title: PatientID:913 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE212493_12


title: PatientID:297 visit: I-WEEK 0

status: Public on Nov 08 2022

type: RNA

city: Spring House

first: Patrick

last: Branigan

state: PA

address: 1400 McKean Road

country: USA

institute: Johnson and Johnson

description:
WB-mRNA
Gene expression data from WB-RNA
XE250703_16

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA expression measure was computed from CEL files interpreted through Brainarray custom CDF pd.hugene21st.hs.entrezg

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Homo sapiens, WB-mRNA

label_protocol: standard Affymetrix protocol

extract_protocol: mRNA was extracted from whole blood collected in PAXgene tubes according to the manufacturer's instructions.

treatment_protocol: Patients received a single intravenous dose of ustekinumab or placebo at week 0 and blood samples were collected at week 0, week 6 and week 8

tag: patientid

tag: visit

value: I-WEEK 0

tag: treatment

value: Placebo

tag: remwk8_i (clinical_remission_week_8)

value: N

tag: crp


title: PatientID:581 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE094743_12

value: I-WEEK 6

value: Ustekinumab


title: PatientID:487 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE179364_12


title: PatientID:70 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE603072_16

value: Y


title: PatientID:268 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE232533_16


title: PatientID:698 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE006463_12


title: PatientID:829 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE212443_16


title: PatientID:415 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE180353_13


title: PatientID:925 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE390304_12


title: PatientID:107 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XF053723_16


title: PatientID:604 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE006423_16


title: PatientID:604 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XE006454_13


title: PatientID:698 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE006413_17


title: PatientID:564 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XE881607_12

value: M-WEEK 8


title: PatientID:930 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XH868866_13


title: PatientID:142 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE250672_16


title: PatientID:307 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD893974_12


title: PatientID:913 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD896775_16


title: PatientID:66 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD987363_16


title: PatientID:229 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD873927_12


title: PatientID:246 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XE003062_16


title: PatientID:64 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD987352_16


title: PatientID:924 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD927714_12


title: PatientID:487 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD785804_13


title: PatientID:256 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD707574_12


title: PatientID:773 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD762215_12


title: PatientID:487 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD829083_17


title: PatientID:289 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD827313_12


title: PatientID:829 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XD896845_13


title: PatientID:357 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD544118_12


title: PatientID:522 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD629295_17


title: PatientID:96 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD685188_12


title: PatientID:677 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD432475_13


title: PatientID:631 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XD442084_13


title: PatientID:858 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XD198915_12


title: PatientID:406 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD253906_16


title: PatientID:206 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD174086_16


title: PatientID:268 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD241653_12


title: PatientID:344 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD685189_12


title: Neutrophils murine bone marrow replicate 3

type: genomic

city: Heidelberg

first: Maximilian

last: Schönung

address: Im Neuenheimer Feld 280

department: Division Translational Medical Oncology

country: Germany

institute: German Cancer Research Center (DKFZ) & National Center for Tumor Diseases (NCT) Heidelberg

hyb_protocol: Standard Illumina protocol for the Infinium Mouse Methylation BeadChip array performed at the German Cancer Research Center (DKFZ) Genomics and Proteomics Core Facility.

data_processing: Illumina Infinium Mouse Methylation BeadChip IDAT files were processed using the RnBeads Bioconductor software package. Background subtraction and intra-array dye bias normalization with an internal reference were performed. Unreliable probes (Greedycut algorithm with detection p-value < 0.01) and probes mapping to sex chromosomes were removed from the dataset.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: FACS-sorted bone marrow neutrophils

extract_protocol: Genomic DNA was isolated using a QIAamp DNA Micro Kit (QIAGEN) according to the manufacturer’s instructions.

tag: gender

value: Female

tag: tissue

value: Bone marrow

tag: cell type

value: Neutrophil


title: PatientID:255 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XD173127_12


title: PatientID:858 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD198855_17


title: JAK2-V617F mutant murine bone marrow replicate 1

scan_protocol: Standard Illumina protocol for the Infinium Mouse Methylation BeadChip array performed at the German Cancer Research Center (DKFZ) Genomics and Proteomics Core Facility.

source_name: Total bone marrow of JAK2-V617F mutant mice


title: Neutrophils murine bone marrow replicate 2

label_protocol: Standard Illumina protocol for the Infinium Mouse Methylation BeadChip array performed at the German Cancer Research Center (DKFZ) Genomics and Proteomics Core Facility.


title: Neutrophils murine bone marrow replicate 1


title: JAK2-V617F mutant murine bone marrow replicate 2


title: PatientID:241 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD095296_16


title: PatientID:443 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XD153506_12


title: PatientID:443 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD153477_16


title: Monocytes murine bone marrow replicate 3

source_name: FACS-sorted bone marrow monocytes

value: Monocyte


title: PatientID:344 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD174079_16


title: PatientID:383 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XD095297_16


title: PatientID:68 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XC967826_13


title: PatientID:75 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XC964619_12


title: Monocytes murine bone marrow replicate 1


title: B-cells murine bone marrow replicate 3

source_name: FACS-sorted bone marrow B-cells

value: B-cell


title: Monocytes murine bone marrow replicate 2


title: PatientID:81 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XC867439_12


title: PatientID:145 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XC816198_12


title: CD8+ T-cells murine bone marrow replicate 2

source_name: FACS-sorted bone marrow CD8+ T-cells

value: CD8+ T-cell


title: B-cells murine bone marrow replicate 1


title: CD8+ T-cells murine bone marrow replicate 3


title: CD45.1 murine bone marrow replicate 1

source_name: Total bone marrow of CD45.1 (B6.SJL-Ptprca Pepcb/BoyCrl) mice


title: PatientID:303 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB900402_12


title: CD4+ T-cells murine bone marrow replicate 3

source_name: FACS-sorted bone marrow CD4+ T-cells

value: CD4+ T-cell


title: CD45.2 murine bone marrow replicate 1

source_name: Total bone marrow of CD45.2 (C57BL/6J) mice


title: PatientID:240 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XC790317_16


title: PatientID:709 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB452844_12


title: PatientID:367 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB450921_12


title: CD8+ T-cells murine bone marrow replicate 1


title: GMP murine bone marrow replicate 2

source_name: FACS-sorted bone marrow granulocyte-monocyte progenitor cells

value: GMP


title: CD4+ T-cells murine bone marrow replicate 2


title: PatientID:480 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB415892_13


title: CMP murine bone marrow replicate 3

source_name: FACS-sorted bone marrow common myeloid progenitor cells

value: CMP


title: GMP murine bone marrow replicate 1


title: CD4+ T-cells murine bone marrow replicate 1


title: SAMPLE 11_x3D_MCF7_BP2

type: SRA

city: Singapore

first: Keng Hwee

last: Chiam

address: 30 Biopolis Street

country: Singapore

institute: Bioinformatics Institute

library_source: transcriptomic

data_processing:
For the first batch, the libraries were run with BGI group’s in-house sequencing platform BGISEQ-500 (20M single-end reads). For the second batch, libraries were run on NovaSeq 6000 (Illumina, USA) to produce 6GB of raw data per sample (20M paired-end reads).
Kallisto version 0.46.0 with a precalculated human index from the ARCHS4 repository was used to obtain transcript counts, which were then mapped to gene-level counts using tximport version 1.22.0 and the GrCH38.87 human genome annotation.
Assembly: GrCH38.87 human genome annotation
Supplementary files format and content: comma-separated values (CSV) file includes read count values for each Sample

source_name: MCF7 spheroids

extract_protocol:
Total RNA was extracted from MCF7 and MCF10A cells in both 2D and 3D cultures using RNeasy plus kits (Qiagen, Germany) according to manufacturer’s instructions. Briefly, cells grown as monolayer were trypsinized and washed with PBS twice followed by RNA extraction using RNeasy Plus Kit. To collect spheroids, medium was removed from 3D cell culture followed by washing with PBS twice gently. Pre-chilled cell recovery solution (Corning, USA) at the volume of 200 μl were added to 8-well chamber slide (Ibidi, Germany). Matrigel matrix was fully depolymerized, and spheroids were released after 30 minutes incubation at 4°C. Suspended spheroids were collected and washed with PBS twice followed by RNA extraction using RNeasy Plus Kit (Qiagen). The integrity and quantity of RNA were determined with NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA) before sending out for RNA sequencing.
Library construction was performed using NEBNext Ultra II RNA Library Prep Kit (Illumina, USA) according to manufacturer’s protocols

tag: cell line

value: MCF7 spheroids

tag: batch

value: Batch 1


title: PatientID:472 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB415723_12

value: Placebo


title: SAMPLE 9_x3D_MCF10A_BP3

source_name: MCF10A spheroids

value: MCF10A spheroids


title: PatientID:367 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB399122_16

value: I-WEEK 0

value: N


title: SAMPLE 8_x3D_MCF10A_BP2


title: SAMPLE 10_x3D_MCF7_BP1


title: PatientID:367 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB399192_12

value: I-WEEK 6

value: Ustekinumab


title: B-cells murine bone marrow replicate 2

value: Female


title: PatientID:989 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB395023_12


title: SAMPLE 7_x3D_MCF10A_BP1


title: GMP murine bone marrow replicate 3

value: Bone marrow


title: CMP murine bone marrow replicate 2


title: MEP murine bone marrow replicate 2

source_name: FACS-sorted bone marrow megakaryocyte–erythroid progenitor cells

value: MEP


title: PatientID:534 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB395013_12


title: PatientID:989 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB394943_16


title: PatientID:472 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB394313_13


title: SAMPLE 6_x2D_MCF7_BP3


title: MEP murine bone marrow replicate 1


title: SAMPLE 4_x2D_MCF7_BP1


title: SAMPLE 3_x2D_MCF10A_BP3


title: PatientID:859 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB393974_12


title: SAMPLE 5_x2D_MCF7_BP2


title: SAMPLE 2_x2D_MCF10A_BP2


title: PatientID:859 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB393823_17


title: MEP murine bone marrow replicate 3


title: PatientID:839 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB393303_12


title: PatientID:729 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB394023_13

value: Y


title: SAMPLE 1_x2D_MCF10A_BP1


title: HUVEC_12

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
TPM abundance estimates, generated with kallisto quant 0.4.6
Assembly: GRCh38.p13
Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.

