemistry).

treatment_protocol: Matched decidual and PBMC samples were sourced from five term normal elective cesarean sections (>37 wks GA) under the approval of Meriter IRB# 2018-10 protocol (three were retained after data quality control). Decidua basalis tissue was dissected from the maternal surface of the placenta and decidua parietalis tissue was scraped from the fetal membrane. Decidual tissue was mechanically and enzymatically dissociated. PBMCs were isolated from whole blood via density gradient centrifugation. PBMC layer was extracted and washed with PBS, counted, adjusted to an optimal concentration of 4 X10^6 cells/mL and cryopreserved.

value: MAIT cells

tag: localization

value: PBMC


title: 85-Basal

source_name: MAIT cells from decidua basalis

value: Decidua basalis


title: 83-Basal


title: GD-rep2

city: Pittsburgh

first: Clayton

middle: Pio

last: Santiago

state: Pennsylvania

address: 1622 Locust Street

department: Ophthalmology

institute: University of Pittsburgh

hyb_protocol: Samples were hybridized with Clariom S Human array (Affymetrix) and scanned at the Center for Innovative Biomedical Resources (CIBR) Genomics Core Facility at the University of Maryland.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
Quality of hybridization was monitored, and raw data were extracted using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0). The overall chip performance was monitored using the Affymetrix Expression Console Software. The raw microarray profiling data was preprocessed and quartile-normalized using the Transcriptome Analysis Console Software.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: GD cells

label_protocol: 500 ng of total RNA was reverse transcribed to cDNA and biotinylated using the GeneChip WT PLUS Reagent Kit.

extract_protocol: Total RNA was extracted from macrophages using a Qiagen RNeasy Mini kit according to the manufacturer’s protocol. After processing with DNase and clean-up procedures, RNA samples were quantified and RNA purity and integrity were evaluated by OD 260/280 ratio and analyzed on an Agilent 2100 Bioanalyzer.

value: macrophages differentiated from iPSC lines derived from a patient with type 2 Gaucher disease (GD)

value: Untreated


title: KPS-B1 (CCSP)

description:
cc10.barcodes.txt
cc10.fragments.bed.gz
cc10.counts.txt.qz
cc10.peaks.txt

data_processing:
Fragmemt file and bam file were processed using 10x Cell Ranger ATAC
Peaks are called using MACS2
Peak count matrix are generated using chromVAR
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: Counts Data is indexed by genes (row), cell (column)
Supplementary_files_format_and_content: Fragments data contains fragment position (1-3 column), and assigned cell barcode (4th column)

source_name: lung adenocarcinoma

growth_protocol: Lung tumors were initiated in KP, KPS-HET and KPS mice through intratracheal instillation of adenoviral Cre recombinase driven by the SPC or CCSP promoters.

extract_protocol:
Moribund mice were sacrificed. Tumor-bearing lungs and macrometastases were enzymatically dissociated and cancer cells were isolated through FACS.
Libraries are contructed using combinatorial sciATAC-seq and droplet-based scATAC-seq protocols.

value: lung adenocarcinoma

value: isolated cancer cells from lungs of KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/fl mice infected with adenoviral Cre

value: mixed B6;129S2


title: Control-1


title: GD-rep1


title: 85-PBMC


title: Blood-IP-R2

first: Yan

last: Li

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

description: IP sample: denaturate 20 minutes

data_processing:
library strategy: Tn5 assisted MeRIP-seq
Reads aligned to genome (hg19) using HISAT (version 2.1.0) with default parameters, converted to BAM file using SamTools, then sorted BAM file using SamTools.
m6A enriched region were detected by exomePeak2 R package, processed across 2 replicates.RNA-Seq data(no IP, input RNA) in the same condition was used as input information
Transcripts reads count were detected by featurecounts.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: human peripheral blood cells

extract_protocol:
Total RNA extraction, TRIzol reagent (Thermo Fisher Scientific, catalog no. 15596026) was used to cell suspension following the standard protocol. Cell lysate, the cells were resuspended in 3μL 0.2% (vol/vol) Triton X-100 (Sigma-Aldrich, cat. no. T9284) lysis buffer with 0.2 μL of Recombinant ribonuclease inhibitor. The lysate was incubated at 72 °C for 3 min and immediately put back on ice. Blood sample, red blood cells was removed by Red Blood Cell Lysis Buffer (Roche, cat. no. 11814389001). The total RNA was extracted using TRIzol reagent.
For library preparation, all reactions were performed in one tube and followed the protocol of TruePrep® RNA Library Prep Kit for Illumina (Vazyme, cat. no. TR501-01) with some modifications. The m6A MeRIP experiments were performed following the recommendations from the EpiMark N6-Methyladenosine Enrichment Kit (NEB #E1610) with some modifications.