source_name: Macrovascular endothelial cell

growth_protocol: iHCPEnC were grown at 37°C, 5% CO2 in Complete Classic MediumTM for endothelial cells without phenol red (Cell Systems, Kirkland, USA) and supplemented with 10% fetal bovine serum, and CultureBoostTM (Cell Systems, Kirkland, USA) containing growth factors, but without hydrocortisone, ascorbate and VEGF, and 1% penicillin/streptomycin (100 U/ml penicillin; 100µg/ml streptomycin). Cells were grown continuously under 0.5 µg/ml puromycin und passaged routinely weekly 1:4.

extract_protocol:
Total RNA was extracted from primary and immortalized human CP endothelial cells using RNeasy Mini kit (Qiagen, Germany)
RNA sequencing was performed according to the manufacturer's protocol (GenXPro GmbH, Germany). The cDNA synthesis was performed by reverse transcription starting from random hexamer oligonucleotides, followed by second strand synthesis and barcoding for Illumina sequencing, 2X 75bp PE of 20 Mio Reads/library.

value: HUVEC

value: Umbilcal vein endothelial cell


title: CMP murine bone marrow replicate 1


title: LSK murine bone marrow replicate 3

source_name: FACS-sorted bone marrow LSK (Lin- Sca1+ cKIT+) cells

value: LSK


title: HUVEC_11

value: Umbilical vein endothelia cell


title: LSK murine bone marrow replicate 2


title: HUVEC_10


title: HBMEC_8

source_name: Immortalized microvascular cell

value: HBMEC

value: Brain microvascular endothelial cell


title: LSK murine bone marrow replicate 1


title: HBMEC_7


title: HBMEC_9


title: iHCPEnC_6

source_name: Immortalized endothelial cell

value: iHCPEnC

value: Immortalized choroid plexus endothelial


title: PatientID:839 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB393273_16

source_name: Homo sapiens, WB-mRNA

value: Placebo


title: iHCPEnC_5


title: iHCPEnC_4


title: HCPEnC_3

source_name: Primary endothelial cells

value: HCPEnC

value: Choroid plexus endothelial cell


title: PatientID:273 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB374671_12

value: I-WEEK 6

value: N


title: HCPEnC_2


title: HCPEnC_1


title: PatientID:750 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB316514_13


title: PatientID:291 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB374702_12

value: Ustekinumab


title: PatientID:807 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB365224_16

value: I-WEEK 0


title: PatientID:741 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB316804_12

value: M-WEEK 8


title: PatientID:750 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB316815_13


title: PatientID:472 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB357171_17


title: PatientID:750 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB316474_16


title: PatientID:273 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB164471_16


title: PatientID:831 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB069584_17

value: Y


title: PatientID:263 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB169951_16


title: PatientID:291 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB164661_16


title: PatientID:536 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB170004_12


title: PatientID:824 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB069954_12


title: SMS-SAN shEZH1-2 rep 3

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to 8x60K whole human genome oligonucleotide microarray (Agilent G4851B), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays (SureScan G4900DA Microarray Scanner), and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: neuroblastoma cell line

label_protocol: Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Human NB cell line IMR32 and SMS-SAN were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Wako) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was extracted at 2 days after shEZH1-expressing lentiviral infection.

treatment_protocol: shCont (pLKO.1) control, shEZH1-1 (TRCN0000002439) or  shEZH1-2 (TRCN0000355735) vectors shRNA contained plasmids,  were purchased from the MISSION(TM) shRNA Library (Sigma-Aldrich). In the preparation of the shRNA/lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the shRNA plasmids and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 105 NB cells were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene.

value: SMS-SAN

tag: lentivirus


title: SMS-SAN shEZH1-1 rep 4


title: SMS-SAN shEZH1-2 rep 2


title: PatientID:875 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB090455_16


title: PatientID:949 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB066424_16


title: SAMPLE 12_x3D_MCF7_BP3

value: MCF7 spheroids

value: Batch 1


title: SMS-SAN shEZH1-2 rep 4


title: PatientID:893 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB090444_16


title: SMS-SAN shEZH1-2 rep 1


title: PatientID:263 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB450911_12


title: PatientID:824 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB069905_17


title: PatientID:741 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XB040595_16


title: SMS-SAN shEZH1-1 rep 2


title: SMS-SAN shEZH1-1 rep 3


title: PatientID:741 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XB040625_12


title: PatientID:263 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA980692_12


title: PatientID:534 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XB402902_13


title: PatientID:480 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA958462_12


title: PatientID:480 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA958442_17


title: SMS-SAN pLKO.1 rep 3

value: shCont (pLKO.1) control


title: PatientID:893 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA804728_13


title: PatientID:536 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA950342_16


title: SMS-SAN pLKO.1 rep 4


title: IMR32 shEZH1-2 rep 4


title: SMS-SAN pLKO.1 rep 1


title: SMS-SAN pLKO.1 rep 2


title: PatientID:839 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA802608_13


title: PatientID:528 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA944652_17


title: PatientID:832 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA802607_12


title: IMR32 shEZH1-2 rep 3


title: PatientID:824 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA761658_12


title: IMR32 shEZH1-1 rep 4


title: PatientID:528 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA786073_13


title: IMR32 pLKO.1 rep 4


title: PatientID:831 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA746037_13


title: IMR32 shEZH1-1 rep 1


title: IMR32 pLKO.1 rep 3


title: IMR32 shEZH1-1 rep 3


title: IMR32 shEZH1-1 rep 2


title: PatientID:291 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA800262_13


title: PatientID:831 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA760225_12


title: PatientID:335 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA744975_12


title: IMR32 shEZH1-2 rep 2


title: PatientID:528 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA779333_13


title: PatientID:776 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA779223_17


title: IMR32 shEZH1-2 rep 1


title: SMS-SAN shEZH1-1 rep 1


title: IDH1-mutated murine bone marrow cells, ivosidenib-resistant, Replicate3

city: Toronto

first: AlexCH

last: Liu

state: Ontario

address: 101 College Street

department: Medical Biophysics

country: Canada

institute: University of Toronto

data_processing:
Adapter sequences were trimmed using Trimmomatic.
Reads were mapped to mm10 reference genome by STAR (v2.5; mismatch=2, RRID:SCR_004463).
Raw counts were quantified by HTSeq (v0.6.1; -m union, RRID:SCR_005514).
Assembly: mm10
Supplementary files format and content: gene_count.csv: Comma-separated values of un-normalized gene counts.

source_name: Bone marrow

growth_protocol: Bone marrow cells from IDH1R132HNPM1c+ mice were gifted to us by the Mark Minden Lab (Princess Margaret Cancer Centre, University Health Network, Toronto, Canada). The bone marrow cells were cultured in X-VIVO 10 medium (Lonza, Cat# 04-380Q) supplemented with 20% (v/v) BIT 9500 serum substitute (Stem Cell Technologies, Cat # 09500), 2 mM Gluta-Plus (Wisent Bioproducts, Cat# 609-066-EL), and the following cytokines: 10 ng/mL hIL-6 (Peprotech), 10 ng/mL mIL-3 (Peprotech), 50 ng/mL mSCF (Peprotech), 50 ng/mL FLT3L (Peprotech) and 25 ng/mL TPO (Peprotech). Antimicrobial agents were not added to the culture medium.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plus Mini Kit.
NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

treatment_protocol: Ivosidenib (5uM) in culture for two months followed by a drug washout period.

value: Bone marrow

value: AML cells

tag: genotype

value: IDH1-R132H, NPM1c


title: IDH1-mutated murine bone marrow cells, ivosidenib-resistant, Replicate1

value: Ivosidenib (5uM) in culture for two months followed by a drug washout period


title: IMR32 pLKO.1 rep 2


title: IDH1-mutated murine bone marrow cells, ivosidenib-sensitive, Replicate3

value: Untreated


title: PatientID:709 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA744185_12

value: Placebo


title: IDH1-mutated murine bone marrow cells, ivosidenib-sensitive, Replicate2


title: IMR32 pLKO.1 rep 1


title: PatientID:709 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA639225_17


title: IDH1-mutated murine bone marrow cells, ivosidenib-resistant, Replicate2


title: PatientID:859 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA740778_13


title: IDH1-mutated murine bone marrow cells, ivosidenib-sensitive, Replicate1


title: PatientID:893 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA611948_13


title: PatientID:318 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA587197_12


title: PatientID:536 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA712014_13


title: PatientID:457 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA599027_12


title: PatientID:243 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA599029_12


title: P2D_H3K4me1

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

library_source: genomic

data_processing:
Bowtie2 to align sequencing reads
MACS2 to identify CUT&Tag peaks and calculate Signal Per Million Reads (SPMR)
Assembly: mm10
Supplementary files format and content: bigWig (bw)
Library strategy: CUT&Tag

source_name: Lung

growth_protocol: Advanced DMEM (Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (FBS, Sigma-Aldrich), GlutaMAX™ Supplement (Gibco, 35050061) and 1x Antibiotic-Antimycotic (Gibco, 15240062).

extract_protocol:
Chromatin immunoprecipitation using antibodies to enrich DNA fragments
The library was constructed with CUT&Tag-IT™ Assay Kit (cat. #53160, Active Motif) according to the manufacturer’s instructions

value: Lung

value: Yes

value: Lung squamous cell carcinoma cell line

value: chip antibody:H3K4me1 (ab8895)


title: PP_H3K4me3

value: chip antibody:H3K4me3 (ab8580)


title: PP_H3K4me1


title: PP_H3K27ac

data_processing:
Bowtie2 to align sequencing reads
MACS2 to identify ChIP-seq peaks and calculate Signal Per Million Reads (SPMR)
Assembly: mm10
Supplementary files format and content: bigWig (bw)

extract_protocol:
Chromatin immunoprecipitation using antibodies to enrich DNA fragments
The library was constructed with KAPA Hyper- Prep Kits (cat. #07962347001, Roche) according to the manufacturer’s instructions

value: chip antibody:H3K27ac (ab4729)


title: P2D_H3K27ac


title: P2D_ATAC-2

data_processing:
Bowtie2 to align sequencing reads
MACS2 to identify ATAC-seq peaks
Assembly: mm10
Supplementary files format and content: bigWig (bw)

extract_protocol:
Assay of transposase accessible chromatin-sequencing to identify the accecible regions on the genome
The library was constructed with Nextera DNA library Prep Kit (cat. #FC-121–1030, Illumina) according to the manufacturer’s instructions


title: P2D_H3K4me3


title: PP_ATAC-2


title: P2D_ATAC-1


title: P53_Kmt2d_tumor-2

data_processing:
Read qualities were evaluated using FASTQC (Babraham Institute) and mapping to mm10 reference genome using STAR program with default parameters
Read counts, TPM and FPKM were calculated using RSEM program 35.
Assembly: mm10
Supplementary files format and content: Tab-delimited gene-by-sample text file with raw gene counts for each sample.

source_name: Lung tumor

extract_protocol:
Cell pellets or tumor nodules were collected and then subjected to total RNA extraction using RNeasy Plus Mini Kit (QIAGEN, 74136) according to the manufacturer’s instructions.
Automated stranded RNA-seq library prep, polyA selection, following manufacturer's protocols.

value: Lung tumor

value: No

value: Lung squamous cell carcinoma tumor


title: PatientID:807 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA567218_12

value: M-WEEK 8

value: Ustekinumab

value: Y


title: PatientID:632 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA570084_12

value: N


title: PatientID:807 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA567539_13

value: I-WEEK 6


title: PatientID:729 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA512143_16

value: I-WEEK 0


title: PatientID:534 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA512504_17


title: PP_ATAC-1


title: P53_Kmt2d_tumor-1


title: PatientID:729 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA503714_13


title: P53_Pten_tumor-3


title: P53_Pten_tumor-2


title: P53_Kmt2d_tumor-3


title: PatientID:832 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA474338_13


title: PatientID:561 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA506323_16


title: PatientID:632 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA569823_13


title: SK-N-DZ shCont

hyb_protocol: 10 micro g of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacture's protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer's protocols.

data_processing: Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: SK-N-DZ, neuroblastoma cell line, mock, shCont

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 2 micro g of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer's protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: Human NB cell lines were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Wako) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was extracted at 8-14 days after shBMI1-expressing lentiviral infection.

treatment_protocol: shCont (pLKO.1) control, shBMI1-1 (TRCN0000020156) vectors shRNA contained plasmids,  were purchased from the MISSION(TM) shRNA Library (Sigma-Aldrich). In the preparation of the shRNA/lentivirus, the packaging cell line HEK 293T (4 × 10^6) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the shRNA plasmids and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene HD transfection reagent (Promega) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 105 NB cells were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene.

value: SK-N-DZ


title: PatientID:540 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA506332_17


title: SK-N-DZ shBMI1-1

source_name: SK-N-DZ, neuroblastoma cell line, shBMI1-1


title: SK-N-BE shBMI1-1

source_name: SK-N-BE, neuroblastoma cell line, shBMI1-1

value: SK-N-BE


title: Dre 2 IP

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description: 2 males, 1 female pooled

data_processing:
After validation (Agilent 2200 TapeStation) and quantification (Invitrogen Qubit System), transcriptome libraries of matching samples were pooled. Pools were quantified via Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on an Illumina HiSeq 4000 sequencing instrument with a 2 × 75-bp paired-end read length protocol.
We applied the community-curated nfcore rnaseq analysis pipeline (version 3.0) (https://nf-co.re/ rnaseq).
The gene-level quantification was carried out using Salmon (version 0.14.1) using the reference genome GRCm38
Differential analysis between ribosomal pulldown (IP) and the hypothalamic background (Input) using differential gene expression analysis with the DESeq2 R package 1.26.0
Assembly: GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Supplementary files format and content: Excel sheet of DESeq2 contrasts IP vs Input for Dre and Drd2 as well as the interaction term of IP vs Input Dre and IP vs Input Drd2
Supplementary files format and content: Excel sheet of Salmon counts

source_name: Hypothalamus

growth_protocol: BacTRAP was performed on hypothalami of male and female POMCDre Drd2Cre R26-lx-rx-EGFP-L10a mice or male and female POMCDre R26-rx-EGFP-L10a mice. Animals were decapitated randomly fed at 11-13 weeks of age, brains quickly removed and hypothalami dissected using a stainless steel brain matrix (World Precision Instruments). Samples were snapfrozen in liquid nitrogen and stored at -80°C until further processing. For POMCDre Drd2Cre R26-lx-rx-EGFP-L10a mice, hypothalami of 18-20 animals with balanced gender proportions were pooled per replicate for a total of 3 replicates. For POMCDre R26-rx-EGFP-L10a mice, hypothalami of 3 animals (2 males, one female) were pooled per replicate for a total of 3 replicates. The

extract_protocol:
The method for purifying translating ribosomes was performed as described by Heiman et al. (https://doi.org/10.1038/nprot.2014.085) with minor modifications: In brief, 375 μL Protein A Dynabeads (Invitrogen, Cat#10001) per replicate were washed three times in wash buffer I (20 mM HEPES/pH 7.4, 5 mM MgCl2, 150 mM KCl, 1% Nonident P-40, 0.5 mM DTT and 100 µg/ml cycloheximide) and subsequently resuspended in 275 µl wash buffer I. An anti-GFP antibody mixture (50 µg of Heintz Lab TRAP anti-GFP 19C8 antibody, Cat# Htz-GFP-19C8; RRID:AB_2716737 and 50 µg of Heintz Lab TRAP anti-GFP 19F7 antibody, Cat# Htz-GFP-19F7; RRID:AB_2716736) was incubated with the beads overnight at 4°C with slow end-over-end mixing. The following day beads were washed three times in wash buffer II (20 mM HEPES/pH 7.4, 5 mM MgCl2, 150 mM KCl, 1% Nonident P-40, 0.5 mM DTT and 200 µg/ml cycloheximide) and subsequently resuspended in 200µl wash buffer II. For lysis buffer preparation 1 tablet of cOmplete mini EDTA-free protease inhibitor cocktail (Sigma-Aldrich, Cat#11836170001) was dissolved in 10 mL 20 mM HEPES/pH 7.4, 5 mM MgCl2, 150 mM KCl, 0.5 mM DTT, 40 U/ml RNasin and 100 µg/ml cycloheximide. Pooled hypothalami were homogenized in 1 mL lysis buffer on a rotating glass/teflon potter homogenizer (Braun Biotech, Potter S) at 4°C twice at 250 rpm and 9 times at 750 rpm. Homogenates were centrifuged in low binding microfuge tubes (Applied Biosystems, Cat# AM12450) at 2,000 g and 4°C for 10 min. Supernatants were consequently mixed on ice with Nonident P-40 (AppliChem, Cat# A1694,0250) and 1,2-diheptanoyl-sn-glycero3-phosphocholine (DHPC; Avanti Polar Lipids, Cat#850306P) at a final concentration of 1% (w/v) and 30 mM, respectively, incubated for 5 min and centrifuged for 10 min at 17,000 g and 4°C. 30 μL of the supernatant was snapfrozen in liquid nitrogen until RNA extraction and served as hypothalamic input sample for each respective IP in the analysis of translational profiling. The remaining supernatant was mixed on ice with 200µl anti-GFP antibody-coated beads and incubated for 1 hour at 4°C with slow end-over-end mixing. Sample-bead complexes (IPs) were collected via magnet and washed four times with wash buffer III (20 mM HEPES/pH 7.4, 5 mM MgCl2, 350 mM KCl, 1% Nonident P-40, 0.5 mM DTT, 100µg/ml cycloheximide). RNA of hypothalamic input and IP samples was extracted using the RNeasy Micro kit (QIAGEN, Cat# 74004). In brief, samples were eluted off the beads by adding 350 μL RLT buffer and incubating for 5 min at room temperature. Subsequently manufacurer’s instructions were followed without alteration. RNA integrity was assessed using a Bioanalyzer instrument (Agilent, 2100 Bioanalyzer).
Pre-amplification was performed via Ovation RNA-Seq system (V2), using total RNA with both poly(T) and random primers for first-strand cDNA synthesis, followed by second-strand cDNA synthesis and isothermal strand-displacement amplification. cDNA libraries were prepared from 1 ng cDNA input according to the Illumina Nextera XT DNA sample preparation protocol.