value: blood cells

tag: tissue source

value: peripheral blood

tag: sample type

value: RNA IP against m6A

tag: denaturation time

value: 20 minutes


title: KPS-HET-B2 (CCSP)

tag: tissue

value: isolated cancer cells from lungs of KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/+ mice infected with adenoviral Cre


title: 83-PBMC


title: Blood-input-R2

description: Input sample

value: no IP (input RNA)

value: no


title: Input library

description: Supplemental_table_1_Essential_gene_analysis.xlsx


title: Blood-IP-R1

description: IP sample: denaturate 20 minutes


title: KP-B2 (CCSP)

value: isolated cancer cells from lungs of KrasLSL-G12D/+; Trp53fl/fl; Smarca4+/+ mice infected with adenoviral Cre


title: Blood-input-R1

description: Input sample


title: TC4886

value: Spleen

value: leukemic B cells


title: Control+C5a-rep2

source_name: control cells treated with C5a

value: macrophages differentiated from iPSC lines derived from healthy controls


title: No drug control library

value: outgrowth for 6 hours in LB


title: TCA0501

value: E{mu}-TCL1 CD19Cre/WTAHRfl/fl


title: MDA-MB-231 shS100A10_5 rep2

city: Nagoya

first: Nishimura

last: Tatsunori

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Graduate School of Medicine

institute: Nagoya University

description: Gene expression of cell

hyb_protocol: cDNA was hybridized to Clarion S array (ThermoFisher Scientific) using the GeneChip WT PLUS Reagent Kit and the GeneChip Hybridization, Wash and Stain Kit (ThermoFisher Scientific).

scan_protocol: The array chips were scanned immediately after washing with GeneChip Scanner 3000 7G (ThermoFisher Scientific).

data_processing:
Raw data (CEL files) were processed with Transcriptome Analysis Console (TAC) 4.0.2 (TheromoFisher SCIENTIFIC).
The data (21448 probes) were filtered manually as follow. The probes, which showed values lower than the back-round in all samples were excluded (the number became 19605 probes). Then, one probe was selected among probes which detect expression of same gene by original perl script. Briefly, the values of all samples were averaged, and the one which showed highest value was chosen. If the averages were same, the probe which showed lower coefficient of variance (CV) was chosen (the number of probes became 18130 probes). Thereafter the probes which detect multiple genes were omitted (the number of probes became 18130 probes). Finally the probes which showed CV higher than 50% in any conditions were excluded; as a total, mRNA expression of 16965 genes were obtained.

label: biotin and streptavidin phycoerythrin

label_protocol: cDNA samples were labeled with a proprietary DNALabeling Reagent that is covalently linked to biotin using GeneChipTM WT Plus Reagent Kit for Cartridge Array (ThermoFisher Scientific) according to the manufacturer's instructions.

growth_protocol: 10% FBS RPMI1640 + penicillin/streptomycin + 2.5ug/ml puromycin

extract_protocol: total RNA was extracted using PureLink RNA mini kit (ThermoFisher Scientific) according to the manufacturer's instructions.

value: breast cancer

value: S100A10 knock-downed


title: 81-Basal

value: MAIT cells

value: Decidua basalis


title: TC0341


title: GD+C5a-rep2

source_name: GD cells treated with C5a

value: macrophages differentiated from iPSC lines derived from a patient with type 2 Gaucher disease (GD)


title: KPS-B1 (SPC)

description:
spc.barcodes.txt
spc.fragments.bed.gz
spc.counts.txt.qz
spc.peaks.txt

value: lung adenocarcinoma

value: isolated cancer cells from lungs of KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/fl mice infected with adenoviral Cre

value: mixed B6;129S2


title: KPS-HET-B2 (SPC)

value: isolated cancer cells from lungs of KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/+ mice infected with adenoviral Cre


title: TCA4771


title: Control-rep2

source_name: control cells

value: Untreated


title: KP-B1 (CCSP)


title: SMARCA4_23_KO_CnR

description: SMARCA4 CUT&RUN

value: KrasG12D/+; Trp53-/-; Smarca4-mutant


title: 482 (PDX)

description:
pdx.barcodes.txt
pdx.fragments.bed.gz
pdx.counts.txt.qz
pdx.peaks.txt

source_name: PDX lung adenocarcinoma


title: SPC-pool

value: isolated cancer cells (pooled) from metastasis of KrasLSL-G12D/+; Trp53fl/fl; Smarca4+/+,  KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/+ and KrasLSL-G12D/+; Trp53fl/fl; Smarca4fl/fl mice infected with adenoviral Cre


title: KPS-HET-B1 (CCSP)


title: KPS-B2 (SPC)


title: KPS-B3 (SPC)


title: KP-B1 (SPC)

value: isolated cancer cells from lungs of KrasLSL-G12D/+; Trp53fl/fl; Smarca4+/+ mice infected with adenoviral Cre


title: KP-B2-M4 (SPC)

value: isolated cancer cells from lungs and metastasis of KrasLSL-G12D/+; Trp53fl/fl; Smarca4+/+ mice infected with adenoviral Cre


title: 146 (PDX)


title: 920 (PDX)


title: BC24h: sampling B control 24h

status: Public on Sep 06 2021

city: São Paulo

first: Caroline

middle: Giacomelli

last: Soares

state: SP

address: Av. Lineu Prestes 580, Bloco 14

department: Department of Food Science and Experimental Nutrition

country: Brazil

institute: School of Pharmaceutical Sciences, University of São Paulo

data_processing:
Libraries were paired-end sequenced using  HiSeq SBS Kit v4 on the HiSeq2500 system (Illumina).
Raw RNA-seq data was checked for its quality through FastQC software and filtered by SeqyClean
Alignment of the reads was performed by the software STAR along with the count of the reads uniquely aligned
Data was normalized by DeSeq2 R package
Genome_build: Papaya1.0, GCF_000150535.2
Supplementary_files_format_and_content: table include normalized data for each sample

organism: Carica papaya

source_name: pulp

extract_protocol:
The total RNA of the fruits pulp was isolated using Concert ™ Plant RNA Reagent (Invitrogen®) and purified by treatment with the DNA-free ™ kit (Invitrogen®), following the protocol described by the manufacturer.
Libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Protocol

treatment_protocol: Treated samples were treated with 100-ppm ethylene for 12 hours in a closed system

value: pulp


title: AC24h: sampling A control 24h


title: KPS-B2 (CCSP)


title: CC24h: sampling C control 24h


title: CT12h: sampling C ethylene-treated 12h


title: KPS-HET-B1 (SPC)


title: 337 (PDX)


title: BT24h: sampling B ethylene-treated 24h


title: CC12h: sampling C control 12h


title: BC12h: sampling B control 12h


title: 68 (PDX)