value: Hypothalamus

value: hypothalamic neurons expressing Pomc

value: POMCDre+/- R26-rx-EGFP-L10a+/-

value: random-fed

tag: age

value: 11-13 weeks


title: P53_Pten_tumor-1


title: Dre 2 Input

description: 2 males, 1 female pooled


title: PatientID:632 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA526254_17


title: PatientID:975 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA474309_17

value: Placebo


title: SK-N-BE shCont

source_name: SK-N-BE, neuroblastoma cell line, mock, shCont


title: PatientID:776 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA424768_13


title: NB-39-nu shBMI1-1

source_name: NB-39-nu, neuroblastoma cell line, shBMI1-1


title: P53_Kmt2d-2

value: Lung

value: Lung basal cell derived organoids


title: NB-39-nu shCont

source_name: NB-39-nu, neuroblastoma cell line, mock, shCont


title: SH-SY5Y shBMI1-1

source_name: SH-SY5Y, neuroblastoma cell line, shBMI1-1


title: PatientID:832 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA474308_16


title: Dre 3 IP

description: 2 males, 1 female pooled


title: Dre 3 Input

description: 2 males, 1 female pooled


title: Dre 1 IP

description: 2 males, 1 female pooled


title: Dre 1 Input

description: 2 males, 1 female pooled


title: PatientID:776 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA419496_13


title: SH-SY5Y shCont

source_name: SH-SY5Y, neuroblastoma cell line, mock, shCont


title: P53_Kmt2d-1

value: No


title: PatientID:210 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA369578_12

value: M-WEEK 8


title: P53-2


title: Drd2 3 IP

description: 9-10 females and 9-10 males pooled

value: hypothalamic neurons co-expressing Drd2 and Pomc


title: Drd2 4 IP

description: 9-10 females and 9-10 males pooled


title: Drd2 4 Input

description: 9-10 females and 9-10 males pooled


title: Drd2 1 IP

description: 9-10 females and 9-10 males pooled


title: Drd2 1 Input

description: 9-10 females and 9-10 males pooled


title: osteoblasts with Staphylococcus aureus infection repeat 3

city: Soochow

first: zhihao

last: chen

address: china

country: China

institute: The Second Affiliated Hospital of Soochow University

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4)
guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Assembly: Hg19
Supplementary files format and content: excel format
Supplementary files format and content: FPKM

growth_protocol: Hfob1.19 cells were seeded in a 6-well plate with 2.5 × 105 cells per well in DMEM/F12 medium (HyClone, USA) containing 10% FBS.

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
RNA libraries were constructed by using rRNA-depleted RNAs with NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
RNA-seq.10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: Hfob1.19 cells were infected with S. aureus at a ratio of 1:25. Following incubation at 37°C for 2 h, cells were incubated with 100 µg/mL gentamicin for 1 h to kill extracellular bacteria

value: osteoblasts

value: osteoblasts with staphylococcus aureus infection


title: osteoblasts with Staphylococcus aureus infection repeat 2


title: PatientID:512 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA346341_12

value: Ustekinumab

value: N


title: Drd2 3 Input

description: 9-10 females and 9-10 males pooled


title: osteoblasts with PBS repeat 3

value: uninfected


title: PatientID:689 visit: I-WEEK 0

description:
WB-mRNA
Gene expression data from WB-RNA
XA233642_17

value: I-WEEK 0


title: patient 1 muscle

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

description:
processed data file:
muscle
TEFM muscle mitocounts

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to the human reference genome (GRCh38) with Salmon and to the human mtDNA only with HiSat2 for in depth analysis of the mitochondrial reads
Salmon mapped reads were further analysed DESeq2
HiSat2 mapped reads were split for each strand using Samtools and coverage between paired reads was obtained with Bedtools bamtobed and genomecov
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files are generated with DESeq2 and show the log2FC of patient versus control samples. Xlsx files contain the counts of each nucleotide for chrM (bedtools genomecov for both strands separately)

source_name: muscle

growth_protocol: Patient and control fibroblasts were cultured in DMEM supplemented with 10% FBS

extract_protocol:
RNA from muscle tissue or cultured fibroblasts was extracted using Trizol
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

tag: subject status/id

value: patient 1

tag: tissue/cell type

value: muscle

tag: molecule subtype

value: rRNA depleted RNA


title: TBLC-blastoids1, scRNAseq

city: Guangzhou

first: xuzhao

last: zhai

address: Kaiyuan avenue

institute: Guangzhou Laboratory

description:
10x Genomics
SC-TBLCs-Blastoids.matrix.txt.gz

library_source: transcriptomic single cell

data_processing:
For bulk RNA-seq, trim_galore was used to trim the adapters,STAR was used for the alignment to the mm10 reference genome, RSEM was used to estimate Raw counts. For single cell RMA-seq, STAR was used for mapping , SEURAT and SCANPY was used for the downstream analysis.
Assembly: mm10
Supplementary files format and content: SC-TBLCs-Blastoids.matrix.txt.gz (barcode-0 corresponds to sample TBLC-blastoids2, barcode-1 corresponds to sample TBLC-blastoids1)

source_name: embryo

extract_protocol:
Libraries of bulk RNA-seq and single cell RNA-seq constructed according to the manufacturer's instructions.
transcriptomic

value: embryo

value: TBLC-blastoids


title: muscle control 2

value: control 2


title: osteoblasts with PBS repeat 2


title: EOfAD-like_21-01556

city: Adelaide

first: Karissa

last: Barthelson

state: South Australia

address: North Terrace Campus

country: Australia

institute: The University of Adelaide

data_processing:
98bp paired end sequencing + 8bp UMI using MGI DNBSEQ-G400 chemistry
Reads were trimmed using fastp v0.23.1 setting a minimum length of 20 and allowing automatic detection of adaptors.
Trimmed reads were aligned to the zebrafish genome (Ensembl release GRCz11.101) using STAR (v2.7.0d)
Alignments were counted using featureCounts (subread v2.0.1)
UMIs (in the header of the fastq files) were deduplicated from the alignments using umi_tools v1.0.1
Assembly: GRCz11 release 101
Supplementary files format and content: raw counts output from featurecouunts

molecule: polyA RNA

organism: Danio rerio

source_name: whole larvae

growth_protocol: The larvae were raised in E3 medium for 7 days, allowing complete larval yolk absorption but not food intake

extract_protocol:
Total RNA was extracted from indivual larvae using the mirVanaTM miRNA isolation Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). DNase treatment was performed on RNA to remove remaining genomic DNA using the DNA-freeTM Kit (Ambion, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA). Only
Stranded polyA libraries prepared by the South Australian Genomics Center (SAGC) using Nugen Universal Plus mRNA-seq (Part No. 0508), protocol M01442 v2. Then underwent Illumina to MGI Library Conversion (MGIEasy Universal Library Conversion Kit, Part No. MGI1000004155)

treatment_protocol: whole larvae were treated with RNAlater solution to stabilise RNA.

value: whole larvae

value: EOfAD-like

tag: developmental stage

value: 7 days post fertilisation

tag: rin


title: TBLC-blastoids2, scRNAseq


title: EOfAD-like_21-01555


title: muscle control 3

value: control 3


title: wt_21-01554

value: WT


title: PatientID:299 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA233654_12

source_name: Homo sapiens, WB-mRNA

tag: patientid

tag: visit

value: I-WEEK 6

value: Placebo


title: osteoblasts with PBS repeat 1

description: C

value: osteoblasts

tag: treatment


title: muscle control 1

value: control 1


title: patient 2 muscle

value: patient 2


title: wt_21-01552


title: PatientID:232 visit: M-WEEK 8

description:
WB-mRNA
Gene expression data from WB-RNA
XA210434_12

value: M-WEEK 8

value: Ustekinumab

tag: remwk8_i (clinical_remission_week_8)

value: N

tag: crp


title: osteoblasts with Staphylococcus aureus infection repeat 1

description: T

value: osteoblasts with staphylococcus aureus infection


title: PatientID:689 visit: I-WEEK 6

description:
WB-mRNA
Gene expression data from WB-RNA
XA230860_12


title: miR4

city: Farmington

first: Antoine

last: Menoret

state: CT

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using HISAT2 v 2.1.0 under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

source_name: CD8+ T cells from mice receiving SEA antigen

extract_protocol:
QIAGEN miRNEasy Micro Kit
Clontech SMART-Seq v4 Ultra-low w/Nextera XT
1x100bp reads

value: CD8+ T cell

value: without miR150 expression

value: SEA


title: miR2


title: miR3


title: miRN

source_name: CD8+ T cells from untreated mice


title: WTN


title: Metastatic BRAF V600E mutant colorectal cancer S143

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

country: Taiwan

institute: National Taiwan University Hospital

scan_protocol: After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the puried target/probe complexes are eluted o the beads and immobilized on the cartridge for data collection. After hybridization, excess probes are washed away using a two step magnetic bead- based puri cation on the nCounter Prep Station. Magnetic beads derivatized with short nucleic acid sequences that are complementary to the Capture Probe and the Reporter Probes are used sequentially. First, the hybridization mixture containing target/probe complexes is allowed to bind to magnetic beads complementary to sequences on the Capture Probe. Wash steps are performed to remove excess Reporter Probes and non-target cellular transcripts. After washing, the Capture Probes and target/probe complexes are eluted o the beads and are hybridized to magnetic beads complementary to sequences on the Reporter Probe. An additional wash is performed to remove excess Capture Probes. Finally, the purified target/probe complexes are eluted out the beads and immobilized on the cartridge for data collection.

data_processing: The raw code counts were normalized by the trimmed mean of M-values normalization method (TMM).

source_name: Colorectal cancer

extract_protocol: Total RNA was extracted from the formalin-fixed paraffin-embedded (FFPE) specimens of primary tumors by using Qiagen’s miRNeasy FFPE Kit (Qiagen, Valencia, CA, USA).