title: AC12h: sampling A control 12h


title: BT12h: sampling B ethylene-treated 12h


title: CT24h: sampling C ethylene-treated 24h


title: AT24h: sampling A ethylene-treated 24h


title: AC0h: sampling A control 0h


title: AT12h: sampling A ethylene-treated 12h


title: BC0h: sampling B control 0h


title: CC0h: sampling C control 0h


title: RWPE1_2D_DHT_rep2

city: London

first: Isabella

last: Barbutti

address: 1 Midland Rd

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Concatenating sequences from two lanes: Concatenate datasets tail-to-head (Galaxy Version 1.0.0) - this step was performed for raw data as well
Renaming sequences: Rename sequences (Galaxy Version 0.0.14+galaxy0)
Removing adapters and low-quality sequences: Trim Galore! Quality and adapter trimmer of reads (Galaxy Version 0.4.3.1). Paired-end, automatic detection of sequences to be trimmed, phred quality score threshold 20, -- length 5
Mapping: Bowtie2 - map reads against reference genome (Galaxy Version 2.3.4.3 +galaxy0). –I 0 –X2000 --fr --dovetail --very-sensitive, hg38full
Removing duplicates: MarkDuplicates examine aligned records in BAM datasets to locate duplicate molecules (Galaxy Version 2.18.2.2)
Removing mitochondrial DNA/read pairs overlapping ENCODE Blacklisted regions: bedtools Intersect intervals find overlapping intervals in various ways (Galaxy Version 2.29.0). Report only those alignments that **do not** overlap with file(s) B TRUE
Adjusting read start sites: alignmentsieve Filter BAM/CRAM files according to specified parameters (Galaxy Version 3.0.2.0). --ATACshift, Output in BEDPE format TRUE
Peak calling: MACS2 callpeak Call peaks from alignment results (Galaxy Version .1.1.20160309.6). --format BED --gsize '2700000000' --nolambda --keep-dup 'all' --bdg --pvalue '0.01' --nomodel --extsize '200' --shift '-100'
Generating bigwig tracks: Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.1)
Genome_build: hg38
Supplementary_files_format_and_content: un-normalised coverage of filtered fragments (reconstructed, duplicate-filtered fragments: see above)

growth_protocol: Cells were cultured in Keratinocyte SFM supplemented with BPE and EGF

extract_protocol:
Assay for transposase accessible chromatin using sequencing (ATAC-seq) was performed as previously described (Buenrostro, 2013) on single cell suspensions. 75000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) at 37°C for 30 minutes. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext High-Fidelity 2x PCR Mastermix (NEB) and the custom primers as published in Buenrostro, 2013. ATAC-seq libraries profiles were visualized using the 12000 DNA assay kit (Agilent) in the Bioanalyzer 2100. The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

treatment_protocol: 0.01 nM DHT was added to the media at 0h, 2h and 4h time points, and cells were collected at 5h time point. Control cells were treated with vehicle (ethanol).

value: Epithelial cells derived from the peripheral zone of a histologically normal adult human prostate

value: DHT for 5 hours


title: RWPE1_2D_DHT_rep1


title: SR_2258_005

city: Kagoshima

first: Yuto

last: Hozaka

address: 8-35-1 Sakuragaoka

department: Digestive Surgery, Breast and Thyroid Surgery

institute: Kagoshima University

data_processing:
Illumina Casava v1.8 2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence using cutadapt v.1.2.1, then mapped to whole genome using bowtie v1.0.0 with parameters -p 4 -S-q-n 1- e 80 -l 30 -a -m 5 --best --strata
The location information of mapping reads was compared with miRBase, Rfam, iGenomes. Annotations were added to reads and distribution of a variety of RNA reads was made up.
The reads mapped in the known miRNAs were counted with Hiseq-count.
The expression levels of miRNAs among samples and groups were compared by edgeR.
Heatplus was used for clustering analysis and creating heatmaps.
Genome_build: hg 19

source_name: colorectal cancer tissues

extract_protocol:
Flesh frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Small RNA Sample Preparation Kit  was used for the construction of sequencing libraries.
miRNA libraries were prepared for sequencing using standard Illumina protocols

value: colon


title: SR_2258_019

source_name: noncancerous tumor-adjacent tissues


title: SR_2258_004


title: SR_2258_001

value: rectum


title: GD+C5a-rep1


title: SR_2258_002


title: SR_2258_020


title: SR_2258_003


title: RWPE1_2D_rep1

value: untreated


title: SR_2258_017


title: SR_2258_016


title: SR_2258_018


title: Data Set 4 AstroTRAPg_20

first: Rob

last: Jackson

state: Massachusetts

address: 136 Harrison Ave.

institute: Tufts University

description:
AstroTRAPg_20
ribosome-bound RNA

data_processing:
base calling: Illumina HiSeq 2000 system
adapter trimming: fastx 0.0.13: fastx_clipper -Q33 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC
alignment: tophat 2.0.9, bowtie2.1.0, samtools 0.1.19: tophat -a 5 -p 12
Counting aligned reads per gene: HTSeq-count 0.6.1
Genome_build: BDGP6
Supplementary_files_format_and_content: text files; counts of mapped reads

organism: Drosophila melanogaster

source_name: Drosophila astrocytes

growth_protocol: Flies were maintained in LD 12:12 and then transferred to DD for timed collections

extract_protocol:
TRAP methods were used to immunoprecipitate ribosomes and bound RNA cargoes from astrocytes of the adult fly head. RNA was extracted using standard procedures for use in library preparation.
Illumina TruSeq v2 kits were employed for library construction. Samples were bar-coded to facilitate sequencing.