tag: gender

value: M

tag: Stage

tag: braf

tag: microsatellite status

value: MSS

tag: pfs (month)

tag: pfs event

tag: os (month)

tag: os event


title: Metastatic BRAF V600E mutant colorectal cancer S141

value: F

tag: age


title: Metastatic BRAF V600E mutant colorectal cancer S140


title: P53-1

source_name: Lung

tag: tissue

value: Lung

tag: cell line

value: No

tag: cell type

value: Lung basal cell derived organoids

tag: genotype


title: MPS-IIIB_21-01551

value: whole larvae

value: MPS-IIIB

tag: developmental stage

value: 7 days post fertilisation

tag: rin


title: Metastatic BRAF V600E mutant colorectal cancer S139


title: miR1

tag: treatment


title: MPS-IIIB_21-01549


title: WT3

value: WT


title: WT4


title: Metastatic BRAF V600E mutant colorectal cancer S137


title: WT2


title: wt_21-01545


title: Metastatic BRAF V600E mutant colorectal cancer S136


title: wt_21-01553


title: Metastatic BRAF V600E mutant colorectal cancer S133


title: Metastatic BRAF V600E mutant colorectal cancer S134


title: wt_21-01543


title: MPS-IIIB_21-01548


title: WT1


title: Metastatic BRAF V600E mutant colorectal cancer S132


title: shXBP1 MC38-OVA tumor-4 [T08]

city: Beijing

first: Likun

last: Wang

address: 15 Datun Road, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
Biomarker Technologies Co, LTD.
Triming of adaptor sequence/low-quality sequence was performed at Biomarker Technologies Co, LTD.
Mapping of trimmed sequence reads was performed at Biomarker Technologies Co, LTD.
Read count extraction and normalization were performed using BMKCloud (www.biocloud.net).
Assembly: GRCm38_release95
Supplementary files format and content: xls file includes count and FPKM values for each Sample

source_name: subcutaneous tumor

growth_protocol: MC38-OVA cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA from B16-OVA or MC38-OVA tumors was isolated with TRNzol Universal Reagent (TIANGEN, China).
RNA libraries were generated at Biomarker Technologies Co, LTD.

treatment_protocol: shNT/shXBP1 MC38-0VA cells were subcutaneously injected into female C57BL/5J mouse.

value: subcutaneous tumor

value: colon adenocarcinoma cell

value: subcutaneous injection into C57BL/6J mouse


title: Metastatic BRAF V600E mutant colorectal cancer S129


title: shXBP1 MC38-OVA tumor-3 [T07]


title: Metastatic BRAF V600E mutant colorectal cancer S126


title: Metastatic BRAF V600E mutant colorectal cancer S130


title: Metastatic BRAF V600E mutant colorectal cancer S125


title: EOfAD-like_21-01542

value: EOfAD-like


title: EOfAD-like_21-01541


title: Metastatic BRAF V600E mutant colorectal cancer S128


title: Metastatic BRAF V600E mutant colorectal cancer S123


title: Metastatic BRAF V600E mutant colorectal cancer S122


title: shXBP1 MC38-OVA tumor-2 [T06]


title: Metastatic BRAF V600E mutant colorectal cancer S135


title: Metastatic BRAF V600E mutant colorectal cancer S107


title: shXBP1 MC38-OVA tumor-1 [T05]


title: Metastatic BRAF V600E mutant colorectal cancer S121


title: MPS-IIIB_21-01544


title: MPS-IIIB_21-01540


title: shNT MC38-OVA tumor-4 [T04]

value: shNT


title: Metastatic BRAF V600E mutant colorectal cancer S100


title: EOfAD-like_21-01539


title: wt_21-01536


title: Metastatic BRAF V600E mutant colorectal cancer S97


title: shNT MC38-OVA tumor-3 [T03]


title: Metastatic BRAF V600E mutant colorectal cancer S95


title: EOfAD-like_21-01535


title: MPS-IIIB_21-01534


title: Metastatic BRAF V600E mutant colorectal cancer S94


title: wt_21-01533


title: shNT MC38-OVA tumor-2 [T02]


title: Metastatic BRAF V600E mutant colorectal cancer S93


title: Metastatic BRAF V600E mutant colorectal cancer S91


title: Metastatic BRAF V600E mutant colorectal cancer S90


title: shNT MC38-OVA tumor-1 [T01]


title: EOfAD-like_21-01532


title: Metastatic BRAF V600E mutant colorectal cancer S89


title: Tet2KD_6

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Assembly: mm10
Supplementary files format and content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: in vitro primary neurons

extract_protocol:
RNA extracted using Qiagen Rneasy extraction
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

value: in vitro primary neurons

value: Tet2 KD


title: Tet2KD_5


title: Tet2KD_4


title: MPS-IIIB_21-01531


title: Metastatic BRAF V600E mutant colorectal cancer S87


title: Metastatic BRAF V600E mutant colorectal cancer S85

value: M


title: Metastatic BRAF V600E mutant colorectal cancer S88

value: MSS


title: Tet2KD_3


title: Metastatic BRAF V600E mutant colorectal cancer S86

value: F


title: Metastatic BRAF V600E mutant colorectal cancer S96


title: EOfAD-like_21-01529


title: MPS-IIIB_21-01530


title: Tet2KD_2


title: Metastatic BRAF V600E mutant colorectal cancer S84


title: Metastatic BRAF V600E mutant colorectal cancer S46


title: Metastatic BRAF V600E mutant colorectal cancer S48


title: Metastatic BRAF V600E mutant colorectal cancer S44


title: Ctl_6

value: shLuc


title: Tet2KD_1


title: Ctl_5


title: Metastatic BRAF V600E mutant colorectal cancer S45


title: Metastatic BRAF V600E mutant colorectal cancer S43


title: control wild type daf-2 RNAi (D1_daf2_A)

first: James

middle: Matthew

last: Jordan

state: NY

department: Medicine

institute: Weill Cornell Medical College, Cornell University

data_processing:
Bowtie 1.1.2 was used to map reads to the WS210 genome with some WS220 features with the following settings: --best --chunkmbs 256 -k 1 -m 2 -S
HTSeq 0.12.4 was used to count reads.
edgeR was used on count tables for differential expression analysis. The original count table was filtered to contain those annotated as genes, reducing the number of genes to 22581.
Genes were further filtered by including only genes with counts per million (CPM) > 1 across 3 libraries. This resulted in 12894 genes.
edgeR exact test was used for four pairwise comparisons, and edgeR GLM was used to find genes that changed differently in different comparison (this could mean up in one comparison and down in another, unchanged in one comparison and up in another, up in one comparison and more up in another,etc.)
Genome_build: WS210 (including transcripts annotated in WS220 mapped back to WS210)
Supplementary_files_format_and_content: RNAseq 1_CPMs_forGEO.csv

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: Worms were maintained without starvation at 20C on OP50 E.coli for at least 4 generations prior to being used in experiments.

extract_protocol:
RNA was extracted using Trizol and chloroform.
Libraries were prepared for sequencing using the NEBNext Ultra RNA Library Prep Kit for Illumina (E7530) with 500ng of starting RNA per library and 12 cycles of PCR.

treatment_protocol: 15 young adult N2 were picked to large OP50 seeded plates x 6 plates and cultured at 20C for 72 hours. Plates were bleached to acquire embryos, which were resuspended in 10 ml virgin S-basal in test tubes at a density of 1/ul. Worms were cultured on carousel at 21-22C for 1 (control) or 8 days. 1000 live animals were recovered on 2x large 25ug/ml Carb, 1mM IPTG, NGM plates seeded with empty vector or daf-2 RNAi HT115 bacteria per condition. Worms were cultured at 20C until eggs appeared on plate (~52 hrs for d1 animals or ~68 hrs for d8 animals) before washing them off the plates with virgin s-basal. Worms were quickly washed twice in 10 ml virgin s-basal and snap frozen in liquid nitrogen.

tag: strain

value: N2 (Bristol)

tag: RNAi

value: daf-2 RNAi

value: no starvation

value: early adult


title: Metastatic BRAF V600E mutant colorectal cancer S40

tag: gender

tag: Stage


title: Metastatic BRAF V600E mutant colorectal cancer S42

tag: braf

tag: microsatellite status


title: Metastatic BRAF V600E mutant colorectal cancer S37

tag: pfs (month)

tag: pfs event


title: Metastatic BRAF V600E mutant colorectal cancer S41

tag: os (month)

tag: os event


title: Ctl_4


title: Metastatic BRAF V600E mutant colorectal cancer S47

tag: age


title: control wild type daf-2 RNAi (D1_daf2_C)


title: Ctl_3


title: Metastatic BRAF V600E mutant colorectal cancer S36


title: control wild type EV (D1_EV_A)

value: empty vector


title: control wild type EV (D1_EV_B)


title: Metastatic BRAF V600E mutant colorectal cancer S25


title: Metastatic BRAF V600E mutant colorectal cancer S28


title: wt_21-01528

tag: tissue

value: whole larvae

value: WT

value: 7 days post fertilisation


title: Ctl_2

tag: cell type


title: Metastatic BRAF V600E mutant colorectal cancer S35


title: Metastatic BRAF V600E mutant colorectal cancer S24


title: control wild type daf-2 RNAi (D1_daf2_B)


title: Metastatic BRAF V600E mutant colorectal cancer S20


title: control wild type EV (D1_EV_C)


title: starved wild type daf-2 RNAi (D8_daf2_A)

value: early-life starvation


title: Ly6C- pCAF repetition 3

city: rehovot

first: Coral

last: Halperin

address: Herzel 234

country: Israel

institute: Weizmann institute of sciences

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 5 reads in at least one sample
Assembly: mm10
Supplementary files format and content: tab delimited text files include mRNA molecule normalized counts values for each sample

source_name: Ly6c- PDPN+ CAFs

growth_protocol: 8  week-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI in the gentleMACS dissociator. The digested cell suspension was strained through a 70µm cell strainer to obtain a single-cell suspension. To isolate CAFs, we performed negative selection against cancer cells (EpCAM) and immune cells (CD45) the Ly6c pCAFs pCAF were selected based on PI−, Ter119−, CD45−, EpCAM−, PDPN+ , LY6C+/-
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: 8 week old BALB/c females were injected under anaesthesia with 100,000 4T1-GFP cells suspended in PBS, directly into the lower left mammary fat pad. To obtain CAFs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.

value: BALB/c

value: Breast tumor

value: Non-immune stromal cells

tag: selection marker

value: Ter119- CD45- EpCAM- PDPN+ LY6C-

value: Orthotopic breast injection of 4T1-luc cells

tag: mouse age

value: 8 weeks


title: Ly6C- pCAF repetition 2


title: Ctl_1

value: in vitro primary neurons


title: Metastatic BRAF V600E mutant colorectal cancer S39

value: F

value: MSS


title: Tet2OE_3

value: Tet2 OE


title: Metastatic BRAF V600E mutant colorectal cancer S18

value: M


title: starved wild type daf-2 RNAi (D8_daf2_B)

value: N2 (Bristol)

value: daf-2 RNAi

value: early adult


title: Ly6C- pCAF repetition 1


title: Ly6C+ pCAF repetition 3

source_name: Ly6c+ PDPN+ CAFs

value: Ter119- CD45- EpCAM- PDPN+ LY6C+


title: Tet2OE_1


title: starved wild type daf-2 RNAi (D8_daf2_C)


title: Metastatic BRAF V600E mutant colorectal cancer S17


title: mRNA-seq___wildtype_S_rep3

city: Martinsried

first: Karl-Uwe

last: Reusswig

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

data_processing:
Sequencing reads were mapped to the S. cerevisiae reference genome (sacCer3) using STAR (v 2.7.10a) with default parameters and converted to sorted BAM files using samtools (v 1.12)
Reads mapping to genes were counted using htseq-count (v 2.0.1) with the parameters '--order=pos --stranded=reverse --mode=intersection-nonempty --nonunique=none --idattr=gene_name --add-chromosome-info"
Downstream analyses were performed using DESeq2 (v 1.36.0)
Assembly: SacCer3
Supplementary files format and content: Count values for individual genes are provided as a tab-delimited .tsv-file.

organism: Saccharomyces cerevisiae

source_name: budding yeast cells

growth_protocol: Cells were grown in YP-media supplemented with 2% raffinose and 0.25 mM adenine at 30 °C to log-phase (OD600 0.5-0.7) and synchronized with α-factor (5-10 µg/ml) for 2:30 h. Cell cycle arrest was assessed by microscopy and by measurement of DNA content (flow cytometry).

extract_protocol:
RNAs were isolated using the MasterPure Yeast RNA Purification Kit (MPY03100) according to the manufacturer's instructions.
Libraries were prepared with 1 µg of total RNA using NEBNext Ultra II Directional RNA library Prep kit (E7765) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490) according to the manufacturer's instructions. A fresh 1:100 dilution of ERCC RNA Spike-In Mix (4456750) was added to the total RNA before library preparation.

treatment_protocol: Replication was induced in G1-arrested cells by adding galactose to the medium (2% final concentration). Release from the G1 arrest was performed by washing once with pre-warmed medium. At the indicated times after treatment, cell pellets were frozen in liquid nitrogen.

value: budding yeast cells

value: arrested in G1 for 2.5 h, then released into fresh medium for 30 min


title: mRNA-seq___wildtype_S_rep4


title: Ly6C+ pCAF repetition 2

value: BALB/c


title: Ctl-GFP_3

value: synGFP


title: Ly6C+ pCAF repetition 1

value: Breast tumor

value: Non-immune stromal cells


title: Ctl-GFP_2


title: starved wild type EV (D8_EV_B)

value: empty vector

value: early-life starvation


title: starved wild type EV (D8_EV_C)


title: mRNA-seq___wildtype_S_rep2


title: Metastatic BRAF V600E mutant colorectal cancer S16


title: Metastatic BRAF V600E mutant colorectal cancer S19


title: Ctl-GFP_1

value: in vitro primary neurons


title: mRNA-seq___wildtype_S_rep1


title: mRNA-seq___wildtype_G1_rep4

value: arrested in G1 for 2.5 h, then induced replication for 3 h


title: mRNA-seq___wildtype_G1_rep3


title: NMF repetition 3 co-cultured with 4T1 cells for 5 days

source_name: Normal mammary fibroblasts

growth_protocol: Fresh mammary fat pad tissue was extracted from 12-week-old female BALB/c mice. The tissue was minced and digested using gentleMACS  dissociation buffer (DMEM with 1mg/ml collagenase II , 1mg/ml collagenase IV, and 0.01mg/ml deoxyribonuclease. To stop the reaction, 20ml of DMEM with 10% FBS and 1% Penicillin- Streptomycin were added to the dissociation buffer followed by filtration with a 70μm strainer. Red blood cells (RBC) were removed by RBC lysis buffer. For the co-culture assay, the cells were cultured on a collagen layer for 1 week of recovery

extract_protocol:
cell suspensions were stained with anti-PDPN antibodies. NMF were isolated by FACS sorting using negative selection for GFP and positive selection for PDPN
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: 3*10^5 Normal mammary fibroblasts were plated in 6 wells in DMEM supplemented with 10% FBS and pen/strep. 24h later 1*10^5 4T1-GFP cells were seeded on top of the NMF. 3 or 5 days later cells were collected into single-cell suspensions.

value: Mammary fat pad

value: Normal mammary fibroblasts

value: GFP- PDPN+

value: co-cultured with 4T1 cells for 5 days

value: 12 weeks


title: SBM

first: Jijun

last: Yu

address: Taiping Road No.27

institute: Basic medical Research Institute

data_processing:
The Cell Ranger Single Cell Software Suite, version  was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.  Cloupe files were generated using the Cell Ranger 6.0.0 version. A description of the pipeline and instructions can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/visualization/latest/cellranger  The CellRanger count command was run on the individual Fastq datasets to produce expression data  R package Seurat v4.0.4 was used for cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction.Data were then log-normalized for the subsequent analyses. Principal component analysis (PCA) was used for dimension reduction, followed by clustering analysis in principal component analysis space using a graph-based clustering approach. UMAP was then used for the two-dimensional visualization of the identified clusters.
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Skull Bone Marrow cells

extract_protocol:
The viability of sorted singlets was determined using trypan blue exclusion. After pelleted, cells were resuspended in 0.04% non-acetylated BSA. The cell suspensions were loaded on a 10x Genomics Chromium instrument (10x Genomics, Pleasanton, CA, USA) to generate single cell Gel-bead-in-Emulsions (GEMs).
Libraries were prepared using the Chromium Single cell 3' Reagent Kits v3.1 (CG000204): Chromium Single Cell 3’ Library & Gel Bead Kit v3.1 (PN-1000128), Chromium Single Cell 3’ Chip Kit v2 (PN-1000127) and Single Index Kit Set A (PN-1000213). Libraries were sequenced on an Illumina NovaSeq 6000 using paired-end sequencing with approximately >90% sequencing saturation.

value: skull

value: leukocytes


title: S006

city: Hamburg

first: Tianran

last: Zhang

address: Falkenried 94

institute: University Medical Center Hamburg-Eppendorf

description: scRNA-seq

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 2.1.0, 10x Genomics, Pleasanton, CA) and the human genome GRCh38 release(function cellranger count). The matrices of cells and the unique molecular identifier (UMI) count were obtained and further processed by the R package Seurat (version 3.0.2)
To remove potential doublets, cutoff values for number of expressed genes (nGene) were determined for samples following visual inspection of the distribution of nGene and nUMI for each cell. The cells with higher nGene values were excluded. We further removed low-quality cells with high mitochondrial genes of all detected genes
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: NASH memory CD45RA− CD4+ T cells

growth_protocol: Fresh samples used in the study were obtained from patients undergoing bariatric surgery and simultaneous liver biopsy at the University Hospital Hamburg-Eppendorf. Lymphocytes from the small intestine were incubated in HBSS containing 1 mM dithioerythritol (DTE), followed by a dissociation step using 1,3 mM EDTA at 37 °C for 30 min. The cells were further separated by a Percoll gradient (GE Healthcare). scRNA-seq was performed on FACS sorted memory CD45RA− CD4+ T cells

extract_protocol:
Cells were loaded on a 10x Chromium single cell instrument.
All steps were performed according to standard protocol of the Chromium single cell 3' v2 kit to generate high-quality cDNA libraries.

value: liver

tag: disease

value: NASH

tag: patient id


title: NMF repetition 3 co-cultured with 4T1 cells for 3 days

tag: strain

value: BALB/c

tag: treatment

value: co-cultured with 4T1 cells for 3 days


title: FBM

source_name: Femur Bone Marrow cells

value: femur


title: S005

description: scRNA-seq

source_name: NAFLD memory CD45RA− CD4+ T cells

value: NAFLD


title: starved wild type EV (D8_EV_A)

value: N2 (Bristol)

tag: RNAi

value: empty vector

value: early adult


title: S004

description: scRNA-seq


title: mRNA-seq___wildtype_G1_rep2

value: budding yeast cells

value: arrested in G1 for 2.5 h, then induced replication for 3 h


title: DURA

source_name: Dura cells

value: cranial dura


title: NMF repetition 2 mono-cultures for 5 days

value: Mammary fat pad

value: Normal mammary fibroblasts

value: GFP- PDPN+

value: mono-cultures for 5 days


title: mRNA-seq___wildtype_G1_rep1


title: NMF repetition 2 co-cultured with 4T1 cells for 5 days

value: co-cultured with 4T1 cells for 5 days

value: 12 weeks


title: S003

description: scRNA-seq

value: liver


title: LUSC Kmt2d Mut-2

extract_protocol:
Cell pellets were collected and then subjected to total RNA extraction using RNeasy Plus Mini Kit (QIAGEN, 74136) according to the manufacturer’s instructions.
Automated stranded RNA-seq library prep, polyA selection, following manufacturer's protocols.

value: Lung

tag: cell line

value: Lung squamous cell carcinoma cell line

tag: genotype

value: No


title: LUSC Kmt2d Mut-1


title: LUSC Kmt2d WT-2

value: PP


title: NMF repetition 2 co-cultured with 4T1 cells for 3 days

value: BALB/c

value: co-cultured with 4T1 cells for 3 days


title: S001

description: scRNA-seq

value: NAFLD


title: Tet2OE_2

value: in vitro primary neurons

value: Tet2 OE


title: LUSC Kmt2d WT-1


title: NMF repetition 3 mono-cultures for 5 days


title: shASAP2-3

city: Shushan District

first: Ming

last: Lu

state: ANHUI SHENG

address: No.81 Meishan Road

institute: Anhui Medical University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38.p13-hg38
Supplementary files format and content: tab-delimited text file include FPKM values for all samples

source_name: THP-6 derived macrophage

growth_protocol: THP-1 cells with or without ASAP2 stable knockdown were differentiated into macrophages with PMA (50 ng/ml, 48 hours).