value: astrocytes

value: adult brain


title: Data Set 4 AstroTRAPg_40

description:
AstroTRAPg_40
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_44

description:
AstroTRAPg_44
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_32

description:
AstroTRAPg_32
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_28

description:
AstroTRAPg_28
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_16

description:
AstroTRAPg_16
ribosome-bound RNA


title: RWPE1_2D_rep2


title: Data Set 4 AstroTRAPg_12

description:
AstroTRAPg_12
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_08

description:
AstroTRAPg_08
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_24

description:
AstroTRAPg_24
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_36

description:
AstroTRAPc_36
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_44

description:
AstroTRAPc_44
ribosome-bound RNA


title: Control-rep1

value: macrophages differentiated from iPSC lines derived from healthy controls


title: Data Set 4 AstroTRAPg_04

description:
AstroTRAPg_04
ribosome-bound RNA


title: MDA-MB-231 shNCT rep1

description: Gene expression of cell

value: breast cancer

value: control


title: MDA-MB-231 shNCT rep2

description: Gene expression of cell


title: MDA-MB-231 shS100A10_1 rep1

description: Gene expression of cell

value: S100A10 knock-downed


title: MDA-MB-231 shS100A10_1 rep2

description: Gene expression of cell


title: Data Set 3 AstroTRAPc_32

description:
AstroTRAPc_32
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_24

description:
AstroTRAPc_24
ribosome-bound RNA


title: Control+C5a-rep1


title: Data Set 3 AstroTRAPc_28

description:
AstroTRAPc_28
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_08

description:
AstroTRAPc_08
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_12

description:
AstroTRAPc_12
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_36

description:
AstroTRAPg_36
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_40_S8_R1_001

description:
SA_TRAP_run2-astroTRAPa_40_S8_R1_001
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_32_S7_R1_001

description:
SA_TRAP_run2-astroTRAPa_32_S7_R1_001
ribosome-bound RNA


title: MDA-MB-231 shS100A10_5 rep1

description: Gene expression of cell


title: Data Set 3 AstroTRAPc_40

description:
AstroTRAPc_40
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_16

description:
AstroTRAPc_16
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_20

description:
AstroTRAPc_20
ribosome-bound RNA


title: Data Set 4 AstroTRAPg_00

description:
AstroTRAPg_00
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_08_S1_R1_001

description:
SA_TRAP_run2-astroTRAPa_08_S1_R1_001
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_44_S9_R1_001

description:
SA_TRAP_run2-astroTRAPa_44_S9_R1_001
ribosome-bound RNA


title: Data Set 1 astroTRAPb_28

description:
astroTRAPb_28
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPb_20_S12_R1_001

description:
SA_TRAP_run2-astroTRAPb_20_S12_R1_001
ribosome-bound RNA


title: Data Set 1 astroTRAPa_40

description:
astroTRAPa_40
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_00_S2_R1_001

description:
SA_TRAP_run2-astroTRAPa_00_S2_R1_001
ribosome-bound RNA


title: Data Set 1 astroTRAPb_04

description:
astroTRAPb_04
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_24_S6_R1_001

description:
SA_TRAP_run2-astroTRAPa_24_S6_R1_001
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_00

description:
AstroTRAPc_00
ribosome-bound RNA


title: Data Set 1 astroTRAPa_00

description:
astroTRAPa_00
ribosome-bound RNA


title: Data Set 2 AstroTRAPe_16

description:
AstroTRAPe_16
ribosome-bound RNA


title: Data Set 1 astroTRAPa_32

description:
astroTRAPa_32
ribosome-bound RNA


title: Data Set 3 AstroTRAPc_04

description:
AstroTRAPc_04
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPb_04_S3_R1_001

description:
SA_TRAP_run2-astroTRAPb_04_S3_R1_001
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPa_36_S11_R1_001