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: THP-6 derived macrophage

value: Macrophage

value: ASAP4 knockdown


title: S008

description: scRNA-seq

value: NASH


title: mRNA-seq___bypassCDKandDDK_rep2

value: budding yeast cells

value: arrested in G1 for 2.5 h, then induced replication for 3 h


title: NMF repetition 1 co-cultured with 4T1 cells for 5 days

value: Mammary fat pad

value: Normal mammary fibroblasts

value: GFP- PDPN+

value: co-cultured with 4T1 cells for 5 days

value: 12 weeks


title: NMF repetition 1 co-cultured with 4T1 cells for 3 days


title: shASAP2-2

source_name: THP-5 derived macrophage

value: THP-5 derived macrophage

value: ASAP3 knockdown


title: mRNA-seq___bypassCDKandDDK_rep1


title: U251_PRMT3_KD_2

city: Cincinnati

first: Qing

middle: Richard

state: Ohio

address: 3333 Burnet Avenue

department: CBDI

institute: cincinnati children's hospital medical center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg19 (human) whole genome using Tophat using default options
Unnormalized gene read counts were generated using Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/). Read count normalization and differential gene expression analysis of count were performed by the DESeq2.
Assembly: hg19

extract_protocol:
Total RNA from Ctrl and KD U251 GBM cells were extracted using Trizol (Life Technologies) protocol followed by purification using an RNeasy Micro Kit (Qiagen).
RNA-seq libraries from Ctrl and KD cells were prepared using Illumina RNA-Seq Preparation Kit.

value: GBM cells

value: PRMT3 knockdown


title: Albino perihperal retina, scRNAseq

first: Revathi

last: Balasubramanian

address: 635 West 165th street

department: Ophthalmology

institute: Columbia University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: E13.5 eye peripheral retina

extract_protocol:
Freshly collected  E13.5 optic cups  were pooled from 3 embryos each for pigmented and albino mice. Cells were dissociated using a Papain digestion protocol. Cells were FAC sorted using TdTomato and single cell suspension was collected in DMEM with 10% FBS for sequencing.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics) for 3' gene expression profiling

value: Developing retina

value: E13.5 eye peripheral retina

value: Swizz ICR


title: shNC-3

source_name: THP-3 derived macrophage

value: THP-3 derived macrophage

value: Macrophage

value: WT


title: U251_PRMT3_KD_1


title: mRNA-seq___bypassCDKandDDK_rep4

value: budding yeast cells


title: FTOc_BPA_Sperm_chr_m6A_Rep2

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

data_processing:
Library strategy: m6A-seq
Raw reads were trimmed with Trimmomatic-0.38, then aligned to the mouse genome and transcriptome (mm10) using HISAT2 (version 2.2.0) with ‘--rna- strandness RF’ parameters. Annotation files downloaded from GENCODE database (https://www.gencodegenes.org/) were used. m6 A peaks were called using MACS with parameter ‘--nomodel’ and ‘--keep-dup 5’.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files

source_name: Sperm

extract_protocol: Not provided

tag: strain background

tag: Sex

value: Male

value: Sperm

tag: antibody


title: shNC-2

source_name: THP-2 derived macrophage

value: THP-2 derived macrophage


title: NMF repetition 1 mono-cultures for 5 days

value: BALB/c

value: Mammary fat pad

value: Normal mammary fibroblasts

value: GFP- PDPN+

value: mono-cultures for 5 days


title: Pigmented peripheral retina,, scRNAseq

description: 10x Genomics


title: NMF Biological rep 4

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 5 reads in at least one sample
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include mRNA molecule count values for each sample

source_name: Normal mammary fat pad

growth_protocol: 8 to 13 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Normal mammary fat pad: Tissue was minced using scissors and placed and disrupted for 25 min at 37oC in a gentleMACS C tube using gentleMACS dissociator, in the presence of enzymatic digestion solution containing 1 mg ml-1 collagenase II, 1 mg ml-1collagenase IV and 70 unit ml-1 DNase. Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation

treatment_protocol: 8 weeks old BALB/c females were injected under anaesthesia with 100,000 4T1-luc cells suspended in PBS, directly into the lower left mammary fat pad. To obtain CAFs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.

value: Normal mammary fat pad

value: Non-immune stromal cells

value: Ter119- CD45- EpCAM-

value: 12 weeks


title: FTOc_BPA_Sperm_chr_m6A_Rep1


title: mRNA-seq___bypassCDKandDDK_rep3

value: arrested in G1 for 2.5 h, then induced replication for 3 h


title: U251_pGreen_Ctrl_2

value: GBM cells

value: Ctrl


title: U251_pGreen_Ctrl_1


title: DLD1-USP7KO-Day1-Dox-Rep3

city: Belfast

first: Yaser

last: Atlasi

address: Lisburn Road

department: patrick G Johnston Centre for Cancer research

institute: Queen's University Belfast

description: DOX-inducible USP7-KO

data_processing:
FASTQ files were aligned against the human reference genome (hg19) using HiSat2 (version 2.1.0; Kim et al., 2019) and mapped reads were assigned to RNAs using HTseq-count with the following settings: -m union -s reverse -t exon. DESeq2 (Love et al., 2014) was used to normalize for library size and normalized reads were further corrected for batch variation between independent experiments using the SVA R package (Leek et al., 2012). Batch-corrected values were used in DESeq2 for differential gene expression analysis. Genes were considered differentially expressed if they fulfilled the following conditions: normalized log2 read counts ≥5, fold change ≥ 2 and FDR < 0.05 at one or more time points.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: deseq2_results

source_name: colorectal cancer cell line

growth_protocol: DLD1 cells were cultured in Roswell Park Memorial Institute 1640 medium (RPMI 1640; Gibco), 10% FBS and 1% Pen/Strep.

extract_protocol:
Each biological triplicate of DLD1 wt, DLD1-USP7-KO and DLD1-KO-Dox-USP7 were grown in a 10 cm2 plate. USP7 expression in DLD1-KO-Dox-USP7 cells was induced by the   GFP-USP7 expression was induced by addition of doxycycline  (1 µg/ml) for 24 hours, three days or 9 days (+Dox). For RNA isolation the medium was removed and 3 ml of TriPure isolation reagent (Roche) was added directly onto the cells.
Samples were prepped with the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting DNA libraries were sequenced according to the Illumina Truseq Rapid V2 protocol on an Illumina HiSeq2500 sequencer.

treatment_protocol: To generate DLD1-KO-Dox-USP7, DLD1-USP7-KO cells were transfected with the GFP-USP7-expressing pTREG-BI-USP7 and the Tet-ON pEF1α-Tet3G plasmids (table xx) linearized with Bsa1. cells were then selected in RPMI containing 400µg/mL G418. For USP7 induction, cells were treated with 1µg/ml doxycycline.

value: colorectal cancer cell line

value: DOX

tag: time point


title: NMF Biological rep 3


title: FTOc_CTL_Sperm_chr_m6A_Rep2

value: Male


title: FTOc_CTL_Sperm_chr_m6A_Rep1

value: Sperm


title: NMF Biological rep 2


title: shNC-1

source_name: THP-1 derived macrophage

value: THP-1 derived macrophage

value: Macrophage

value: WT


title: WT_BPA-Sperm-chr_m6A-Rep1


title: WT_BPA-Sperm-chr_m6A-Rep2


title: DLD1-USP7KO-Day1-Dox-Rep2

description: DOX-inducible USP7-KO


title: eNK-EXO treated NK cells,biol rep2

city: Guiyang

first: Heyong

last: Luo

address: Dongqing road

institute: Guizhou Medical University

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Differential expression analysis was performed using the DESeq2
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0)
Assembly: human NCBI genome 36
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: human cells

growth_protocol: NK cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer . RNA integrity was assessed using the Agilent 2100 Bioanalyzer
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: NK cells were treated with 80 µg/mL eNK-EXO for 24 h

value: NK cells

value: immune cells

value: eNK-EXO treated for 24h


title: eNK-EXO treated NK cells,biol rep1


title: NMF Biological rep 1

value: BALB/c

value: Normal mammary fat pad


title: eNK-EXO treated NK cells,biol rep3


title: AS_NK cells,biol rep3

value: AS_NK cells


title: pCAF Biological rep 3

source_name: PDPN+ CAFs

value: Breast tumor

value: Non-immune stromal cells

value: Ter119- CD45- EpCAM- PDPN-

value: Orthotopic breast injection of 4T1-luc cells

value: 8 weeks


title: shASAP2-1

source_name: THP-4 derived macrophage

value: THP-4 derived macrophage

value: ASAP2 knockdown


title: WT_CTL-Sperm-chr_m6A-Rep2

value: Male

value: Sperm


title: pCAF Biological rep 2

value: Ter119- CD45- EpCAM- PDPN+


title: AS_NK cells,biol rep2

value: WT


title: WT_CTL-Sperm-chr_m6A-Rep1


title: DLD1-USP7KO-Day9-Dox-Rep2

description: DOX-inducible USP7-KO

value: colorectal cancer cell line

value: DOX


title: DLD1-USP7KO-Day1-Dox-Rep1

description: DOX-inducible USP7-KO


title: pCAF Biological rep 1


title: AS_NK cells,biol rep1

value: immune cells


title: DLD1-USP7KO-Day9-Dox-Rep1

description: DOX-inducible USP7-KO


title: FTOc-BPAF3-Sperm-ATAC-Rep2

data_processing:
All libraries were sequenced using an Illumina sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm10 using Bowtie2. ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools. To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS) and mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Genome_build: mm10 (GRCm38)

extract_protocol:
ATAC-seq was carried out using the Omni-ATAC protocol. After cells were counted, the nuclei were isolated with Lysis Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. The purified nuclei pellet was then resuspended in the transposase reaction mix containing 0.05% digitonin and incubated for 30 min at 37°C. Following incubation, cells were treated with Proteinase K at 55°C for 2 h, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Libraries were paired-end sequenced on Illumina Hiseq2500 v4 or NovaSeq 6000 instruments.
Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.


title: NK cells,biol rep3

value: NK cells


title: DLD1-USP7KO-Day3-Dox-Rep3

description: DOX-inducible USP7-KO


title: HA-JICD1_H3K9Ac

city: Seoul

first: Jung Yun

last: Kim

address: 145 Anam-ro, Seungbuk-gu

country: South Korea

institute: Korea University

data_processing:
High-throughput sequencing was performed as single-end 75 sequencing using Illumina NextSeq 500.
The reads were trimmed and aligned using Bowtie2. Bowtie2 indices were either generated from the genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
We used Model-based Analysis of ChIP-seq (MACS) to identify peaks from the alignment file.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH fires include quantitative data across genomic regions

source_name: Ink4a/Arf-/- astrocytes

extract_protocol:
Lysates were clarified from sonicated and constructed using NEBNext® UltraTM DNA Library Prep Kit for Illumina (Cat. #E7370, New England Biolabs)
Libraries were prepared according to NEBNext® UltraTM DNA Library Prep Kit for Illumina (Cat. #E7370, New England Biolabs)

value: FVB/N crossed with a C57B6 and BALB/C F1

value: astrocytes

tag: chip antibody

value: HA3K9Ac antibody (Cat. #07-352, EMD Millipore)


title: NK cells,biol rep2


title: FTOc-BPAF3-Sperm-ATAC-Rep1


title: FTOc-BPAF2-sperm-ATAC-Rep2


title: NK cells,biol rep1


title: DLD1-USP7KO-Day3-Dox-Rep1

description: DOX-inducible USP7-KO


title: HA-JICD1_HA

value: HA antibody (Cat. #3724s, Cell Signaling Technology)


title: DLD1-USP7KO-Day9-Dox-Rep3

description: DOX-inducible USP7-KO


title: FTOc-BPAF2-sperm-ATAC-Rep1


title: DLD1-USP7KO-NoDox-Rep3

description: DOX-inducible USP7-KO

value: No-treatment


title: FTOc_BPAF1-sperm-ATAC-Rep2


title: Con_HA


title: DLD1-USP7KO-NoDox-Rep2

description: DOX-inducible USP7-KO


title: FTOc_BPAF1-sperm-ATAC-Rep1


title: TRiP_F_3

city: Greenwood

first: Rebecca

middle: A

last: MacPherson

state: SC

address: 114 Gregor Mendel Circle, Dr. Trudy Mackay

department: Center for Human Genetics

institute: Clemson University

data_processing:
The default Illumina BaseSpace NovaSeq sequencing pipeline was used to demultiplex the barcoded sequencing reads. We then merged S1 flow cell lanes together, as well as reads from different flow cell runs.
Filtering: We filtered out short and low-quality reads using the AfterQC pipeline (v0.9.7) (Chen et al., 2017) and quantified remaining levels of rRNA via the bbduk command (Bushnell, 2014).
Alignment: Reads were aligned to the reference genome (D. melanogaster v6.13) using GMAP-GSNAP (Wu et al., 2016) and these unique alignments to Drosophila genes were counted using the featurecounts pipeline from the Subread package (Liao et al., 2013; Wu et al 2016).
Assembly: dm6 v6.13
Supplementary files format and content: read_counts_forGEO.csv

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Each sample contained 30 whole flash-frozen 3-5 day old flies, homogenized using a Fisherbrand™ Bead Mill (ThermoFisher Scientific, Waltham MA). RNA was extracted using the the Qiagen RNeasy Plus Mini Kit (Qiagen, Hilden, Germany), resuspended in RNase-free water, and kept at -80°C until further use.
Libraries were synthesized from RNA using the Universal RNA-seq with Nuquant + UDI kit (Tecan Genomics, Inc., CA) according to manufacturer recommendations. 100ng of total RNA was converted into cDNA using the integrated DNase treatment and sheared into 350bp fragments using the Covaris ME220 Focused-ultrasonicator (Covaris, Woburn, MA). We performed Ribosomal RNA depletion and bead selection using Drosophila AnyDeplete probes and RNAClean XP beads (Beckman Coulter, Brea, CA), respectively. Libraries were purified after 17 cycles of PCR amplification. We measured library fragment sizes on the Agilent Tapestation using the Agilent High Sensitivity DNA 1000 kit (Agilent Technologies) and quantified library concentration using the Qubit 1X dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific).

tag: background strain

value: whole body

value: Female

tag: replicate

tag: molecule subtype

value: rRNA depleted RNA


title: FTOc-CTL-sperm-ATAC-Rep2

tag: tissue


title: DLD1-USP7KO-NoDox-Rep1

description: DOX-inducible USP7-KO

tag: cell type


title: FTOc-CTL-sperm-ATAC-Rep1


title: Lateral habenula tissue

city: durham

first: Anne

last: West

state: NC

address: 311 research drive

institute: Duke University

data_processing:
fastq generation with CellRanger mkfastq (v3.0.2) from raw bcl data (Illumina NextSeq 550 mid-output)
transcriptome alignment and count matrix generation with CellRanger count (v3.0.2) and mm10-3.0.0_pre-mrna.gtf
Genome_build: mm10
Supplementary_files_format_and_content: Filtered_feature_bc_matrix - This contains the matrix, features, and bar code files for further processing

source_name: Lateral habenula

growth_protocol: CAG-Sun1/sfGFP x Gad2-IRES-CRE mice

extract_protocol:
Lateral habenula tissue was dissected fresh before nuclei were isolated and FANS sorted for GFP expression. 10,000 GFP+ nuclei were sorted into final volume of 40uL before loading 10X Chromium controller with 3' Gene Expression (v3) kit for single nucleus RNA-seq
Libraries were constructed according to the 10X Genomics protocol for 3' Gene Expression (v3)

treatment_protocol: naiive adult mice

value: Untreated

value: Lateral habenula

tag: molecule type

value: Single-nuclear RNA


title: TRiP_F_1


title: DLD1-USP7KO-Day3-Dox-Rep2

description: DOX-inducible USP7-KO


title: DLD1-WT-Rep2

description: parental

value: parental


title: TRiP_M_3

value: Male


title: ZKSCAN1_GFP

city: Paris

first: Noémie

last: Robil

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Reads aligned with STAR on hg19 genome
FeatureCounts was used to count reads per gene on FastDB 2018_1 annotations
Normalization was performed using DESeq2 on R.
Supplementary files format and content: Tab-delimited text files

source_name: HEK293T cells

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany).  Circular RNA was enriched by removing rRNA (rRNA minus kit, Thermo Fisher) and digesting RNAs with RNAse R.
The libraries were sequenced from both ends of the fragments for a total of 150nt from each end a NovaSeq SP flow-cell (Illumina). The fastq read files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA). The quality of the demultiplexed fastq files was evaluated with the FastQC software, which generates reports with the quality scores, base composition, k-mer, GC and N contents, sequence duplication levels and overrepresented sequences.
RNAseq of circular RNAs

value: HEK293T cells

value: GFP


title: ZKSCAN1_ADAR1


title: Con_H3K9Ac


title: ZKSCAN1_ADAR3


title: ZKSCAN1_ADAR2


title: TAU_ADAR3

value: TAU


title: DLD1-WT-Rep1

description: parental

value: colorectal cancer cell line


title: BPA_Sperm_CTCF_Rep1_R1

description: chromatin IP against CTCF

data_processing:
All reads were mapped to unique genomic regions using Bowtie2 (Langmead and Salzberg, 2012) and the mm10 genome. PCR duplicates were removed using Picard Tools.
Genome_build: mm10

extract_protocol: Cells were crosslinked with 1% formaldehyde in 1xPBS for 10 min at RT, and the reaction was quenched with 125 mM glycine for 10 min at RT. After washing with PBS, cells were lysed with 5 mM PIPES, 85 mM KCl, 0.5% NP40 and 1x protease inhibitors (P8107S, NEB) on ice for 15 min. After centrifugation, cells were resuspended in RIPA buffer (1x PBS; 1% NP40; 0.5% sodium deoxycholate; 0.1% SDS; 1x protease inhibitors) and incubated on ice for 20 min. The purified chromatin was sonicated to 300-500 bp using a Diagenode Bioruptor. After 25 cycles (30 seconds on and 60 seconds off), the supernatant containing sheared chromatin was collected. Immunoprecipitation was performed overnight at 4°C with antibodies. Libraries for Illumina sequencing were constructed using the following standard protocol. Fragment ends were repaired using the NEBNext End Repair Module and adenosine was added at the 3’ ends using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA was incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers. Two independent biological replicates per sample were then sequenced using paired-end 50 bp on Illumina Hiseq2500 v4 or NovaSeq 6000 instruments.

tag: chip-antibody

value: CTCF

value: Sperm