description:
SA_TRAP_run2-astroTRAPa_36_S11_R1_001
ribosome-bound RNA


title: Data Set 1 astroTRAPa_36

description:
astroTRAPa_36
ribosome-bound RNA


title: Data Set 1 astroTRAPb_20

description:
astroTRAPb_20
ribosome-bound RNA


title: Data Set 2 SA_TRAP_run2-astroTRAPb_12_S4_R1_001

description:
SA_TRAP_run2-astroTRAPb_12_S4_R1_001
ribosome-bound RNA


title: Data Set 1 astroTRAPa_08

description:
astroTRAPa_08
ribosome-bound RNA


title: Data Set 1 astroTRAPa_24

description:
astroTRAPa_24
ribosome-bound RNA


title: Data Set 1 AstroTRAPd_16

description:
AstroTRAPd_16
ribosome-bound RNA


title: MO-9-GMP

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

country: France

institute: APHP Hôpital Robert Debré

data_processing:
Full Fastq files were aligned to the reference human genome hg19/GRCh37 with tophat2 (-p 24 -r 150 -g 2 --library-type fr-firststrand)
Gene expressionwas quantified using the full Gencode v26lift37. We used HTSeq (Anders et al., 2015) to obtain the number of reads associated to each gene in the Gencode v26lift37 database (restricted to protein-coding genes, antisense and lincRNAs).
Bioconductor DESeq package (Anders and Huber, 2010) was used to import raw HTSeq counts for each sample into R statistical software and extract the count matrix.
After normalizing for library size, the count matrix was normalized by the coding length of genes to compute FPKM scores (number of fragments per kilobase of exon model and millions of mapped reads).
Only smples without abnormally elevated numbers of genes FPKM>2 or <0.5 are were used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: raw counts in txt format
Supplementary_files_format_and_content: FPKM table in txt formal

source_name: Bone Marrow

extract_protocol:
total RNA was extracted from mononuclear cells or sorted HSPC (1000 to 10000 cells) using the RNeasy Mini or Micro Kit (Qiagen).
Libraries were prepared with TruSeq® Stranded Total RNASample preparation kit (Illumina) according to supplier’s recommendations. Briefly the ribosomal RNA fraction was removed from 1μg of total RNA using the Ribo-Zero™ Gold Kit (Epicentre). Fragmentation was then achieved using divalent cations under elevated temperature to obtain approximately 300bp pieces. Double strand cDNA synthesis was performed using reverse transcriptase and random primers, Illumina adapters were ligated and cDNA library was PCR amplified for sequencing. Paired-end 75b sequencing was then carried out on a HiSeq4000 (Illumina).

treatment_protocol: CD34+ cells were selected from mononucleated cells using the Easysep Human CD34 positive selection kit and Easysep magnet (StemCell Technologies, Vancouver, Canada) following the manufacturer's instructions. Cells were phenotyped on a BD FACSCantoTM II analyzer (BD Biosciences) using marker combinations that have been validated in fetal and adult bone marrow (Notta et al., 2011, 2016): HSC CD34+CD38-CD45RA-CD90+, MPP CD34+CD38-CD45RA-CD90-CD49f-, CMP CD34+CD38+CD45RA-CD135+, GMP CD34+CD38+CD45RA+CD135+ and MEP CD34+CD38+CD45RA-CD135- .

value: Bone Marrow

tag: disease state

value: healthy children

value: Sorted GMP

value: WT


title: Data Set 1 astroTRAPa_44

description:
astroTRAPa_44
ribosome-bound RNA


title: MO-6-MEP

value: Sorted MEP


title: Data Set 1 astroTRAPb_12

description:
astroTRAPb_12
ribosome-bound RNA


title: MO-9-MEP


title: MO-24-CSH

value: Sorted HSC


title: MO-05-MEP


title: MO-06-CSH


title: MO-23-CSH


title: MO-04-GMP


title: MO-05-CSH


title: MO-27-MPP

value: Sorted MPP


title: LMMJ-20-MEP

value: PTPN11 mutated


title: MO-05-CMP

value: Sorted CMP


title: Data Set 2 SA_TRAP_run2-astroTRAPb_28_S5_R1_001

description:
SA_TRAP_run2-astroTRAPb_28_S5_R1_001
ribosome-bound RNA


title: LMMJ-24-CMP


title: MO-04-CMP


title: LMMJ-20-GMP


title: MO-6-CMP


title: MO-04-CSH


title: MO-6-GMP


title: LMMJ-20-CMP


title: LMMJ-24-MEP


title: LMMJ-15-CMP


title: MO-05-GMP


title: LMMJ-15-MPP


title: LMMJ-15-MEP


title: LMMJ-24-GMP


title: mRNA - Embryos stage 24- stage 30 rep 1

city: Mancheste

first: Llilians

last: Calvo

address: Oxford Rd

institute: University of Manchester

data_processing:
small RNA:
Adaptors were removed and read ranging from 18 to 26 nucleotides were kepts using Cutadapt v. 1.18
tRNAs were predicted using tRNAscan-SE (v2.0; option -e)
Reads were mapped to tRNAs and rRNAs and only unmapped reads were kept using Bowtie (v1.1.1)
Reads were mapped to Parhyale predicted microRNAs using Bowtie (v1.1.1)
Quantification was performed using salmon quant from salmon (v0.14.1) (37) in alignment mode
polyA RNA
Paired-end RNA-seq reads from each developmental library were mapped to the Parhyale genome STAR (v2.7.2b)
To quantify mRNAs, reads mapped to the genome and to annotated Parhyale transcripts were quantified using salmon quant from salmon (v0.14.1) in mapping base mode
Genome_build: GCA_001587735.2 Phaw_5.0
Supplementary_files_format_and_content: Tab-delimited sf files include RPM (small RNA) or TPM values for each sample as generated from salmon

organism: Parhyale hawaiensis

source_name: Parhyale hawaiensis pooled staged embryos

growth_protocol: Animals (Parhyale hawaiensis) were reared in standard plastic aquarium tanks containing artificial sea water (aquarium salt and deionised water) at a salinity of 30 PPT, and kept at ∼26◦C.

extract_protocol:
Embryos were extracted from females anaesthetised using clove oil (Sigma) diluted 1:10000 in sea water. Embryos were washed in filtered seawater and manually staged using a Leica Stereo Fluorescence microscope. Isolated embryos were stored in RNAlater (Sigma) and total RNA was then extracted using the SPLIT RNA Extraction Kit (Lexogen) following the manufacturer’s instructions.
Small RNA libraries (4 replicates per time-point) were built using the Small RNA-Seq Library Prep Kit (Lexogen). Long library fragments and linker-linker artefacts were removed using a purification module with magnetic beads (Lexogen). Long mRNA libraries (2 replicates per time-point) were built using the TruSeq Stranded mRNA HT Sample Prep Kit (Illumina).

value: laboratory strain - wild type

tag: age

value: Embryos stage 24- stage 30


title: LMMJ-15-CSH

value: untreated


title: MO-04-MEP


title: LMMJ-20-MPP


title: LMMJ-07-MEP


title: LMMJ-07-GMP


title: mRNA - Embryos stage 21- stage 23 rep 2

value: Embryos stage 21- stage 23


title: mRNA - Embryos stage 21- stage 23 rep 1


title: LMMJ-07-CMP


title: mRNA -  Embryos stage 17 rep 2

value: Embryos stage 17


title: mRNA - Embryos stage 24- stage 30 rep 2


title: LMMJ-15-GMP


title: mRNA - Embryos stage 17 rep 1


title: mRNA - Embryos stage 14 rep 2

value: Embryos stage 14


title: mRNA - Embryos stage 14 rep 1


title: PSO38B-04T-LS-019_N715-S506_S35_L005_R

city: San Francisco

first: Wilson

last: Liao

state: CA

address: 2340 Sutter St.

department: Dermatology

institute: University of California, San Francisco

data_processing:
Mapping to GRCh38 performed using STAR v2.4.2a
Raw gene counts calculated using HTSeq v0.6.1p1  on the GENCODE 25 annotation of GRCh38
Samples with < 1 million reads, < 10,000 detected genes, or < 60% mappable reads were excluded
Genes expressed at < 5 reads in fewer than 20% of samples were excluded
Genome_build: GRCh38
Supplementary_files_format_and_content: CountData_SecukinumabPsoRnaSeq_20210324.tsv  (Matrix table with raw gene counts for every gene and every sample)

source_name: skin

extract_protocol:
Sequencing libraries were constructed using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech cat. 634894). Bulk RNA was extracted from whole skin tissue using Qiagen RNeasy fibrous tissue mini kit (cat. 74704). Reverse transcription was performed on poly-adenylated RNA from cell lysate for up to 1,000 cells followed by second strand synthesis to make full length cDNA. cDNA was then later amplified by PCR using cycle numbers determined by cell numbers. Amplified cDNA was purified by AMPure XP beads (Beckman Coulter) and followed by Qubit quantification.
Sequencing libraries were constructed using the Illumina Nextera DNA kit with 0.4 ng of amplified cDNA for sorted lymphocytes and 0.3 ng for cDNA synthesized from bulk skin RNA.

tag: sequencing batch

tag: sequencing lane

value: bulk

tag: subject id

value: lesion

tag: clinical status

tag: sorted cells

tag: used for analysis

value: TRUE


title: mRNA - Embryos stage 8- stage 11 rep 2

value: Embryos stage 8- stage 11


title: PSO38B-04T-LS-019_N714-S505_S34_L005_R

tag: cell type


title: mRNA - Embryos stage 6 rep 1

value: Embryos stage 6


title: LMMJ-04-CMP

value: Bone Marrow

tag: treatment

tag: cell line


title: mRNA - Embryos stage 6 rep 2

tag: strain/genotype


title: LMMJ-04-CSH


title: PSO38B-04T-LS-019_N712-S503_S33_L005_R

value: Teff


title: LMMJ-04-MEP

value: Sorted MEP


title: PSO38B-04T-LS-019_N710-S511_S39_L005_R


title: PSO38B-04T-LS-019_N711-S502_S32_L005_R

value: Treg


title: mRNA - Embryos stage 1- stage 4 rep 2

value: Embryos stage 1- stage 4

tag: molecule subtype

value: small RNA


title: PSO38B-04T-LS-019_N707-S510_S38_L005_R

value: FALSE


title: LMMJ-04-GMP

tag: tissue source

value: Sorted GMP

value: PTPN11 mutated


title: PSO38B-04T-LS-019_N705-S507_S36_L005_R


title: PSO38B-04T-LS-019_N706-S508_S37_L005_R


title: mRNA - Embryos stage 1- stage 4 rep 1

value: laboratory strain - wild type


title: small RNA -  Embryos stage 21- stage 23 rep 4

value: Embryos stage 21- stage 23


title: PSO38A-04T-LS-019_N706-S508_S29_L004_R


title: PSO38A-04T-LS-019_N707-S510_S30_L004_R


title: small RNA -  Embryos stage 24- stage 30 rep 3

value: Embryos stage 24- stage 30


title: mRNA - Embryos stage 8- stage 11 rep 1


title: small RNA -  Embryos stage 21- stage 23 rep 3


title: PSO38A-04T-LS-019_N705-S507_S28_L004_R


title: small RNA -  Embryos stage 24- stage 30 rep 4


title: small RNA -  Embryos stage 21- stage 23 rep 2


title: PSO38A-04T-LS-019_N704-S506_S27_L004_R

value: bulk


title: PSO38A-04T-LS-019_N703-S505_S26_L004_R

value: lesion


title: small RNA -  Embryos stage 17 rep 4

value: Embryos stage 17


title: small RNA -  Embryos stage 17 rep 3


title: PSO38A-04T-LS-019_N701-S502_S24_L004_R

value: TRUE


title: small RNA -  Embryos stage 21- stage 23 rep 1


title: PSO38A-04T-LS-019_N710-S511_S31_L004_R


title: PSO38A-04T-LS-019_N702-S503_S25_L004_R


title: small RNA -  Embryos stage 24- stage 30 rep 2


title: small RNA -  Embryos stage 17 rep 2


title: small RNA -  Embryos stage 24- stage 30 rep 1


title: small RNA -  Embryos stage 17 rep 1


title: PSO36B-04T-MF-17_N712-S503_S17_L003_R


title: small RNA -  Embryos stage 14 rep 3

value: Embryos stage 14


title: PSO36B-04T-MF-17_N715-S506_S19_L003_R


title: PSO36B-04T-MF-17_N714-S505_S18_L003_R


title: PSO36B-04T-MF-17_N711-S502_S16_L003_R


title: small RNA -  Embryos stage 14 rep 4


title: PSO36B-04T-MF-17_N707-S510_S22_L003_R


title: small RNA -  Embryos stage 14 rep 2


title: small RNA -  Embryos stage 14 rep 1